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Mishina K, Kai H, Hamada M, Haraguchi Y, Oono Y, Ordon F, Komatsuda T. Series of resistance genes in barley ( Hordeum vulgare L.) that control Barley yellow mosaic virus multiplication and the root-to-leaf systemic movement. Plant Dis 2024. [PMID: 38173257 DOI: 10.1094/pdis-07-23-1451-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The infection of young winter barley (Hordeum vulgare L.) root system in winter by Barley yellow mosaic virus (BaYMV) can lead to high yield losses. Resistance breeding is critical for managing this virus, but there are only a few reports on resistance genes that describe how the genes control BaYMV propagation and the systemic movement from the roots to the leaves. Here we report a real-time quantitative PCR analysis of the virus in barley roots and leaves carrying BaYMV resistance genes (rym1-rym15 and an unknown gene) to elucidate the molecular mechanisms underlying the barley response to BaYMV. The resistance mechanism directly targets the virus. Moreover, the resistance genes/cultivars were classified into the following three groups according to their BaYMV titer: (1) immune (BaYMV was undetectable in the roots or leaves); (2) partially immune (BaYMV was detected in the roots, but not in the leaves); (3) susceptible (BaYMV was detected in the roots and leaves). Our results clarified the functions of the resistance genes in barley roots and leaves following a BaYMV infection. We anticipate our analysis to be a starting point for more understanding the correspondence between resistance genes of Triticeae and the soil-borne viruses.
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Affiliation(s)
| | | | | | | | - Youko Oono
- NARO, 13516, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan, 305-8517;
| | - Frank Ordon
- Julius Kuhn-Institut, 98882, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany;
| | - Takao Komatsuda
- Shandong Academy of Agricultural Sciences, 74641, Ji'nan, China
- Tsukuba, Japan;
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Deblieck M, Ordon F, Serfling A. Mapping of prehaustorial resistance against wheat leaf rust in einkorn ( Triticum monococcum), a progenitor of wheat. Front Plant Sci 2023; 14:1252123. [PMID: 37936932 PMCID: PMC10626456 DOI: 10.3389/fpls.2023.1252123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/25/2023] [Indexed: 11/09/2023]
Abstract
Wheat leaf rust (Puccinia triticina) is one of the most significant fungal diseases of wheat, causing substantial yield losses worldwide. Infestation is currently being reduced by fungicide treatments and mostly vertical resistance. However, these measures often break down when the fungal virulence pattern changes, resulting in a breakdown of vertical resistances. In contrast, the prehaustorial resistance (phr) that occurs in the einkorn-wheat leaf rust interaction is race-independent, characterized by an early defense response of plants during the prehaustorial phase of infestation. Einkorn (Triticum monococcum) is closely related to Triticum urartu as a progenitor of wheat and generally shows a high level of resistance against leaf rust of wheat. Hence, einkorn can serve as a valuable source to improve the level of resistance to the pathogen in future wheat lines. In particular, einkorn accession PI272560 is known to exhibit a hypersensitive prehaustorial effector triggered immune reaction, preventing the infection of P. triticina. Remarkably, this effector-triggered immune reaction turned out to be atypical as it is non-race-specific (horizontal). To genetically dissect the prehaustorial resistance (phr) in PI272560, a biparental F2 population of 182 plants was established after crossing PI272560 with the susceptible T. boeoticum accession 36554. Three genetic maps comprising 2,465 DArT-seq markers were constructed, and a major QTL was detected on chromosome 5A. To locate underlying candidate genes, marker sequences flanking the respective QTL were aligned to the T. urartu reference genome and transcriptome data available from the parental accessions were used. Within the QTL interval of approximately 16.13 million base pairs, the expression of genes under inoculated and non-inoculated conditions was analyzed via a massive analysis of cDNA (MACE). Remarkably, a single gene located 3.4 Mbp from the peak marker within the major QTL was upregulated (20- to 95-fold) after the inoculation in the resistant accession in comparison to the susceptible T. boeoticum accession. This gene belongs to a berberine bridge enzyme-like protein that is suspected to interact on the plant surface with glycoside hydrolases (GH) secreted by the fungus and to induce a hypersensitive defense reaction in the plant after fungal infections.
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Sabir K, Rose T, Wittkop B, Stahl A, Snowdon RJ, Ballvora A, Friedt W, Kage H, Léon J, Ordon F, Stützel H, Zetzsche H, Chen TW. Stage-specific genotype-by-environment interactions determine yield components in wheat. Nat Plants 2023; 9:1688-1696. [PMID: 37735253 DOI: 10.1038/s41477-023-01516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/18/2023] [Indexed: 09/23/2023]
Abstract
In cereal crops, environmental fluctuations affect different physiological processes during various developmental phases associated with the formation of yield components. Because these effects are coupled with cultivar-specific phenology, studies investigating environmental responses in different cultivars can give contradictory results regarding key phases impacting yield performance. To dissect how genotype-by-environment interactions affect grain yield in winter wheat, we estimated the sensitivities of yield components to variation in global radiation, temperature and precipitation in 220 cultivars across 81 time-windows ranging from double ridge to seed desiccation. Environmental sensitivity responses were prominent in the short-term physiological subphases of spike and kernel development, causing phenologically dependent, stage-specific genotype-by-environment interactions. Here we reconcile contradicting findings from previous studies and show previously undetected effects; for example, the positive impact of global radiation on kernel weight during canopy senescence. This deep insight into the three-way interactions between phenology, yield formation and environmental fluctuations provides comprehensive new information for breeding and modelling cereal crops.
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Affiliation(s)
- Khadija Sabir
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Till Rose
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Henning Kage
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Frank Ordon
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Hartmut Stützel
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Holger Zetzsche
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Tsu-Wei Chen
- Group of Intensive Plant Food Systems, Albrecht Daniel Thaer Institut of Agricultural and Horticultural Science, Humboldt University Berlin, Berlin, Germany.
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Gauthier K, Pankovic D, Nikolic M, Hobert M, Germeier CU, Ordon F, Perovic D, Niehl A. Nutrients and soil structure influence furovirus infection of wheat. Front Plant Sci 2023; 14:1200674. [PMID: 37600210 PMCID: PMC10436314 DOI: 10.3389/fpls.2023.1200674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Abstract
Soil-borne wheat mosaic virus (SBWMV) and Soil-borne cereal mosaic virus (SBCMV), genus Furovirus, family Virgaviridae, cause significant crop losses in cereals. The viruses are transmitted by the soil-borne plasmodiophorid Polymyxa graminis. Inside P. graminis resting spores, the viruses persist in the soil for long time, which makes the disease difficult to combat. To open up novel possibilities for virus control, we explored the influence of physical and chemical soil properties on infection of wheat with SBWMV and SBCMV. Moreover, we investigated, whether infection rates are influenced by the nutritional state of the plants. Infection rates of susceptible wheat lines were correlated to soil structure parameters and nutrient contents in soil and plants. Our results show that SBWMV and SBCMV infection rates decrease the more water-impermeable the soil is and that virus transmission depends on pH. Moreover, we found that contents of several nutrients in the soil (e.g. phosphorous, magnesium, zinc) and in planta (e.g. nitrogen, carbon, boron, sulfur, calcium) affect SBWMV and SBCMV infection rates. The knowledge generated may help paving the way towards development of a microenvironment-adapted agriculture.
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Affiliation(s)
- Kevin Gauthier
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Brunswick, Germany
| | - Dejana Pankovic
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Miroslav Nikolic
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Mirko Hobert
- State Institute for Agriculture and Horticulture Saxony-Anhalt, Centre for Agricultural Investigations, Bernburg, Germany
| | - Christoph U. Germeier
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Quedlinburg, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Dragan Perovic
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Annette Niehl
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Brunswick, Germany
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Soleimani B, Lehnert H, Trebing S, Habekuß A, Ordon F, Stahl A, Will T. Identification of Markers Associated with Wheat Dwarf Virus (WDV) Tolerance/Resistance in Barley ( Hordeum vulgare ssp. vulgare) Using Genome-Wide Association Studies. Viruses 2023; 15:1568. [PMID: 37515254 PMCID: PMC10385604 DOI: 10.3390/v15071568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Wheat dwarf virus (WDV) causes an important vector transmitted virus disease, which leads to significant yield losses in barley production. Due to the fact that, at the moment, no plant protection products are approved to combat the vector Psammotettix alienus, and this disease cannot be controlled by chemical means, the use of WDV-resistant or -tolerant genotypes is the most efficient method to control and reduce the negative effects of WDV on barley growth and production. In this study, a set of 480 barley genotypes were screened to identify genotypic differences in response to WDV, and five traits were assessed under infected and noninfected conditions. In total, 32 genotypes showed resistance or tolerance to WDV. Subsequently, phenotypic data of 191 out of 480 genotypes combined with 34,408 single-nucleotide polymorphisms (SNPs) were used for a genome-wide association study to identify quantitative trait loci (QTLs) and markers linked to resistance/tolerance to WDV. Genomic regions significantly associated with WDV resistance/tolerance in barley were identified on chromosomes 3H, 4H, 5H, and 7H for traits such as relative virus titer, relative performance of total grain weight, plant height, number of ears per plant, and thousand grain weight.
