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Schwertfirm G, Schneider M, Haase F, Riedel C, Lazzaro M, Ruge-Wehling B, Schweizer G. Genome-wide association study revealed significant SNPs for anthracnose resistance, seed alkaloids and protein content in white lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:155. [PMID: 38858311 PMCID: PMC11164739 DOI: 10.1007/s00122-024-04665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume alternative to soybean in Central Europe, but its cultivation is risky due to the fungal disease anthracnose that can cause severe yield damage. In addition, management of seed alkaloids is critical for human nutrition and animal feed. We report on a white lupin collection of genebank accessions, advanced breeding lines and cultivars that was genotyped and phenotypically characterized for anthracnose resistance and seed alkaloids and protein levels. Using genotyping by sequencing (GBS), SeqSNP-targeted GBS, BiomarkX genotyping and Sanger sequencing, a genetic resource of genome-wide SNPs for white lupin was established. We determined anthracnose resistance in two years field trials at four locations with infection rows and measured seed alkaloids and protein levels by near-infrared spectroscopy (NIRS). Few white lupin breeding lines showed anthracnose resistance comparable or better than Celina and Frieda, currently the best commercial cultivars in Germany. NIRS estimates for seed alkaloids and protein levels revealed variation in the white lupin collection. Using genome-wide association studies (GWAS), we identified SNPs significantly associated with anthracnose resistance in the field representing known and new genomic regions. We confirmed the pauper locus and detected new SNP markers significantly associated with seed alkaloids. For the first time, we present loci associated with total grain protein content. Finally, we tested the potential of genomic prediction (GP) in predicting the phenotype of these three quantitative traits. Application of results and resources are discussed in the context of fostering breeding programs for white lupin.
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Affiliation(s)
- Grit Schwertfirm
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany.
| | - Michael Schneider
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Florian Haase
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Christine Riedel
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Kleeberg 14, 94099, Ruhstorf a. d. Rott, Germany
| | - Mariateresa Lazzaro
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Brigitte Ruge-Wehling
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Guenther Schweizer
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
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2
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Mancinotti D, Czepiel K, Taylor JL, Golshadi Galehshahi H, Møller LA, Jensen MK, Motawia MS, Hufnagel B, Soriano A, Yeheyis L, Kjaerulff L, Péret B, Staerk D, Wendt T, Nelson MN, Kroc M, Geu-Flores F. The causal mutation leading to sweetness in modern white lupin cultivars. SCIENCE ADVANCES 2023; 9:eadg8866. [PMID: 37540741 PMCID: PMC10403207 DOI: 10.1126/sciadv.adg8866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
Lupins are high-protein crops that are rapidly gaining interest as hardy alternatives to soybean; however, they accumulate antinutritional alkaloids of the quinolizidine type (QAs). Lupin domestication was enabled by the discovery of genetic loci conferring low QA levels (sweetness), but the precise identity of the underlying genes remains uncertain. We show that pauper, the most common sweet locus in white lupin, encodes an acetyltransferase (AT) unexpectedly involved in the early QA pathway. In pauper plants, a single-nucleotide polymorphism (SNP) strongly impairs AT activity, causing pathway blockage. We corroborate our hypothesis by replicating the pauper chemotype in narrow-leafed lupin via mutagenesis. Our work adds a new dimension to QA biosynthesis and establishes the identity of a lupin sweet gene for the first time, thus facilitating lupin breeding and enabling domestication of other QA-containing legumes.