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Affiliation(s)
- Behnaz Soleimani
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Sarah Trebing
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Torsten Will
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI)-Federal Research Center for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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Hoffie RE, Perovic D, Habekuß A, Ordon F, Kumlehn J. Novel resistance to the Bymovirus BaMMV established by targeted mutagenesis of the PDIL5-1 susceptibility gene in barley. Plant Biotechnol J 2023; 21:331-341. [PMID: 36221782 PMCID: PMC9884012 DOI: 10.1111/pbi.13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The Potyviridae are the largest family of plant-pathogenic viruses. Members of this family are the soil-borne bymoviruses barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), which, upon infection of young winter barley seedlings in autumn, can cause yield losses as high as 50%. Resistance breeding plays a major role in coping with these pathogens. However, some viral strains have overcome the most widely used resistance. Thus, there is a need for novel sources of resistance. In ancient landraces and wild relatives of cultivated barley, alleles of the susceptibility factor PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (PDIL5-1) were identified to confer resistance to all known strains of BaYMV and BaMMV. Although the gene is highly conserved throughout all eukaryotes, barley is thus far the only species for which PDIL5-1-based virus resistance has been reported. Whereas introgression by crossing to the European winter barley breeding pool is tedious, time-consuming and additionally associated with unwanted linkage drag, the present study exemplifies an approach to targeted mutagenesis of two barley cultivars employing CRISPR-associated endonuclease technology to induce site-directed mutations similar to those described for PDIL5-1 alleles that render certain landraces resistant. Homozygous primary mutants were produced in winter barley, and transgene-free homozygous M2 mutants were produced in spring barley. A variety of mutants carrying novel PDIL5-1 alleles were mechanically inoculated with BaMMV, by which all frameshift mutations and certain in-frame mutations were demonstrated to confer resistance to this virus. Under greenhouse conditions, virus-resistant mutants showed no adverse effects in terms of growth and yield.
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Affiliation(s)
- Robert Eric Hoffie
- Plant Reproductive BiologyLeibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Dragan Perovic
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Antje Habekuß
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Frank Ordon
- Institute for Resistance Research and Stress ToleranceJulius Kuehn Institute (JKI)Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Jochen Kumlehn
- Plant Reproductive BiologyLeibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
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Matros A, Schikora A, Ordon F, Wehner G. QTL for induced resistance against leaf rust in barley. Front Plant Sci 2023; 13:1069087. [PMID: 36714737 PMCID: PMC9877528 DOI: 10.3389/fpls.2022.1069087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
Leaf rust caused by Puccinia hordei is one of the major diseases of barley (Hordeum vulgare L.) leading to yield losses up to 60%. Even though, resistance genes Rph1 to Rph28 are known, most of these are already overcome. In this context, priming may promote enhanced resistance to P. hordei. Several bacterial communities such as the soil bacterium Ensifer (syn. Sinorhizobium) meliloti are reported to induce resistance by priming. During quorum sensing in populations of gram negative bacteria, they produce N-acyl homoserine-lactones (AHL), which induce resistance in plants in a species- and genotype-specific manner. Therefore, the present study aims to detect genotypic differences in the response of barley to AHL, followed by the identification of genomic regions involved in priming efficiency of barley. A diverse set of 198 spring barley accessions was treated with a repaired E. meliloti natural mutant strain expR+ch producing a substantial amount of AHL and a transformed E. meliloti strain carrying the lactonase gene attM from Agrobacterium tumefaciens. For P. hordei resistance the diseased leaf area and the infection type were scored 12 dpi (days post-inoculation), and the corresponding relative infection and priming efficiency were calculated. Results revealed significant effects (p<0.001) of the bacterial treatment indicating a positive effect of priming on resistance to P. hordei. In a genome-wide association study (GWAS), based on the observed phenotypic differences and 493,846 filtered SNPs derived from the Illumina 9k iSelect chip, genotyping by sequencing (GBS), and exome capture data, 11 quantitative trait loci (QTL) were identified with a hot spot on the short arm of the barley chromosome 6H, associated to improved resistance to P. hordei after priming with E. meliloti expR+ch. Genes in these QTL regions represent promising candidates for future research on the mechanisms of plant-microbe interactions.
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Affiliation(s)
- Andrea Matros
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Adam Schikora
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Pfrieme AK, Ruckwied B, Habekuß A, Will T, Stahl A, Pillen K, Ordon F. Corrigendum: Identification and validation of Quantitative Trait Loci for Wheat dwarf virus resistance in wheat ( Triticum spp.). Front Plant Sci 2022; 13:1088938. [PMID: 36600912 PMCID: PMC9806797 DOI: 10.3389/fpls.2022.1088938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.828639.].
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Affiliation(s)
- Anne-Kathrin Pfrieme
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Britta Ruckwied
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Antje Habekuß
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Torsten Will
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Andreas Stahl
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute for Agricultural and Nutritional Sciences, Plant Breeding, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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Deblieck M, Szilagyi G, Andrii F, Saranga Y, Lauterberg M, Neumann K, Krugman T, Perovic D, Pillen K, Ordon F. Dissection of a grain yield QTL from wild emmer wheat reveals sub-intervals associated with culm length and kernel number. Front Genet 2022; 13:955295. [DOI: 10.3389/fgene.2022.955295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat (Triticum turgidum ssp. dicoccoides), conferring high grain yield under well-watered and water-limited conditions, was transferred to the elite durum wheat cultivar Uzan (T. turgidum ssp. durum) by a marker-assisted backcross breeding approach. The 2B introgression line turned out to be higher yielding but also exhibited negative traits that likely result from trans-, cis-, or linkage drag effects from the wild emmer parent. In this study, the respective 2BS QTL was subjected to fine-mapping, and a set of 17 homozygote recombinants were phenotyped at BC4F5 generation under water-limited and well-watered conditions at an experimental farm in Israel and at a high-throughput phenotyping platform (LemnaTec-129) in Germany. In general, both experimental setups allowed the identification of sub-QTL intervals related to culm length, kernel number, thousand kernel weight, and harvest index. Sub-QTLs for kernel number and harvest index were detected specifically under either drought stress or well-watered conditions, while QTLs for culm length and thousand-kernel weight were detected in both conditions. Although no direct QTL for grain yield was identified, plants with the sub-QTL for kernel number showed a higher grain yield than the recurrent durum cultivar Uzan under well-watered and mild drought stress conditions. We, therefore, suggest that this sub-QTL might be of interest for future breeding purposes.
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Lauterberg M, Saranga Y, Deblieck M, Klukas C, Krugman T, Perovic D, Ordon F, Graner A, Neumann K. Precision phenotyping across the life cycle to validate and decipher drought-adaptive QTLs of wild emmer wheat ( Triticum turgidum ssp. dicoccoides) introduced into elite wheat varieties. Front Plant Sci 2022; 13:965287. [PMID: 36311121 PMCID: PMC9598872 DOI: 10.3389/fpls.2022.965287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Drought events or the combination of drought and heat conditions are expected to become more frequent due to global warming, and wheat yields may fall below their long-term average. One way to increase climate-resilience of modern high-yielding varieties is by their genetic improvement with beneficial alleles from crop wild relatives. In the present study, the effect of two beneficial QTLs introgressed from wild emmer wheat and incorporated in the three wheat varieties BarNir, Zahir and Uzan was studied under well-watered conditions and under drought stress using non-destructive High-throughput Phenotyping (HTP) throughout the life cycle in a single pot-experiment. Plants were daily imaged with RGB top and side view cameras and watered automatically. Further, at two time points, the quantum yield of photosystem II was measured with a top view FluorCam. The QTL carrying near isogenic lines (NILs) were compared with their corresponding parents by t-test for all non-invasively obtained traits and for the manually determined agronomic and yield parameters. Data quality of phenotypic traits (repeatability) in the controlled HTP experiment was above 85% throughout the life cycle and at maturity. Drought stress had a strong effect on growth in all wheat genotypes causing biomass reduction from 2% up to 70% at early and late points in the drought period, respectively. At maturity, the drought caused 47-55% decreases in yield-related traits grain weight, straw weight and total biomass and reduced TKW by 10%, while water use efficiency (WUE) increased under drought by 29%. The yield-enhancing effect of the introgressed QTLs under drought conditions that were previously demonstrated under field/screenhouse conditions in Israel, could be mostly confirmed in a greenhouse pot experiment using HTP. Daily precision phenotyping enabled to decipher the mode of action of the QTLs in the different genetic backgrounds throughout the entire wheat life cycle. Daily phenotyping allowed a precise determination of the timing and size of the QTLs effect (s) and further yielded information about which image-derived traits are informative at which developmental stage of wheat during the entire life cycle. Maximum height and estimated biovolume were reached about a week after heading, so experiments that only aim at exploring these traits would not need a longer observation period. To obtain information on different onset and progress of senescence, the CVa curves represented best the ongoing senescence of plants. The QTL on 7A in the BarNir background was found to improve yield under drought by increased biomass growth, a higher photosynthetic performance, a higher WUE and a "stay green effect."
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Affiliation(s)
- Madita Lauterberg
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Christian Klukas
- Digitalization in Research and Development (ROM), BASF SE, Ludwigshafen am Rhein, Germany
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. Front Plant Sci 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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Wang Y, Habekuß A, Jayakodi M, Mascher M, Snowdon RJ, Stahl A, Fuß J, Ordon F, Perovic D. High-Resolution Mapping of Barley mild mosaic virus Resistance Gene rym15. Front Plant Sci 2022; 13:908170. [PMID: 35720548 PMCID: PMC9201720 DOI: 10.3389/fpls.2022.908170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), which are transmitted by the soil-borne plasmodiophorid Polymyxa graminis, cause high yield losses in barley. In previous studies, the recessive BaMMV resistance gene rym15, derived from the Japanese landrace Chikurin Ibaraki 1, was mapped on chromosome 6HS of Hordeum vulgare. In this study, 423 F4 segmental recombinant inbred lines (RILs) were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri (139 RILs) and Uschi (284 RILs). A set of 32 competitive allele-specific PCR (KASP) assays, designed using single nucleotide polymorphisms (SNPs) from the barley 50 K Illumina Infinium iSelect SNP chip, genotyping by sequencing (GBS) and whole-genome sequencing (WGS), was used as a backbone for construction of two high-resolution maps. Using this approach, the target locus was narrowed down to 0.161 cM and 0.036 cM in the Igri × Chikurin Ibaraki 1 (I × C) and Chikurin Ibaraki 1 × Uschi (C × U) populations, respectively. Corresponding physical intervals of 11.3 Mbp and 0.281 Mbp were calculated for I × C and C × U, respectively, according to the Morex v3 genome sequence. In the 0.281 Mbp target region, six high confidence (HC) and two low confidence (LC) genes were identified. Genome assemblies of BaMMV-susceptible cultivars Igri and Golden Promise from the barley pan-genome, and a HiFi assembly of Chikurin Ibaraki 1 together with re-sequencing data for the six HC and two LC genes in susceptible parental cultivar Uschi revealed functional SNPs between resistant and susceptible genotypes only in two of the HC genes. These SNPs are the most promising candidates for the development of functional markers and the two genes represent promising candidates for functional analysis.