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Affiliation(s)
- Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Katarzyna Czepiel
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, Poznań, Poland
| | - Jemma L. Taylor
- Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Hajar Golshadi Galehshahi
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | | | | | - Mohammed Saddik Motawia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Bárbara Hufnagel
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alexandre Soriano
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | | | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Benjamin Péret
- IPSiM, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Dan Staerk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Toni Wendt
- Traitomic A/S, J.C. Jacobsens Gade 14, 1799 Copenhagen, Denmark
| | - Matthew N. Nelson
- Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, Poznań, Poland
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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3
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Alkemade JA, Baroncelli R, Messmer MM, Hohmann P. Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose. MOLECULAR PLANT PATHOLOGY 2023; 24:616-627. [PMID: 37078402 DOI: 10.1111/mpp.13332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
- Centre for Studies on Bioinspired Agro-Enviromental Technology, Università di Napoli Federico II, Portici, 80055, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Bonaplanta, BioCrops Innovations SL, Manresa, Spain
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4
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Annicchiarico P, de Buck AJ, Vlachostergios DN, Heupink D, Koskosidis A, Nazzicari N, Crosta M. White Lupin Adaptation to Moderately Calcareous Soils: Phenotypic Variation and Genome-Enabled Prediction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1139. [PMID: 36903997 PMCID: PMC10005150 DOI: 10.3390/plants12051139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
White lupin is a promising high-protein crop, the cultivation of which is limited by a lack of adaptation to soils that are even just mildly calcareous. This study aimed to assess the phenotypic variation, the trait architecture based on a GWAS, and the predictive ability of genome-enabled models for grain yield and contributing traits of a genetically-broad population of 140 lines grown in an autumn-sown environment of Greece (Larissa) and a spring-sown environment of the Netherlands (Ens) that featured moderately calcareous and alkaline soils. We found large genotype × environment interaction and modest or nil genetic correlation for line responses across locations for grain yield, a lime susceptibility score, and other traits, with the exception of individual seed weight and plant height. The GWAS identified significant SNP markers associated with various traits that were markedly inconsistent across locations, while providing direct or indirect evidence for widespread polygenic trait control. Genomic selection proved to be a feasible strategy, owing to a moderate predictive ability for yield and lime susceptibility in Larissa (the site featuring greater lime soil stress). Other supporting results for breeding programs where the identification of a candidate gene for lime tolerance and the high reliability of genome-enabled predictions for individual seed weight.
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Affiliation(s)
- Paolo Annicchiarico
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics, 26900 Lodi, Italy
| | | | - Dimitrios N. Vlachostergios
- Institute of Industrial and Forage Crops, Hellenic Agricultural Organization “Demeter”, 41335 Larissa, Greece
| | | | - Avraam Koskosidis
- Institute of Industrial and Forage Crops, Hellenic Agricultural Organization “Demeter”, 41335 Larissa, Greece
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics, 26900 Lodi, Italy
| | - Margherita Crosta
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics, 26900 Lodi, Italy
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5
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Pecetti L, Annicchiarico P, Crosta M, Notario T, Ferrari B, Nazzicari N. White Lupin Drought Tolerance: Genetic Variation, Trait Genetic Architecture, and Genome-Enabled Prediction. Int J Mol Sci 2023; 24:ijms24032351. [PMID: 36768674 PMCID: PMC9916572 DOI: 10.3390/ijms24032351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
White lupin is a high-protein crop requiring drought tolerance improvement. This study focused on a genetically-broad population of 138 lines to investigate the phenotypic variation and genotype × environment interaction (GEI) for grain yield and other traits across drought-prone and moisture-favourable managed environments, the trait genetic architecture and relevant genomic regions by a GWAS using 9828 mapped SNP markers, and the predictive ability of genomic selection (GS) models. Water treatments across two late cropping months implied max. available soil water content of 60-80% for favourable conditions and from wilting point to 15% for severe drought. Line yield responses across environments featured a genetic correlation of 0.84. Relatively better line yield under drought was associated with an increased harvest index. Two significant QTLs emerged for yield in each condition that differed across conditions. Line yield under stress displayed an inverse linear relationship with the onset of flowering, confirmed genomically by a common major QTL. An adjusted grain yield computed as deviation from phenology-predicted yield acted as an indicator of intrinsic drought tolerance. On the whole, the yield in both conditions and the adjusted yield were polygenic, heritable, and exploitable by GS with a high predictive ability (0.62-0.78). Our results can support selection for climatically different drought-prone regions.
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6
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Jha UC, Nayyar H, von Wettberg EJB, Naik YD, Thudi M, Siddique KHM. Legume Pangenome: Status and Scope for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223041. [PMID: 36432770 PMCID: PMC9696634 DOI: 10.3390/plants11223041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 05/31/2023]
Abstract
In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur 208024, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Eric J. B. von Wettberg
- Department and Plant and Soil Science, Gund Institute for the Environment, The University of Vermont, Burlington, VT 05405, USA
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
- Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Department of Agricultural Biotechnology and Molecular Biology, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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7
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Surkova SY, Samsonova MG. Mechanisms of Vernalization-Induced Flowering in Legumes. Int J Mol Sci 2022; 23:ijms23179889. [PMID: 36077286 PMCID: PMC9456104 DOI: 10.3390/ijms23179889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes.
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8
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Plewiński P, Rychel-Bielska S, Kozak B, Maureira-Butler IJ, Iqbal MM, Nelson MN, Książkiewicz M. FLOWERING LOCUS T indel variants confer vernalization-independent and photoperiod-insensitive flowering of yellow lupin ( Lupinus luteus L.). HORTICULTURE RESEARCH 2022; 9:uhac180. [PMID: 36338848 PMCID: PMC9627521 DOI: 10.1093/hr/uhac180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Ongoing climate change has considerably reduced the seasonal window for crop vernalization, concurrently expanding cultivation area into northern latitudes with long-day photoperiod. To address these changes, cool season legume breeders need to understand molecular control of vernalization and photoperiod. A key floral transition gene integrating signals from these pathways is the Flowering locus T (FT). Here, a recently domesticated grain legume, yellow lupin (Lupinus luteus L.), was explored for potential involvement of FT homologues in abolition of vernalization and photoperiod requirements. Two FTa (LlutFTa1a and LlutFTa1b) and FTc (LlutFTc1 and LlutFTc2) homologues were identified and sequenced for two contrasting parents of a reference recombinant inbred line (RIL) population, an early-flowering cultivar Wodjil and a late-flowering wild-type P28213. Large deletions were detected in the 5' promoter regions of three FT homologues. Quantitative trait loci were identified for flowering time and vernalization response in the RIL population and in a diverse panel of wild and domesticated accessions. A 2227 bp deletion found in the LlutFTc1 promoter was linked with early phenology and vernalization independence, whereas LlutFTa1a and LlutFTc2 indels with photoperiod responsiveness. Comparative mapping highlighted convergence of FTc1 indel evolution in two Old World lupin species, addressing both artificial selection during domestication and natural adaptation to short season environmental conditions. We concluded that rapid flowering in yellow lupin is associated with the de-repression of the LlutFTc1 homologue from the juvenile phase, putatively due to the elimination of all binding sites in the promoter region for the AGAMOUS-like 15 transcription factor.
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Affiliation(s)
- Piotr Plewiński
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Iván J Maureira-Butler
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Muhammad Munir Iqbal
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, 6009, WA, Australia
- Genomics WA, Joint initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, QEII campus, Nedlands, 6009, Western Australia, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
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9
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Alkemade JA, Nazzicari N, Messmer MM, Annicchiarico P, Ferrari B, Voegele RT, Finckh MR, Arncken C, Hohmann P. Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1011-1024. [PMID: 34988630 PMCID: PMC8942938 DOI: 10.1007/s00122-021-04014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 05/11/2023]
Abstract
GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
| | | | - Barbara Ferrari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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10
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Osorio CE, Till BJ. A Bitter-Sweet Story: Unraveling the Genes Involved in Quinolizidine Alkaloid Synthesis in Lupinus albus. FRONTIERS IN PLANT SCIENCE 2022; 12:795091. [PMID: 35154186 PMCID: PMC8826574 DOI: 10.3389/fpls.2021.795091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 05/05/2023]
Abstract
Alkaloids are part of a structurally diverse group of over 21,000 cyclic nitrogen-containing secondary metabolites that are found in over 20% of plant species. Lupinus albus are naturally containing quinolizidine alkaloid (QA) legumes, with wild accessions containing up to 11% of QA in seeds. Notwithstanding their clear advantages as a natural protecting system, lupin-breeding programs have selected against QA content without proper understanding of quinolizidine alkaloid biosynthetic pathway. This review summarizes the current status in this field, with focus on the utilization of natural mutations such as the one contained in pauper locus, and more recently the development of molecular markers, which along with the advent of sequencing technology, have facilitated the identification of candidate genes located in the pauper region. New insights for future research are provided, including the utilization of differentially expressed genes located on the pauper locus, as candidates for genome editing. Identification of the main genes involved in the biosynthesis of QA will enable precision breeding of low-alkaloid, high nutrition white lupin. This is important as plant based high quality protein for food and feed is an essential for sustainable agricultural productivity.