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Affiliation(s)
- Yaping Wang
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Janina Fuß
- Institute for Clinical Molecular Biology, Competence Centre for Genomic Analysis (CCGA), Kiel University, Kiel, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
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Teklemariam SS, Bayissa KN, Matros A, Pillen K, Ordon F, Wehner G. The genetic diversity of Ethiopian barley genotypes in relation to their geographical origin. PLoS One 2022; 17:e0260422. [PMID: 35622864 PMCID: PMC9140232 DOI: 10.1371/journal.pone.0260422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Ethiopia is recognized as a center of diversity for barley, and its landraces are known for the distinct genetic features compared to other barley collections. The genetic diversity of Ethiopian barley likely results from the highly diverse topography, altitude, climate conditions, soil types, and farming systems. To get detailed information on the genetic diversity a panel of 260 accessions, comprising 239 landraces and 21 barley breeding lines, obtained from the Ethiopian biodiversity institute (EBI) and the national barley improvement program, respectively were studied for their genetic diversity using the 50k iSelect single nucleotide polymorphism (SNP) array. A total of 983 highly informative SNP markers were used for structure and diversity analysis. Three genetically distinct clusters were obtained from the structure analysis comprising 80, 71, and 109 accessions, respectively. Analysis of molecular variance (AMOVA) revealed the presence of higher genetic variation (89%) within the clusters than between the clusters (11%), with moderate genetic differentiation (PhiPT = 0.11) and five accessions were detected as first-generation migrants using Monte Carlo resampling methods. The Mantel test revealed that the genetic distance between accessions is poorly associated with their geographical distance. Despite the observed weak correlation between geographic distance and genetic differentiation, for some regions like Gonder, Jimma, Gamo-Gofa, Shewa, and Welo, more than 50% of the landraces derived from these regions are assigned to one of the three clusters.
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Affiliation(s)
- Surafel Shibru Teklemariam
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Agricultural Research Center, Melkassa, Ethiopia
| | - Kefyalew Negisho Bayissa
- Ethiopian Institute of Agricultural Research (EIAR), National Agricultural Biotechnology Research Center, Holetta, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Federal Research Centre on Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
- * E-mail:
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14
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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). Front Plant Sci 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Terraillon J, Frisch M, Falke KC, Jaiser H, Spiller M, Cselényi L, Krumnacker K, Boxberger S, Habekuß A, Kopahnke D, Serfling A, Ordon F, Zenke-Philippi C. Genomic Prediction Can Provide Precise Estimates of the Genotypic Value of Barley Lines Evaluated in Unreplicated Trials. Front Plant Sci 2022; 13:735256. [PMID: 35528936 PMCID: PMC9072862 DOI: 10.3389/fpls.2022.735256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Genomic prediction has been established in breeding programs to predict the genotypic values of selection candidates without phenotypic data. First results in wheat showed that genomic predictions can also prove useful to select among material for which phenotypic data are available. In such a scenario, the selection candidates are evaluated with low intensity in the field. Genome-wide effects are estimated from the field data and are then used to predict the genotypic values of the selection candidates. The objectives of our simulation study were to investigate the correlations r(y, g) between genomic predictions y and genotypic values g and to compare these with the correlations r(p, g) between phenotypic values p and genotypic values g. We used data from a yield trial of 250 barley lines to estimate variance components and genome-wide effects. These parameters were used as basis for simulations. The simulations included multiple crossing schemes, population sizes, and varying sizes of the components of the masking variance. The genotypic values g of the selection candidates were obtained by genetic simulations, the phenotypic values p by simulating evaluation in the field, and the genomic predictions y by RR-BLUP effect estimation from the phenotypic values. The correlations r(y, g) were greater than the correlations r(p, g) for all investigated scenarios. We conclude that using genomic predictions for selection among candidates tested with low intensity in the field can proof useful for increasing the efficiency of barley breeding programs.
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Affiliation(s)
- Jérôme Terraillon
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - K. Christin Falke
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - Heidi Jaiser
- Saatzucht Josef Breun GmbH & Co. KG, Herzogenaurach, Germany
| | | | - László Cselényi
- W. von Borries-Eckendorf GmbH & Co. KG, Leopoldshöhe, Germany
| | | | | | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Carola Zenke-Philippi
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
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Pfrieme AK, Ruckwied B, Habekuß A, Will T, Stahl A, Pillen K, Ordon F. Identification and Validation of Quantitative Trait Loci for Wheat Dwarf Virus Resistance in Wheat ( Triticum spp.). Front Plant Sci 2022; 13:828639. [PMID: 35498699 PMCID: PMC9047360 DOI: 10.3389/fpls.2022.828639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/09/2022] [Indexed: 05/26/2023]
Abstract
Wheat dwarf virus (WDV) is transmitted by the leafhopper Psammotettix alienus. As a major pathogen in wheat and other cereals, WDV causes high yield losses in many European countries. Due to climate change, insect-transmitted viruses will become more important and the restrictions in the use of insecticides efficient against P. alienus renders growing of WDV resistant/tolerant varieties the only effective strategy to control WDV. So far, there is little information about the possible sources of resistance and no known information about the genome regions responsible for the resistance. In a screening for WDV resistance using artificial inoculation in gauze houses, a panel of 500 wheat accessions including cultivars, gene bank accessions, and wild relatives of wheat was phenotyped for virus titer, infection rate, as well as plant height and yield parameters relative to healthy controls of the same genotype. Additionally, 85 T. aestivum-Ae. tauschii intogression lines were tested for WDV resistance in the greenhouse. A subset of 250 hexaploid wheat accessions was genotyped with the 15k iSelect SNP Chip. By genome-wide association study (GWAS), the quantitative trait loci (QTL) for partial WDV resistance were identified. Within these studies, one cultivar was identified showing an average infection rate of only 5.7%. By analyzing single seed descent (SSD) and doubled haploid (DH) populations comprising 153 and 314 individuals for WDV resistance and by genotyping these with the 25k iSelect SNP Chip, QTL for yield per plant, thousand-grain weight, and relative virus titer were validated on chromosomes 1B, 2B, 3B, 4B, 4A, 5A, 6A, and 7A. These results will be the basis for marker-assisted selection for WDV resistance to replacing the laborious, time-consuming, and technically challenging phenotyping with WDV bearing leafhoppers.
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Affiliation(s)
- Anne-Kathrin Pfrieme
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Britta Ruckwied
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Antje Habekuß
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Torsten Will
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Andreas Stahl
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute for Agricultural and Nutritional Sciences, Plant Breeding, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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Skoppek CI, Punt W, Heinrichs M, Ordon F, Wehner G, Boch J, Streubel J. The barley HvSTP13GR mutant triggers resistance against biotrophic fungi. Mol Plant Pathol 2022; 23:278-290. [PMID: 34816582 PMCID: PMC8743016 DOI: 10.1111/mpp.13161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 05/29/2023]
Abstract
High-yielding and stress-resistant crops are essential to ensure future food supply. Barley is an important crop to feed livestock and to produce malt, but the annual yield is threatened by pathogen infections. Pathogens can trigger an altered sugar partitioning in the host plant, which possibly leads to an advantage for the pathogen. Hampering these processes represents a promising strategy to potentially increase resistance. We analysed the response of the barley monosaccharide transporter HvSTP13 towards biotic stress and its potential use for plant protection. The expression of HvSTP13 increased on bacterial and fungal pathogen-associated molecular pattern (PAMP) application, suggesting a PAMP-triggered signalling that converged on the transcriptional induction of the gene. Promoter studies indicate a region that is probably targeted by transcription factors downstream of PAMP-triggered immunity pathways. We confirmed that the nonfunctional HvSTP13GR variant confers resistance against an economically relevant biotrophic rust fungus in barley. Our experimental setup provides basal prerequisites to further decode the role of HvSTP13 in response to biological stress. Moreover, in line with other studies, our experiments indicate that the alteration of sugar partitioning pathways, in a host-pathogen interaction, is a promising approach to achieve broad and durable resistance in plants.
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Affiliation(s)
- Caroline Ines Skoppek
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
| | - Wilko Punt
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
- Present address:
Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Marleen Heinrichs
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
- Present address:
Department of Cellular BiochemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Frank Ordon
- Institute for Resistance Research and Stress ToleranceJulius Kühn Institute – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Gwendolin Wehner
- Institute for Resistance Research and Stress ToleranceJulius Kühn Institute – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Jens Boch
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
| | - Jana Streubel
- Department of Plant BiotechnologyInstitute of Plant GeneticsLeibniz Universität HannoverHanoverGermany
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Rollar S, Geyer M, Hartl L, Mohler V, Ordon F, Serfling A. Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust ( Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population. Front Plant Sci 2021; 12:684671. [PMID: 35003147 PMCID: PMC8733622 DOI: 10.3389/fpls.2021.684671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/19/2021] [Indexed: 05/20/2023]
Abstract
Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.
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Affiliation(s)
- Sandra Rollar
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Hoffie RE, Otto I, Perovic D, Budhagatapalli N, Habekuß A, Ordon F, Kumlehn J. Targeted Knockout of Eukaryotic Translation Initiation Factor 4E Confers Bymovirus Resistance in Winter Barley. Front Genome Ed 2021; 3:784233. [PMID: 34913048 PMCID: PMC8667817 DOI: 10.3389/fgeed.2021.784233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/04/2021] [Indexed: 12/03/2022] Open
Abstract
The Eukaryotic Translation Initiation Factor 4E (EIF4E) is a well-known susceptibility factor for potyvirus infections in many plant species. The barley yellow mosaic virus disease, caused by the bymoviruses Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), can lead to yield losses of up to 50% in winter barley. In autumn, the roots of young barley plants are infected by the soil-borne plasmodiophoraceous parasite Polymyxa graminis L. that serves as viral vector. Upon viral establishment and systemic spreading into the upper parts of the plants, yellow mosaics occur as first symptoms on leaves. In the further course of plant development, the disease entails leaf necrosis and increased susceptibility to frost damage. Thanks to the rym4 and rym5 allelic variants of the HvEIF4E gene, more than two thirds of current European winter barley cultivars are resistant to BaYMV and BaMMV. However, several strains of BaYMV and BaMMV have already overcome rym4- and rym5-mediated resistance. Accordingly, new resistance-conferring alleles are needed for barley breeding. Therefore, we performed targeted mutagenesis of the EIF4E gene by Cas9 endonuclease in BaMMV/BaYMV-susceptible winter barley cv. “Igri”. Small insertions were generated, resulting in a shift of the translational reading frame, thereby causing the loss-of-function of EIF4E. The mutations occurred in the homozygous state already in the primary mutants. Their progeny proved invariably homozygous and fully resistant to mechanical inoculation with BaMMV. EIF4E knockout plants showed normal growth habit and produced grains, yet exhibited a yield penalty.
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Affiliation(s)
- Robert Eric Hoffie
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingrid Otto
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Nagaveni Budhagatapalli
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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20
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Wang Y, Habekuß A, Snowdon RJ, Ordon F, Perovic D. Delineating the elusive BaMMV resistance gene rym15 in barley by medium-resolution mapping. Mol Breed 2021; 41:76. [PMID: 37309517 PMCID: PMC10236098 DOI: 10.1007/s11032-021-01270-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2 populations from 90.56 to 93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250 s:92r (I × C, χ2 = 0.659) and 140 s:40r (C × U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01270-9.
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Affiliation(s)
- Yaping Wang
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
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Naz AA, Bungartz A, Serfling A, Kamruzzaman M, Schneider M, Wulff BBH, Pillen K, Ballvora A, Oerke EC, Ordon F, Léon J. Lr21 diversity unveils footprints of wheat evolution and its new role in broad-spectrum leaf rust resistance. Plant Cell Environ 2021; 44:3445-3458. [PMID: 34212402 DOI: 10.1111/pce.14144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Aegilops tauschii, the progenitor of the wheat D genome, contains extensive diversity for biotic and abiotic resistance. Lr21 is a leaf rust resistance gene, which did not enter the initial gene flow from Ae. tauschii into hexaploid wheat due to restrictive hybridization events. Here, we used population genetics and high-resolution comparative genomics to study evolutionary and functional divergence of Lr21 in diploid and hexaploid wheats. Population genetics identified the original Lr21, lr21-1 and lr21-2 alleles and their evolutionary history among Ae. tauschii accessions. Comparative genetics of Lr21 variants between Ae. tauschii and cultivated genotypes suggested at least two independent polyploidization events in bread wheat evolution. Further, a recent re-birth of a unique Lr21-tbk allele and its neofunctionalization was discovered in the hexaploid wheat cv. Tobak. Altogether, four independent alleles were investigated and validated for leaf rust resistance in diploid, synthetic hexaploid and cultivated wheat backgrounds. Besides seedling resistance, we uncover a new role of the Lr21 gene in conferring an adult plant field resistance. Seedling and adult plant resistance turned out to be correlated with developmentally dependent variation in Lr21 expression. Our results contribute to understand Lr21 evolution and its role in establishing a broad-spectrum leaf rust resistance in wheat.
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Affiliation(s)
- Ali A Naz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
- Plant Breeding, University of Applied Sciences, Osnabreuck, Germany
| | - Annemarie Bungartz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Quedlinburg, Germany
| | - Mohammad Kamruzzaman
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Michael Schneider
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | | | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Erich-Christian Oerke
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Quedlinburg, Germany
| | - Jens Léon
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
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22
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Beukert U, Pfeiffer N, Ebmeyer E, Hinterberger V, Lueck S, Serfling A, Ordon F, Schulthess AW, Reif JC. Efficiency of a Seedling Phenotyping Strategy to Support European Wheat Breeding Focusing on Leaf Rust Resistance. Biology (Basel) 2021; 10:628. [PMID: 34356483 PMCID: PMC8301088 DOI: 10.3390/biology10070628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/26/2022]
Abstract
Leaf rust resistance is of high importance for a sustainable European wheat production. The expression of known resistance genes starts at different developmental stages of wheat. Breeding for resistance can be supported by a fast, precise, and resource-saving phenotyping. The examination of detached leaf assays of juvenile plants inoculated under controlled conditions and phenotyped by a robotic- and computer-based, high-throughput system is a promising approach in this respect. Within this study, the validation of the phenotyping workflow was conducted based on a winter wheat set derived from Central Europe and examined at different plant developmental stages. Moderate Pearson correlations of 0.38-0.45 comparing leaf rust resistance of juvenile and adult plants were calculated and may be mainly due to different environmental conditions. Specially, the infection under controlled conditions was limited by the application of a single rust race at only one time point. Our results suggest that the diversification with respect to the applied rust race spectrum is promising to increase the consistency of detached leaf assays and the transferability of its results to the field.
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Affiliation(s)
- Ulrike Beukert
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), 06484 Quedlinburg, Germany; (U.B.); (A.S.); (F.O.)
| | - Nina Pfeiffer
- KWS LOCHOW GmbH, 29303 Bergen, Germany; (N.P.); (E.E.)
| | | | - Valentin Hinterberger
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (V.H.); (S.L.); (A.W.S.)
| | - Stefanie Lueck
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (V.H.); (S.L.); (A.W.S.)
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), 06484 Quedlinburg, Germany; (U.B.); (A.S.); (F.O.)
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), 06484 Quedlinburg, Germany; (U.B.); (A.S.); (F.O.)
| | - Albert Wilhelm Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (V.H.); (S.L.); (A.W.S.)
| | - Jochen Christoph Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (V.H.); (S.L.); (A.W.S.)
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23
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Pidon H, Wendler N, Habekuβ A, Maasberg A, Ruge-Wehling B, Perovic D, Ordon F, Stein N. High-resolution mapping of Rym14 Hb, a wild relative resistance gene to barley yellow mosaic disease. Theor Appl Genet 2021; 134:823-833. [PMID: 33263784 PMCID: PMC7925471 DOI: 10.1007/s00122-020-03733-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/18/2020] [Indexed: 05/11/2023]
Abstract
We mapped the Rym14Hb resistance locus to barley yellow mosaic disease in a 2Mbp interval. The co-segregating markers will be instrumental for marker-assisted selection in barley breeding. Barley yellow mosaic disease is caused by Barley yellow mosaic virus and Barley mild mosaic virus and leads to severe yield losses in barley (Hordeum vulgare) in Central Europe and East-Asia. Several resistance loci are used in barley breeding. However, cases of resistance-breaking viral strains are known, raising concerns about the durability of those genes. Rym14Hb is a dominant major resistance gene on chromosome 6HS, originating from barley's secondary genepool wild relative Hordeum bulbosum. As such, the resistance mechanism may represent a case of non-host resistance, which could enhance its durability. A susceptible barley variety and a resistant H. bulbosum introgression line were crossed to produce a large F2 mapping population (n = 7500), to compensate for a ten-fold reduction in recombination rate compared to intraspecific barley crosses. After high-throughput genotyping, the Rym14Hb locus was assigned to a 2Mbp telomeric interval on chromosome 6HS. The co-segregating markers developed in this study can be used for marker-assisted introgression of this locus into barley elite germplasm with a minimum of linkage drag.
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Affiliation(s)
- Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany.
| | - Neele Wendler
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574, Einbeck, Germany
| | - Antje Habekuβ
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Anja Maasberg
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Brigitte Ruge-Wehling
- Institute for Breeding Research On Agricultural Crops, Julius Kühn Institute (JKI), Groß Lüsewitz, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Von Siebold Straße 8, 37075, Göttingen, Germany.
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24
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Abstract
Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.
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Affiliation(s)
- Kefyalew Negisho
- Ethiopian Institute of Agricultural Research (EIAR), National Agricultural Biotechnology Research Center, Holeta, Ethiopia
| | - Surafel Shibru
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Research Center, Melkassa, Ethiopia
| | - Klaus Pillen
- Martin-Luther-University, Institute of Agricultural and Nutritional Sciences, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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25
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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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26
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Abstract
Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.
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Affiliation(s)
| | | | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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27
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Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. Theor Appl Genet 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
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Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
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Zetzsche H, Friedt W, Ordon F. Breeding progress for pathogen resistance is a second major driver for yield increase in German winter wheat at contrasting N levels. Sci Rep 2020; 10:20374. [PMID: 33230232 PMCID: PMC7683597 DOI: 10.1038/s41598-020-77200-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023] Open
Abstract
Breeding has substantially increased the genetic yield potential, but fungal pathogens are still major constraints for wheat production. Therefore, breeding success for resistance and its impact on yield were analyzed on a large panel of winter wheat cultivars, representing breeding progress in Germany during the last decades, in large scale field trials under different fungicide and nitrogen treatments. Results revealed a highly significant effect of genotype (G) and year (Y) on resistances and G × Y interactions were significant for all pathogens tested, i.e. leaf rust, strip rust, powdery mildew and Fusarium head blight. N-fertilization significantly increased the susceptibility to biotrophic and hemibiotrophic pathogens. Resistance was significantly improved over time but at different rates for the pathogens. Although the average progress of resistance against each pathogen was higher at the elevated N level in absolute terms, it was very similar at both N levels on a relative basis. Grain yield was increased significantly over time under all treatments but was considerably higher without fungicides particularly at high N-input. Our results strongly indicate that wheat breeding resulted in a substantial increase of grain yield along with a constant improvement of resistance to fungal pathogens, thereby contributing to an environment-friendly and sustainable wheat production.