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Affiliation(s)
- Claudia E. Osorio
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
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11
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Hufnagel B, Soriano A, Taylor J, Divol F, Kroc M, Sanders H, Yeheyis L, Nelson M, Péret B. Pangenome of white lupin provides insights into the diversity of the species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2532-2543. [PMID: 34346542 PMCID: PMC8633493 DOI: 10.1111/pbi.13678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Accepted: 07/22/2021] [Indexed: 05/21/2023]
Abstract
White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.
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Affiliation(s)
- Bárbara Hufnagel
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
- Present address:
CIRADUMR AGAP InstitutSEAPAG TeamPetit‐BourgGuadeloupeF‐97170French West Indies
| | | | | | - Fanchon Divol
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
| | - Magdalena Kroc
- Institute of Plant Genetics Polish Academy of SciencesPoznanPoland
| | | | | | | | - Benjamin Péret
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
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Zafeiriou I, Polidoros AN, Baira E, Kasiotis KM, Machera K, Mylona PV. Mediterranean White Lupin Landraces as a Valuable Genetic Reserve for Breeding. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112403. [PMID: 34834766 PMCID: PMC8619254 DOI: 10.3390/plants10112403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 05/21/2023]
Abstract
Legumes crops are important for sustainable agriculture and global food security. Among them white lupin (Lupinus albus L.), is characterized by exceptional protein content of high nutritional value, competitive to that of soybean (Glycine max) and is well adapted to rainfed agriculture. However, its high seed-quinolizidine alkaloid (QA) content impedes its direct integration to human diet and animal feed. Additionally, its cultivation is not yet intensive, remains confined to local communities and marginal lands in Mediterranean agriculture, while adaptation to local microclimates restrains its cultivation from expanding globally. Hence, modern white lupin breeding aims to exploit genetic resources for the development of "sweet" elite cultivars, resilient to biotic adversities and well adapted for cultivation on a global level. Towards this aim, we evaluated white lupin local landrace germplasm from Greece, since the country is considered a center of white lupin diversity, along with cultivars and breeding lines for comparison. Seed morphological diversity and molecular genetic relationships were investigated. Most of the landraces were distinct from cultivars, indicating the uniqueness of their genetic make-up. The presence of pauper "sweet" marker allele linked to low seed QA content in some varieties was detected in one landrace, two breeding lines, and the cultivars. However, QA content in the examined genotypes did not relate with the marker profile, indicating that the marker's predictive power is limited in this material. Marker alleles for vernalization unresponsiveness were detected in eight landraces and alleles for anthracnose resistance were found in two landraces, pointing to the presence of promising germplasm for utilization in white lupin breeding. The rich lupin local germplasm genetic diversity and the distinct genotypic composition compared to elite cultivars, highlights its potential use as a source of important agronomic traits to support current breeding efforts and assist its integration to modern sustainable agriculture.
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Affiliation(s)
- Ioannis Zafeiriou
- Institute of Plant Breeding & Genetic Resources, HAO-DEMETER, 57001 Thermi, Greece;
| | - Alexios N. Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eirini Baira
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (E.B.); (K.M.K.); (K.M.)
| | - Konstantinos M. Kasiotis
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (E.B.); (K.M.K.); (K.M.)
| | - Kyriaki Machera
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (E.B.); (K.M.K.); (K.M.)