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Affiliation(s)
- Holger Zetzsche
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484, Quedlinburg, Germany.
| | - Wolfgang Friedt
- iFZ Research Centre for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus Liebig University, 35392, Giessen, Germany
| | - Frank Ordon
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484, Quedlinburg, Germany
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29
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Deblieck M, Fatiukha A, Grundman N, Merchuk-Ovnat L, Saranga Y, Krugman T, Pillen K, Serfling A, Makalowski W, Ordon F, Perovic D. GenoTypeMapper: graphical genotyping on genetic and sequence-based maps. Plant Methods 2020; 16:123. [PMID: 32944061 PMCID: PMC7488165 DOI: 10.1186/s13007-020-00665-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. RESULTS We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. CONCLUSIONS In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.
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Affiliation(s)
- Mathieu Deblieck
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Andrii Fatiukha
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Norbert Grundman
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Lianne Merchuk-Ovnat
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Yehoshua Saranga
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, 76100 Rehovot, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Abba Khoushy Ave 199, 3498838 Haifa, Israel
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Wojciech Makalowski
- Faculty of Medicine, Institute of Bioinformatics, Westfälische Wilhelms-Universität Münster, Niels-Stensen Strasse 14, 48149 Münster, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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30
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Beukert U, Liu G, Thorwarth P, Boeven PHG, Longin CFH, Zhao Y, Ganal M, Serfling A, Ordon F, Reif JC. The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat. Theor Appl Genet 2020; 133:2171-2181. [PMID: 32281003 PMCID: PMC7311497 DOI: 10.1007/s00122-020-03588-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/31/2020] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Hybrid wheat breeding is a promising strategy to improve the level of leaf rust and stripe rust resistance in wheat. Leaf rust and stripe rust belong to the most important fungal diseases in wheat production. Due to a dynamic development of new virulent races, epidemics appear in high frequency and causes significant losses in grain yield and quality. Therefore, research is needed to develop strategies to breed wheat varieties carrying highly efficient resistances. Stacking of dominant resistance genes through hybrid breeding is such an approach. Within this study, we investigated the genetic architecture of leaf rust and stripe rust resistance of 1750 wheat hybrids and their 230 parental lines using a genome-wide association study. We observed on average a lower rust susceptibility for hybrids in comparison to their parental inbred lines and some hybrids outperformed their better parent with up to 56%. Marker-trait associations were identified on chromosome 3D and 4A for leaf rust and on chromosome 2A, 2B, and 6A for stripe rust resistance by using a genome-wide association study with a Bonferroni-corrected threshold of P < 0.10. Detected loci on chromosomes 4A and 2A were located within previously reported genomic regions affecting leaf rust and stripe rust resistance, respectively. The degree of dominance was for most associations favorable in the direction of improved resistance. Thus, resistance can be increased in hybrid wheat breeding by fixing complementary leaf rust and stripe rust resistance genes with desired dominance effects in opposite parental pools.
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Affiliation(s)
- Ulrike Beukert
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Guozheng Liu
- BASF Agricultural Solutions Belgium NV, Technologiepark 101, 9052, Zwijnaarde, Ghent, Belgium
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - Philipp H G Boeven
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany.
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31
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Jiang C, Kan J, Ordon F, Perovic D, Yang P. Bymovirus-induced yellow mosaic diseases in barley and wheat: viruses, genetic resistances and functional aspects. Theor Appl Genet 2020; 133:1623-1640. [PMID: 32008056 DOI: 10.1007/s00122-020-03555-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/24/2020] [Indexed: 05/20/2023]
Abstract
Bymovirus-induced yellow mosaic diseases seriously threaten global production of autumn-sown barley and wheat, which are two of the presently most important crops around the world. Under natural field conditions, the diseases are caused by infection of soil-borne plasmodiophorid Polymyxa graminis-transmitted bymoviruses of the genus Bymovirus of the family Potyviridae. Focusing on barley and wheat, this article summarizes the achievements on taxonomy, geography and host specificity of these disease-conferring viruses, as well as the genetics of resistance in barley, wheat and wild relatives. Moreover, based on recent progress of barley and wheat genomics, germplasm resources and large-scale sequencing, the exploration and isolation of corresponding resistant genes from wheat and barley as well as relatives, no matter what a large and complicated genome is present, are becoming feasible and are discussed. Furthermore, the foreseen advances on cloning of the resistance or susceptibility-encoding genes, which will provide the possibility to explore the functional interaction between host plants and soil-borne viral pathogens, are discussed as well as the benefits for marker-assisted resistance breeding in barley and wheat.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China.
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32
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Beukert U, Thorwarth P, Zhao Y, Longin CFH, Serfling A, Ordon F, Reif JC. Comparing the Potential of Marker-Assisted Selection and Genomic Prediction for Improving Rust Resistance in Hybrid Wheat. Front Plant Sci 2020; 11:594113. [PMID: 33193553 PMCID: PMC7655876 DOI: 10.3389/fpls.2020.594113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/05/2020] [Indexed: 05/20/2023]
Abstract
Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with those of genome-wide prediction. The hybrid wheat population included 1,744 single crosses from 236 parental lines. The genotypes were fingerprinted using a 15k SNP array and evaluated for leaf rust and stripe rust resistance in multi-location field trials. We observed a high congruency of putative quantitative trait loci (QTL) for leaf rust resistance between both populations. This was not the case for stripe rust resistance. Accordingly, prediction accuracy of the detected QTL was moderate for leaf rust but low for stripe rust resistance. Genome-wide selection increased the prediction accuracy slightly for stripe rust albeit at a low level but not for leaf rust. Thus, our findings suggest that marker-assisted selection seems to be a robust and efficient tool to improve leaf rust resistance in European wheat hybrids.
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Affiliation(s)
- Ulrike Beukert
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Jochen C. Reif,
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33
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Soleimani B, Lehnert H, Keilwagen J, Plieske J, Ordon F, Naseri Rad S, Ganal M, Beier S, Perovic D. Comparison Between Core Set Selection Methods Using Different Illumina Marker Platforms: A Case Study of Assessment of Diversity in Wheat. Front Plant Sci 2020; 11:1040. [PMID: 32754184 PMCID: PMC7381318 DOI: 10.3389/fpls.2020.01040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Collections of plant genetic resources stored in genebanks are an important source of genetic diversity for improvement in plant breeding programs and for conservation of natural variation. The establishment of reduced representative collections from a large set of genotypes is a valuable tool that provides cost-effective access to the diversity present in the whole set. Software like Core Hunter 3 is available to generate high quality core sets. In addition, general clustering approaches, e.g., k-medoids, are available to subdivide a large data set into small groups with maximum genetic diversity between groups. Illumina genotyping platforms are a very efficient tool for the assessment of genetic diversity of plant genetic resources. The accumulation of genotyping data over time using commercial genotyping platforms raises the question of how such huge amount of information can be efficiently used for creating core collections. In the present study, after developing a 15K wheat Infinium array with 12,908 SNPs and genotyping a set of 479 hexaploid winter wheat lines (Triticum aestivum), a larger data set was created by merging 411 lines previously genotyped with the 90K iSelect array. Overlaying the markers from the 15K and 90K arrays enabled the identification of a common set of 12,806 markers, suggesting that the 15K array is a valuable and cost-effective resource for plant breeding programs. Finally, we selected genetically diverse core sets out of these 890 wheat genotypes derived from five collections based on the common markers from the 15K and 90K SNP arrays. Two different approaches, k-medoids and Core Hunter 3 were compared,and k-medoids was identified as an efficient method for selecting small core sets out of a large collection of genotypes while retaining the genetic diversity of the original population.
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Affiliation(s)
- Behnaz Soleimani
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute, Quedlinburg, Germany
| | - Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | | | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute, Quedlinburg, Germany
| | - Sara Naseri Rad
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | | | - Sebastian Beier
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute, Quedlinburg, Germany
- *Correspondence: Dragan Perovic,
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34
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Novakazi F, Afanasenko O, Anisimova A, Platz GJ, Snowdon R, Kovaleva O, Zubkovich A, Ordon F. Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres). Theor Appl Genet 2019; 132:2633-2650. [PMID: 31209538 DOI: 10.1007/s00122-019-03378-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/09/2019] [Indexed: 05/28/2023]
Abstract
A total of 449 barley accessions were phenotyped for Pyrenophora teres f. teres resistance at three locations and in greenhouse trials. Genome-wide association studies identified 254 marker-trait associations corresponding to 15 QTLs. Net form of net blotch is one of the most important diseases of barley and is present in all barley growing regions. Under optimal conditions, it causes high yield losses of 10-40% and reduces grain quality. The most cost-effective and environmentally friendly way to prevent losses is growing resistant cultivars, and markers linked to effective resistance factors can accelerate the breeding process. Here, 449 barley accessions expressing different levels of resistance comprising landraces and commercial cultivars from the centres of diversity were selected. The set was phenotyped for seedling resistance to three isolates in controlled-environment tests and for adult plant resistance at three field locations (Belarus, Germany and Australia) and genotyped with the 50 k iSelect chip. Genome-wide association studies using 33,818 markers and a compressed mixed linear model to account for population structure and kinship revealed 254 significant marker-trait associations corresponding to 15 distinct QTL regions. Four of these regions were new QTL that were not described in previous studies, while a total of seven regions influenced resistance in both seedlings and adult plants.
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Affiliation(s)
- Fluturë Novakazi
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Olga Afanasenko
- All-Russian Research Institute of Plant Protection, 196608 shosse Podbelski 3, Saint Petersburg, Russia
| | - Anna Anisimova
- All-Russian Research Institute of Plant Protection, 196608 shosse Podbelski 3, Saint Petersburg, Russia
| | - Gregory J Platz
- Queensland Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Olga Kovaleva
- Federal Research Center the N. I. Vavilov All-Russian Institute of Plant Genetic Resources, 42-44, B. Morskaya Street, Saint Petersburg, Russia, 190000
| | - Alexandr Zubkovich
- Republican Unitary Enterprise, The Research and Practical Center of the National Academy of Sciences of Belarus for Arable Farming, Timiriazeva Street 1, 222160, Zhodino, Belarus
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur-Straße 27, 06484, Quedlinburg, Germany.
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35
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Voss-Fels KP, Stahl A, Wittkop B, Lichthardt C, Nagler S, Rose T, Chen TW, Zetzsche H, Seddig S, Majid Baig M, Ballvora A, Frisch M, Ross E, Hayes BJ, Hayden MJ, Ordon F, Leon J, Kage H, Friedt W, Stützel H, Snowdon RJ. Breeding improves wheat productivity under contrasting agrochemical input levels. Nat Plants 2019; 5:706-714. [PMID: 31209285 DOI: 10.1038/s41477-019-0445-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 05/10/2019] [Indexed: 05/22/2023]
Abstract
The world cropping area for wheat exceeds that of any other crop, and high grain yields in intensive wheat cropping systems are essential for global food security. Breeding has raised yields dramatically in high-input production systems; however, selection under optimal growth conditions is widely believed to diminish the adaptive capacity of cultivars to less optimal cropping environments. Here, we demonstrate, in a large-scale study spanning five decades of wheat breeding progress in western Europe, where grain yields are among the highest worldwide, that breeding for high performance in fact enhances cultivar performance not only under optimal production conditions but also in production systems with reduced agrochemical inputs. New cultivars incrementally accumulated genetic variants conferring favourable effects on key yield parameters, disease resistance, nutrient use efficiency, photosynthetic efficiency and grain quality. Combining beneficial, genome-wide haplotypes could help breeders to more efficiently exploit available genetic variation, optimizing future yield potential in more sustainable production systems.
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Affiliation(s)
- Kai P Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Carolin Lichthardt
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Sabrina Nagler
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Till Rose
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Tsu-Wei Chen
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Holger Zetzsche
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Sylvia Seddig
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Mirza Majid Baig
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Matthias Frisch
- Institute for Agronomy and Plant Breeding II, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Elizabeth Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Matthew J Hayden
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Frank Ordon
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Jens Leon
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Henning Kage
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
| | - Hartmut Stützel
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany.
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
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36
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Voss-Fels KP, Stahl A, Wittkop B, Lichthardt C, Nagler S, Rose T, Chen TW, Zetzsche H, Seddig S, Majid Baig M, Ballvora A, Frisch M, Ross E, Hayes BJ, Hayden MJ, Ordon F, Leon J, Kage H, Friedt W, Stützel H, Snowdon RJ. Breeding improves wheat productivity under contrasting agrochemical input levels. Nat Plants 2019; 5:706-714. [PMID: 31209285 DOI: 10.5281/zenodo.1316947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 05/10/2019] [Indexed: 05/27/2023]
Abstract
The world cropping area for wheat exceeds that of any other crop, and high grain yields in intensive wheat cropping systems are essential for global food security. Breeding has raised yields dramatically in high-input production systems; however, selection under optimal growth conditions is widely believed to diminish the adaptive capacity of cultivars to less optimal cropping environments. Here, we demonstrate, in a large-scale study spanning five decades of wheat breeding progress in western Europe, where grain yields are among the highest worldwide, that breeding for high performance in fact enhances cultivar performance not only under optimal production conditions but also in production systems with reduced agrochemical inputs. New cultivars incrementally accumulated genetic variants conferring favourable effects on key yield parameters, disease resistance, nutrient use efficiency, photosynthetic efficiency and grain quality. Combining beneficial, genome-wide haplotypes could help breeders to more efficiently exploit available genetic variation, optimizing future yield potential in more sustainable production systems.
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Affiliation(s)
- Kai P Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Carolin Lichthardt
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Sabrina Nagler
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Till Rose
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Tsu-Wei Chen
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany
| | - Holger Zetzsche
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Sylvia Seddig
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Mirza Majid Baig
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
| | - Matthias Frisch
- Institute for Agronomy and Plant Breeding II, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Elizabeth Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Matthew J Hayden
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, Victoria, Australia
| | - Frank Ordon
- Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Jens Leon
- Institute of Crop Science and Resource Conservation, Chair of Plant Breeding, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Henning Kage
- Department of Agronomy and Crop Science, Christian Albrechts University of Kiel, Kiel, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
| | - Hartmut Stützel
- Institute of Horticultural Production Systems, Leibniz University Hannover, Hannover, Germany.
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
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Shi L, Jiang C, He Q, Habekuß A, Ordon F, Luan H, Shen H, Liu J, Feng Z, Zhang J, Yang P. Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV. Theor Appl Genet 2019; 132:1777-1788. [PMID: 30815718 DOI: 10.1007/s00122-019-03314-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/15/2019] [Indexed: 05/25/2023]
Abstract
A novel rare allele of the barley host factor gene eIF4E for BaMMV/BaYMV infection was identified in an Iranian landrace that showed broad resistance to barley yellow mosaic virus disease, and molecular markers facilitating efficient selection were developed. The soil-borne yellow mosaic virus disease caused by different strains of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) is a major threat to winter barley (Hordeum vulgare) production in Europe and East Asia. However, the exploration of resistant germplasm or casual genes for barley breeding is rather limited in relation to the rapid diversification of viral strains. Here, we identified an Iranian barley landrace 'HOR3298,' which represented complete resistance to BaYMV and BaMMV. In contrast to rym4 and rym5, which act as the predominant source in Europe and East Asia for breeding resistant cultivars over decades and which have been overcome by several virulent isolates, this landrace showed broad-spectrum resistance to multiple isolates of BaYMV/BaMMV in the fields of Germany and China. By employment of bulked segregant RNA sequencing, test for allelism, and haplotype analysis, a recessive resistance gene in 'HOR3298' was genetically mapped coincident with the host factor eukaryotic translation initiation factor 4E (eIF4E, causal gene of rym4 and rym5). The eIF4EHOR3298 allele encoded for a novel haplotype that contained an exclusive nucleotide mutation (G565A) in the coding sequence. The easily handled markers were developed based on the exclusively rare variation, providing precise selection of this allele. Thus, this work provided a novel reliable resistance source and the feasible marker-assisted selection assays that can be used in breeding for barley yellow mosaic virus disease resistance in cultivated barley.
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Affiliation(s)
- Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Antje Habekuß
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Haiye Luan
- Institute of Agricultural Sciences of Coastal Area Jiangsu, Yancheng, 224002, China
| | - Huiquan Shen
- Institute of Agricultural Sciences of Coastal Area Jiangsu, Yancheng, 224002, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Fazlikhani L, Keilwagen J, Kopahnke D, Deising H, Ordon F, Perovic D. High Resolution Mapping of Rph MBR1012 Conferring Resistance to Puccinia hordei in Barley ( Hordeum vulgare L.). Front Plant Sci 2019; 10:640. [PMID: 31191570 PMCID: PMC6541035 DOI: 10.3389/fpls.2019.00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/29/2019] [Indexed: 06/01/2023]
Abstract
Isolation of disease resistance genes in barley was hampered by the large genome size, but has become easy due to the availability of the reference genome sequence. During the last years, many genomic resources, e.g., the Illumina 9K iSelect, the 50K Infinium arrays, the Barley Genome Zipper, POPSEQ, and genotyping by sequencing (GBS), were developed that enable enhanced gene isolation in combination with the barley genome sequence. In the present study, we developed a fine map of the barley leaf rust resistance gene Rph MBR1012. 537 segmental homozygous recombinant inbred lines (RILs) derived from 4775 F2-plants were used to construct a high-resolution mapping population (HRMP). The Barley Genome Zipper, the 9K iSelect chip, the 50K Infinium chip and GBS were used to develop 56 molecular markers located in the target interval of 8 cM. This interval was narrowed down to about 0.07 cM corresponding to 0.44 Mb of the barley reference genome. Eleven low-confidence and 18 high-confidence genes were identified in this interval. Five of these are putative disease resistance genes and were subjected to allele-specific sequencing. In addition, comparison of the genetic map and the reference genome revealed an inversion of 1.34 Mb located distally to the resistance locus. In conclusion, the barley reference sequence and the respective gene annotation delivered detailed information about the physical size of the target interval, the genes located in the target interval and facilitated the efficient development of molecular markers for marker-assisted selection for RphMBR1012.
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Affiliation(s)
- Leila Fazlikhani
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Holger Deising
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
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Lehnert H, Serfling A, Friedt W, Ordon F. Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat ( Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions. Front Plant Sci 2018; 9:1728. [PMID: 30568663 PMCID: PMC6290350 DOI: 10.3389/fpls.2018.01728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/07/2018] [Indexed: 05/06/2023]
Abstract
In the majority of wheat growing areas worldwide, the incidence of drought stress has increased significantly resulting in a negative impact on plant development and grain yield. Arbuscular mycorrhizal symbiosis is known to improve drought stress tolerance of wheat. However, quantitative trait loci (QTL) involved in the response to drought stress conditions in the presence of mycorrhizae are largely unknown. Therefore, a diverse set consisting of 94 bread wheat genotypes was phenotyped under drought stress and well watered conditions in the presence and absence of mycorrhizae. Grain yield and yield components, drought stress related traits as well as response to mycorrhizae were assessed. In parallel, wheat accessions were genotyped by using the 90k iSelect chip, resulting in a set of 15511 polymorphic and mapped SNP markers, which were used for genome-wide association studies (GWAS). In general, drought stress tolerance of wheat was significantly increased in the presence of mycorrhizae compared to drought stress tolerance in the absence of mycorrhizae. However, genotypes differed in their response to mycorrhizae under drought stress conditions. Several QTL regions on different chromosomes were detected associated with grain yield and yield components under drought stress conditions. Furthermore, two genome regions on chromosomes 3D and 7D were found to be significantly associated with the response to mycorrhizae under drought stress conditions. Overall, the results reveal that inoculation of wheat with mycorrhizal fungi significantly improves drought stress tolerance and that QTL regions associated with the response to mycorrhizae under drought stress conditions exist in wheat. Further research is necessary to validate detected QTL regions. However, this study may be the starting point for the identification of candidate genes associated with drought stress tolerance and response to mycorrhizae under drought stress conditions. Maybe in future, these initial results will help to contribute to use mycorrhizal fungi effectively in agriculture and combine new approaches i.e., use of genotypic variation in response to mycorrhizae under drought stress conditions with existing drought tolerance breeding programs to develop new drought stress tolerant genotypes.