| | - Photini V. Mylona
- Institute of Plant Breeding & Genetic Resources, HAO-DEMETER, 57001 Thermi, Greece;
- Correspondence: ; Tel.: +30-2310-478-904
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Scharff LB, Saltenis VLR, Jensen PE, Baekelandt A, Burgess AJ, Burow M, Ceriotti A, Cohan J, Geu‐Flores F, Halkier BA, Haslam RP, Inzé D, Klein Lankhorst R, Murchie EH, Napier JA, Nacry P, Parry MAJ, Santino A, Scarano A, Sparvoli F, Wilhelm R, Pribil M. Prospects to improve the nutritional quality of crops. Food Energy Secur 2021. [DOI: 10.1002/fes3.327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Lars B. Scharff
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Vandasue L. R. Saltenis
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Poul Erik Jensen
- Department of Food Science University of Copenhagen Frederiksberg Denmark
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | | | - Meike Burow
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology National Research Council (CNR) Milan Italy
| | | | - Fernando Geu‐Flores
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Barbara Ann Halkier
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | | | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
| | - Erik H. Murchie
- School of Biosciences University of Nottingham Loughborough UK
| | | | - Philippe Nacry
- BPMPUniv MontpellierINRAECNRSMontpellier SupAgro Montpellier France
| | | | - Angelo Santino
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR) Lecce Italy
| | - Aurelia Scarano
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR) Lecce Italy
| | - Francesca Sparvoli
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology Julius Kühn‐Institut – Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Mathias Pribil
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
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14
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Alkemade JA, Messmer MM, Arncken C, Leska A, Annicchiarico P, Nazzicari N, Książkiewicz M, Voegele RT, Finckh MR, Hohmann P. A High-Throughput Phenotyping Tool to Identify Field-Relevant Anthracnose Resistance in White Lupin. PLANT DISEASE 2021; 105:1719-1727. [PMID: 33337235 DOI: 10.1094/pdis-07-20-1531-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The seed- and air-borne pathogen Colletotrichum lupini, the causal agent of lupin anthracnose, is the most important disease in white lupin (Lupinus albus) worldwide and can cause total yield loss. The aims of this study were to establish a reliable high-throughput phenotyping tool to identify anthracnose resistance in white lupin germplasm and to evaluate a genomic prediction model, accounting for previously reported resistance quantitative trait loci, on a set of independent lupin genotypes. Phenotyping under controlled conditions, performing stem inoculation on seedlings, showed to be applicable for high throughput, and its disease score strongly correlated with field plot disease assessments (r = 0.95, P < 0.0001) and yield (r = -0.64, P = 0.035). Traditional one-row field disease phenotyping showed no significant correlation with field plot disease assessments (r = 0.31, P = 0.34) and yield (r = -0.45, P = 0.17). Genomically predicted resistance values showed no correlation with values observed under controlled or field conditions, and the parental lines of the recombinant inbred line population used for constructing the prediction model exhibited a resistance pattern opposite to that displayed in the original (Australian) environment used for model construction. Differing environmental conditions, inoculation procedures, or population structure may account for this result. Phenotyping a diverse set of 40 white lupin accessions under controlled conditions revealed eight accessions with improved resistance to anthracnose. The standardized area under the disease progress curves (sAUDPC) ranged from 2.1 to 2.8, compared with the susceptible reference accession with a sAUDPC of 3.85. These accessions can be incorporated into white lupin breeding programs. In conclusion, our data support stem inoculation-based disease phenotyping under controlled conditions as a time-effective approach to identify field-relevant resistance, which can now be applied to further identify sources of resistance and their underlying genetics.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Agata Leska
- Getreidezüchtung Peter Kunz (gzpk), Feldbach, Switzerland
| | | | - Nelson Nazzicari
- CREA, Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | | | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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15
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Quantitative Control of Early Flowering in White Lupin ( Lupinus albus L.). Int J Mol Sci 2021; 22:ijms22083856. [PMID: 33917799 PMCID: PMC8068107 DOI: 10.3390/ijms22083856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 12/03/2022] Open
Abstract
White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.
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Zhang R, Chen Z, Zhang L, Yao W, Xu Z, Liao B, Mi Y, Gao H, Jiang C, Duan L, Ji A. Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata. Front Genet 2021; 11:601689. [PMID: 33537059 PMCID: PMC7848199 DOI: 10.3389/fgene.2020.601689] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/22/2020] [Indexed: 11/22/2022] Open
Abstract
Andrographolide, which is enriched in the leaves of Andrographis paniculata, has been known as “natural antibiotic” due to its pharmacological activities such as anti-inflammatory, antimicrobial and antioxidant effects. Several key enzymes in andrographolide biosynthetic pathway have been studied since the genome sequences were released, but its regulatory mechanism remains unknown. WRKY transcription factors proteins have been reported to regulate plant secondary metabolism, development as well as biotic and abiotic stresses. Here, WRKY transcription factors related to andrographolide biosynthesis were systematically identified, including sequences alignment, phylogenetic analysis, chromosomal distribution, gene structure, conserved motifs, synteny, alternative splicing event and Gene ontology (GO) annotation. A total of 58 WRKYs were identified in Chuanxinlian genome and phylogenetically classified into three groups. Moreover, nine WRKY genes underwent alternative splicing events. Furthermore, the combination of binding site prediction, gene-specific expression patterns, and phylogenetic analysis suggested that 7 WRKYs (ApWRKY01, ApWRKY08, ApWRKY12, ApWRKY14, ApWRKY19, ApWRKY20, and ApWRKY50) might regulate andrographolide biosynthesis. This study laid a foundation for understanding the regulatory mechanism of andrographolide biosynthesis and the improvement and breeding of Andrographis paniculata varieties.