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Affiliation(s)
- Heike Lehnert
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Albrecht Serfling
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Wolfgang Friedt
- IFZ Research Centre for Biosystems, Land Use and Nutrition, Plant Breeding Department, Justus Liebig University, Gießen, Germany
| | - Frank Ordon
- Institute of Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), Quedlinburg, Germany
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40
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Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P, Schüler D, Sharma R, Pasam RK, Rutten T, Guo G, Xu D, Zhang J, Herren G, Müller T, Krattinger SG, Keller B, Jiang Y, González MY, Zhao Y, Habekuß A, Färber S, Ordon F, Lange M, Börner A, Graner A, Reif JC, Scholz U, Mascher M, Stein N. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 2018; 51:319-326. [PMID: 30420647 DOI: 10.1038/s41588-018-0266-x] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/26/2018] [Indexed: 01/22/2023]
Abstract
Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.
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Affiliation(s)
- Sara G Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Agriculture and Food, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | - Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Elena Rey Mazón
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martín Basterrechea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,University of Dundee at the James Hutton Institute, Invergowrie, UK
| | - Raj K Pasam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maria Y González
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Sandra Färber
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,Center for Integrated Breeding Research, Georg-August-Universität Göttingen, Göttingen, Germany.
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41
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Majka M, Serfling A, Czembor P, Ślusarkiewicz-Jarzina A, Kwiatek MT, Ordon F, Wiśniewska H. Resistance of ( Aegilops tauschii × Secale cereale) × Triticosecale Hybrids to Leaf Rust ( Puccinia triticina) Determined on the Macroscopic and Microscopic Level. Front Plant Sci 2018; 9:1418. [PMID: 30319677 PMCID: PMC6168713 DOI: 10.3389/fpls.2018.01418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Leaf rust caused by Puccinia triticina Eriks belongs to the most important fungal pathogens of wheat (Triticum aestivum L.) and triticale (× Triticosecale). Effective resistance to leaf rust is both, cost-effective and environmentally safe. Many wild Aegilops species carry unknown resistances against fungal diseases and are characterized by a high genetic variability. The main goal of this work was to examine the resistance of (Aegilops tauschii × Secale cereale) × Triticosecale hybrids to leaf rust in inoculation tests with different races of P. triticina. Hybrid plants were selected for the presence of 2D chromosome/s in the triticale background using fluorescence and genomic in situ hybridization. The presence of leaf rust resistance genes was confirmed with closely linked molecular markers, i.e., Xgdm35 and Xgwm296. 14 genotypes of BC2F4 - BC2F6 hybrid plants with the monosomic addition of chromosome 2D (M2DA) were analyzed together with nine control lines. Resistance was determined at the macroscopic and microscopic level at the seedling and adult plant stage (flag leaf). In general, results revealed limited resistance of hybrid plants at the seedling stage, followed by an increase of the resistance level at later stages of plant development. This indicates that respective hybrid plants may exhibit APR resistance conferred by Lr22a introgressed from Ae. tauschii. On the basis of the macroscopic and microscopic analysis, this kind of resistance turned out to be additive and race-specific. We selected four monosomic 2D addition triticale genotypes highly resistant to P. triticina infection at the two main stages of plant development. From the selected genotypes, we obtained 26 doubled haploid lines among which two lines with doubled additional chromosomes 2D of Ae. tauschii can be used for further breeding to increase leaf rust resistance of cultivated triticale.
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Affiliation(s)
- Maciej Majka
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Paweł Czembor
- Department of Genetics and Plant Breeding, Plant Breeding and Acclimatization Institute – National Research Institute, Błonie, Poland
| | | | - Michał Tomasz Kwiatek
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Halina Wiśniewska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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42
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Babben S, Schliephake E, Janitza P, Berner T, Keilwagen J, Koch M, Arana-Ceballos FA, Templer SE, Chesnokov Y, Pshenichnikova T, Schondelmaier J, Börner A, Pillen K, Ordon F, Perovic D. Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes. BMC Genomics 2018; 19:409. [PMID: 29843596 PMCID: PMC5975666 DOI: 10.1186/s12864-018-4795-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT. RESULTS Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirmed and new AA substitutions in CBF-A3, CBF-A15, VRN-B3, PPD-B1 and PPD-D1 located at highly conserved sites were detected. Since these results rely on phenotypic data obtained at five locations in 2 years, detection of significant associations of FT to AA changes in CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1 may be exploited in marker assisted breeding for frost tolerance in winter wheat. CONCLUSIONS A set of 65 primer pairs for the genes mentioned above from a previous study was BLASTed against the IWGSC RefSeq resulting in the identification of 39 primer combinations covering the full length of 19 genes. This work demonstrates the usefulness of the IWGSC RefSeq in specific primer development for highly conserved gene families in hexaploid wheat and, that a candidate gene association genetics approach based on the sequence data is an efficient tool to identify new alleles of genes important for the response to abiotic stress in wheat.
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Affiliation(s)
- Steve Babben
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Edgar Schliephake
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Philipp Janitza
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Thomas Berner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Jens Keilwagen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Michael Koch
- Deutsche Saatveredelung AG (DSV), Weißenburger Str. 5, 59557 Lippstadt, Nordrhein-Westfalen Germany
| | - Fernando Alberto Arana-Ceballos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and Reproduction, Correnstraße 3, 06466 Seeland OT Gatersleben, Saxony-Anhalt Germany
| | - Sven Eduard Templer
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9B, 50931 Cologne, Nordrhein-Westfalen Germany
| | - Yuriy Chesnokov
- Agrophysical Research Institute (AFI), Grazhdanskii prosp. 14, 195220 St. Petersburg, Russia
| | - Tatyana Pshenichnikova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Jörg Schondelmaier
- Saaten-Union Biotec GmbH, Hovedisser Str. 94, 33818 Leopoldshoehe, Nordrhein-Westfalen Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and Reproduction, Correnstraße 3, 06466 Seeland OT Gatersleben, Saxony-Anhalt Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 3, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Frank Ordon
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Dragan Perovic
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
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Paulmann MK, Kunert G, Zimmermann MR, Theis N, Ludwig A, Meichsner D, Oelmüller R, Gershenzon J, Habekuss A, Ordon F, Furch ACU, Will T. Barley yellow dwarf virus Infection Leads to Higher Chemical Defense Signals and Lower Electrophysiological Reactions in Susceptible Compared to Tolerant Barley Genotypes. Front Plant Sci 2018; 9:145. [PMID: 29563918 PMCID: PMC5845851 DOI: 10.3389/fpls.2018.00145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
Barley yellow dwarf virus (BYDV) is a phloem limited virus that is persistently transmitted by aphids. Due to huge yield losses in agriculture, the virus is of high economic relevance. Since the control of the virus itself is not possible, tolerant barley genotypes are considered as the most effective approach to avoid yield losses. Although several genes and quantitative trait loci are known and used in barley breeding for virus tolerance, little is known about molecular and physiological backgrounds of this trait. Therefore, we compared the anatomy and early defense responses of a virus susceptible to those of a virus-tolerant cultivar. One of the very early defense responses is the transmission of electrophysiological reactions. Electrophysiological reactions to BYDV infection might differ between susceptible and tolerant cultivars, since BYDV causes disintegration of sieve elements in susceptible cultivars. The structure of vascular bundles, xylem vessels and sieve elements was examined using microscopy. All three were significantly decreased in size in infected susceptible plants where the virus causes disintegration of sieve elements. This could be associated with an uncontrolled ion exchange between the sieve-element lumen and apoplast. Further, a reduced electrophysiological isolation would negatively affect the propagation of electrophysiological reactions. To test the influence of BYDV infection on electrophysiological reactions, electropotential waves (EPWs) induced by leaf-tip burning were recorded using aphids as bioelectrodes. EPWs in infected susceptible plants disappeared already after 10 cm in contrast to those in healthy susceptible or infected tolerant or healthy tolerant plants. Another early plant defense reaction is an increase in reactive oxygen species (ROS). Using a fluorescent dye, we found a significant increase in ROS content in infected susceptible plants but not in infected tolerant plants. Similar results were found for the phytohormones abscisic acid and three jasmonates. Salicylic acid levels were generally higher after BYDV infection compared to uninfected plants. Heat stimulation caused an increase in jasmonates. By shedding light on the plant defense mechanisms against BYDV, this study, provides further knowledge for breeding virus tolerant plants.
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Affiliation(s)
- Maria K. Paulmann
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Grit Kunert
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Matthias R. Zimmermann
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Nina Theis
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Biology, Elms College, Chicopee, MA, United States
| | - Anatoli Ludwig
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Doreen Meichsner
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Antje Habekuss
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Quedlinburg, Germany
| | - Alexandra C. U. Furch
- Department of Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Torsten Will
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Quedlinburg, Germany
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Vatter T, Maurer A, Perovic D, Kopahnke D, Pillen K, Ordon F. Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM). PLoS One 2018; 13:e0191666. [PMID: 29370232 PMCID: PMC5784946 DOI: 10.1371/journal.pone.0191666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/09/2018] [Indexed: 11/18/2022] Open
Abstract
The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.