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Affiliation(s)
- Rongrong Zhang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenzhen Chen
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Libing Zhang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Yao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhichao Xu
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Baosheng Liao
- Key Laboratory of Bioactive Substances and Resources, Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yaolei Mi
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co. Ltd., Ganzhou, China
| | - Han Gao
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Chunhong Jiang
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co. Ltd., Ganzhou, China
| | - Lixin Duan
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Aijia Ji
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
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17
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The Puzzling Fate of a Lupin Chromosome Revealed by Reciprocal Oligo-FISH and BAC-FISH Mapping. Genes (Basel) 2020; 11:genes11121489. [PMID: 33322080 PMCID: PMC7764521 DOI: 10.3390/genes11121489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Old World lupins constitute an interesting model for evolutionary research due to diversity in genome size and chromosome number, indicating evolutionary genome reorganization. It has been hypothesized that the polyploidization event which occurred in the common ancestor of the Fabaceae family was followed by a lineage-specific whole genome triplication (WGT) in the lupin clade, driving chromosome rearrangements. In this study, chromosome-specific markers were used as probes for heterologous fluorescence in situ hybridization (FISH) to identify and characterize structural chromosome changes among the smooth-seeded (Lupinus angustifolius L., Lupinus cryptanthus Shuttlew., Lupinus micranthus Guss.) and rough-seeded (Lupinus cosentinii Guss. and Lupinus pilosus Murr.) lupin species. Comparative cytogenetic mapping was done using FISH with oligonucleotide probes and previously published chromosome-specific bacterial artificial chromosome (BAC) clones. Oligonucleotide probes were designed to cover both arms of chromosome Lang06 of the L. angustifolius reference genome separately. The chromosome was chosen for the in-depth study due to observed structural variability among wild lupin species revealed by BAC-FISH and supplemented by in silico mapping of recently released lupin genome assemblies. The results highlighted changes in synteny within the Lang06 region between the lupin species, including putative translocations, inversions, and/or non-allelic homologous recombination, which would have accompanied the evolution and speciation.
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18
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Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time. Sci Rep 2020; 10:19174. [PMID: 33154532 PMCID: PMC7645761 DOI: 10.1038/s41598-020-76197-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Anthracnose susceptibility and ill-adapted flowering time severely affect Lupinus luteus yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with Lupinus angustifolius; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with L. angustifolius. Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the Lanr1 gene and Flowering-locus-T of L. angustifolius. This suggests orthologous genes for both traits in the L. luteus genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in L. luteus, and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.