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Affiliation(s)
- Thomas Vatter
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Doris Kopahnke
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Quedlinburg, Germany
- * E-mail:
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Osthushenrich T, Frisch M, Zenke-Philippi C, Jaiser H, Spiller M, Cselényi L, Krumnacker K, Boxberger S, Kopahnke D, Habekuß A, Ordon F, Herzog E. Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley. Front Plant Sci 2018; 9:1899. [PMID: 30627135 PMCID: PMC6309237 DOI: 10.3389/fpls.2018.01899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/07/2018] [Indexed: 05/10/2023]
Abstract
Background: The expected genetic variance is an important criterion for the selection of crossing partners which will produce superior combinations of genotypes in their progeny. The advent of molecular markers has opened up new vistas for obtaining precise predictors for the genetic variance of a cross, but fast prediction methods that allow plant breeders to select crossing partners based on already available data from their breeding programs without complicated calculations or simulation of breeding populations are still lacking. The main objective of the present study was to demonstrate the practical applicability of an analytical approach for the selection of superior cross combinations with experimental data from a barley breeding program. We used genome-wide marker effects to predict the yield means and genetic variances of 14 DH families resulting from crosses of four donor lines with five registered elite varieties with the genotypic information of the parental lines. For the validation of the predicted parameters, the analytical approach was extended by the masking variance as a major component of phenotypic variance. The predicted parameters were used to fit normal distribution curves of the phenotypic values and to conduct an Anderson-Darling goodness-of-fit test for the observed phenotypic data of the 14 DH families from the field trial. Results: There was no evidence that the observed phenotypic values deviated from the predicted phenotypic normal distributions in 13 out of 14 crosses. The correlations between the observed and the predicted means and the observed and predicted variances were r = 0.95 and r = 0.34, respectively. After removing two crosses with downward outliers in the phenotypic data, the correlation between the observed and predicted variances increased to r = 0.76. A ranking of the 14 crosses based on the sum of predicted mean and genetic variance identified the 50% best crosses from the field trial correctly. Conclusions: We conclude that the prediction accuracy of the presented approach is sufficiently high to identify superior crosses even with limited phenotypic data. We therefore expect that the analytical approach based on genome-wide marker effects is applicable in a wide range of breeding programs.
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Affiliation(s)
- Tanja Osthushenrich
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - Carola Zenke-Philippi
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
| | - Heidi Jaiser
- Saatzucht Josef Breun GmbH & Co. KG, Herzogenaurach, Germany
| | | | - László Cselényi
- W. von Borries-Eckendorf GmbH & Co. KG, Leopoldshöhe, Germany
| | | | | | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Eva Herzog
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany
- *Correspondence: Eva Herzog
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Vatter T, Maurer A, Kopahnke D, Perovic D, Ordon F, Pillen K. A nested association mapping population identifies multiple small effect QTL conferring resistance against net blotch (Pyrenophora teres f. teres) in wild barley. PLoS One 2017; 12:e0186803. [PMID: 29073176 PMCID: PMC5658061 DOI: 10.1371/journal.pone.0186803] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/06/2017] [Indexed: 12/02/2022] Open
Abstract
The net form of net blotch caused by the necrotrophic fungus Pyrenophora teres f. teres is a major disease of barley, causing high yield losses and reduced malting and feed quality. Exploiting the allelic richness of wild barley proved to be a valuable tool to broaden the genetic base of resistance of modern elite cultivars. In this study, a SNP-based nested association mapping (NAM) study was conducted to map QTL for P. teres resistance in the barley population HEB-25 comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area followed by calculation of the average ordinate (AO) and scoring of the reaction type (RT) in two-year field trials a large variability of net blotch resistance across and within families of HEB-25 was observed. Genotype response to net blotch infection showed a range of 48.2% for AO (0.9-49.1%) and 6.4 for RT (2.2-8.6). NAM based on 5,715 informative SNPs resulted in the identification of 24 QTL for resistance against net blotch. Out of these, six QTL are considered novel showing no correspondence to previously reported QTL for net blotch resistance. Overall, variation of net blotch resistance in HEB-25 turned out to be controlled by small effect QTL. Results indicate the presence of alleles in HEB-25 differing in their effect on net blotch resistance. Results provide valuable information regarding the genetic architecture of the complex barley-P. teres f. teres interaction as well as for the improvement of net blotch resistance of elite barley cultivars.
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Affiliation(s)
- Thomas Vatter
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
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Thorwarth P, Ahlemeyer J, Bochard AM, Krumnacker K, Blümel H, Laubach E, Knöchel N, Cselényi L, Ordon F, Schmid KJ. Genomic prediction ability for yield-related traits in German winter barley elite material. Theor Appl Genet 2017; 130:1669-1683. [PMID: 28534096 DOI: 10.1007/s00122-017-2917-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 05/04/2017] [Indexed: 05/25/2023]
Abstract
Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L.) elite material families and old cultivars, which reflect the breeding history of barley in Germany. Crosses of parents selected from the training set were used to create a set of double-haploid families consisting of 750 genotypes. Those were used to confirm prediction ability estimates based on a cross-validation with the training set material using 11 different genomic prediction models. Population structure was inferred with dimensionality reduction methods like discriminant analysis of principle components and the influence of population structure on prediction ability was investigated. In addition to the size of the training set, marker density is of crucial importance for genomic prediction. We used genome-wide linkage disequilibrium and persistence of linkage phase as indicators to estimate that 11,203 evenly spaced markers are required to capture all QTL effects. Although a 9k SNP array does not contain a sufficient number of polymorphic markers for long-term genomic selection, we obtained fairly high prediction accuracies ranging from 0.31 to 0.71 for the traits earing, hectoliter weight, spikes per square meter, thousand kernel weight and yield and show that they result from the close genetic relatedness of the material. Our work contributes to designing long-term genetic prediction programs for barley breeding.
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Affiliation(s)
- Patrick Thorwarth
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Jutta Ahlemeyer
- Deutsche Saatveredelung AG, Weissenburger Str. 5, 59557, Lippstadt, Germany
| | | | | | - Hubert Blümel
- Secoba Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany
| | - Eberhard Laubach
- Nordsaat-Saatzucht GmbH, Hofweg 8, 23899, Gudow-Segrahn, Germany
| | - Nadine Knöchel
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - László Cselényi
- W. von Borries-Eckendorf GmbH & Co. KG, Hovedisser Str. 92, 33818, Leopoldshöhe, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.
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Meise P, Jozefowicz AM, Uptmoor R, Mock HP, Ordon F, Schum A. Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro. J Proteomics 2017; 166:68-82. [PMID: 28733104 DOI: 10.1016/j.jprot.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/10/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
Abstract
Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific. SIGNIFICANCE Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars.
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Affiliation(s)
- Philipp Meise
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany
| | - Anna Maria Jozefowicz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Physiology and Cell Biology, Applied Biochemistry, OT Gatersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Ralf Uptmoor
- University of Rostock, Faculty of Agricultural and Environmental Science, Justus-von-Liebig-Weg 6, 18055 Rostock, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Physiology and Cell Biology, Applied Biochemistry, OT Gatersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Frank Ordon
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany
| | - Annegret Schum
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, OT Groß Lüsewitz, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany.
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Lehnert H, Serfling A, Enders M, Friedt W, Ordon F. Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum). New Phytol 2017; 215:779-791. [PMID: 28517039 DOI: 10.1111/nph.14595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 05/23/2023]
Abstract
Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study. Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed. The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.
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Affiliation(s)
- Heike Lehnert
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Matthias Enders
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Wolfgang Friedt
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | - Frank Ordon
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
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50
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Templer SE, Ammon A, Pscheidt D, Ciobotea O, Schuy C, McCollum C, Sonnewald U, Hanemann A, Förster J, Ordon F, von Korff M, Voll LM. Metabolite profiling of barley flag leaves under drought and combined heat and drought stress reveals metabolic QTLs for metabolites associated with antioxidant defense. J Exp Bot 2017; 68:1697-1713. [PMID: 28338908 PMCID: PMC5441916 DOI: 10.1093/jxb/erx038] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Barley (Hordeum vulgare L.) is among the most stress-tolerant crops; however, not much is known about the genetic and environmental control of metabolic adaptation of barley to abiotic stresses. We have subjected a genetically diverse set of 81 barley accessions, consisting of Mediterranean landrace genotypes and German elite breeding lines, to drought and combined heat and drought stress at anthesis. Our aim was to (i) investigate potential differences in morphological, physiological, and metabolic adaptation to the two stress scenarios between the Mediterranean and German barley genotypes and (ii) identify metabolic quantitative trait loci (mQTLs). To this end, we have genotyped the investigated barley lines with an Illumina iSelect 9K array and analyzed a set of 57 metabolites from the primary C and N as well as antioxidant metabolism in flag leaves under control and stress conditions. We found that drought-adapted genotypes attenuate leaf carbon metabolism much more strongly than elite lines during drought stress adaptation. Furthermore, we identified mQTLs for flag leaf γ-tocopherol, glutathione, and succinate content by association genetics that co-localize with genes encoding enzymes of the pathways producing these antioxidant metabolites. Our results provide the molecular basis for breeding barley cultivars with improved abiotic stress tolerance.
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Affiliation(s)
- Sven Eduard Templer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute of Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Alexandra Ammon
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - David Pscheidt
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Otilia Ciobotea
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Christian Schuy
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Christopher McCollum
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Anja Hanemann
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, D-91074 Herzogenaurach, Germany
| | - Jutta Förster
- SAATEN-UNION BIOTEC GmbH, Hovedisser Strasse 92, D-33818 Leopoldshöhe, Germany
| | - Frank Ordon
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute of Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany
| | - Maria von Korff
- Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine-Universität Düsseldorf, Institute for Plant Genetics, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Lars Matthias Voll
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Staudtstr. 5, D-91058 Erlangen, Germany
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