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Rychel-Bielska S, Plewiński P, Kozak B, Galek R, Ksia̧żkiewicz M. Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin ( Lupinus angustifolius L.). FRONTIERS IN PLANT SCIENCE 2020; 11:572135. [PMID: 33193508 PMCID: PMC7663182 DOI: 10.3389/fpls.2020.572135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a moderate-yielding legume crop known for its high grain protein content and contribution to soil improvement. It is cultivated under photoperiods ranging from 9 to 17 h, as a spring-sown (in colder locations) or as an autumn-sown crop (in warmer regions). Wild populations require a prolonged cold period, called vernalization, to induce flowering. The key achievement of L. angustifolius domestication was the discovery of two natural mutations (named Ku and Jul) conferring vernalization independence. These mutations are overlapping deletion variants in the promoter of LanFTc1, a homolog of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene. The third deletion, named here as Pal, was recently found in primitive germplasm. In this study, we genotyped L. angustifolius germplasm that differs in domestication status and geographical origin for LanFTc1 alleles, which we then phenotyped to establish flowering time and vernalization responsiveness. The Ku and Jul lines were vernalization-independent and early flowering, wild (ku) lines were vernalization-dependent and late flowering, whereas the Pal line conferred intermediate phenotype. Three lines representing ku, Pal, and Ku alleles were subjected to gene expression surveys under 8- and 16-h photoperiods. FT homologs (LanFTa1, LanFTa2, LanFTc1, and LanFTc2) and some genes selected by recent expression quantitative trait loci mapping were analyzed. Expression profiles of LanFTc1 and LanAGL8 (AGAMOUS-like 8) matched observed differences in flowering time between genotypes, highlighted by high induction after vernalization in the ku line. Moreover, these genes revealed altered circadian clock control in Pal line under short days. LanFD (FD) and LanCRLK1 (CALCIUM/CALMODULIN-REGULATED RECEPTOR-LIKE KINASE 1) were negatively responsive to vernalization in Ku and Pal lines but positively responsive or variable in ku, whereas LanUGT85A2 (UDP-GLUCOSYL TRANSFERASE 85A2) was significantly suppressed by vernalization in all lines. Such a pattern suggests the opposite regulation of these gene pairs in the vernalization pathway. LanCRLK1 and LanUGT85A2 are homologs of A. thaliana genes involved in the FLOWERING LOCUS C (FLC) vernalization pathway. Lupins, like many other legumes, do not have any FLC homologs. Therefore, candidate genes surveyed in this study, namely LanFTc1, LanAGL8, LanCRLK1, and LanUGT85A2, may constitute anchors for further elucidation of molecular components contributing to vernalization response in legumes.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Michał Ksia̧żkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Iqbal MM, Erskine W, Berger JD, Nelson MN. Phenotypic characterisation and linkage mapping of domestication syndrome traits in yellow lupin (Lupinus luteus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2975-2987. [PMID: 32683474 PMCID: PMC7497344 DOI: 10.1007/s00122-020-03650-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/01/2020] [Indexed: 05/03/2023]
Abstract
The transformation of wild plants into domesticated crops usually modifies a common set of characters referred to as 'domestication syndrome' traits such as the loss of pod shattering/seed dehiscence, loss of seed dormancy, reduced anti-nutritional compounds and changes in growth habit, phenology, flower and seed colour. Understanding the genetic control of domestication syndrome traits facilitates the efficient transfer of useful traits from wild progenitors into crops through crossing and selection. Domesticated forms of yellow lupin (Lupinus luteus L.) possess many domestication syndrome traits, while their genetic control remains a mystery. This study aimed to reveal the genetic control of yellow lupin domestication traits. This involved phenotypic characterisation of those traits, defining the genomic regions controlling domestication traits on a linkage map and performing a comparative genomic analysis of yellow lupin with its better-understood relatives, narrow-leafed lupin (L. angustifolius L.) and white lupin (L. albus L.). We phenotyped an F9 recombinant inbred line (RIL) population of a wide cross between Wodjil (domesticated) × P28213 (wild). Vernalisation responsiveness, alkaloid content, flower and seed colour in yellow lupin were each found to be controlled by single loci on linkage groups YL-21, YL-06, YL-03 and YL-38, respectively. Aligning the genomes of yellow with narrow-leafed lupin and white lupin revealed well-conserved synteny between these sister species (76% and 71%, respectively). This genomic comparison revealed that one of the key domestication traits, vernalisation-responsive flowering, mapped to a region of conserved synteny with the vernalisation-responsive flowering time Ku locus of narrow-leafed lupin, which has previously been shown to be controlled by an FT homologue. In contrast, the loci controlling alkaloid content were each found at non-syntenic regions among the three species. This provides a first glimpse into the molecular control of flowering time in yellow lupin and demonstrates both the power and the limitation of synteny as a tool for gene discovery in lupins.
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Affiliation(s)
- Muhammad Munir Iqbal
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, WA, 6009, Australia.
| | - William Erskine
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jens D Berger
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia.
- Royal Botanic Gardens, Kew, Wakehurst Place Ardingly, West Sussex, RH17 6TN, UK.
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21
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Rychel-Bielska S, Nazzicari N, Plewiński P, Bielski W, Annicchiarico P, Książkiewicz M. Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.). J Appl Genet 2020; 61:531-545. [PMID: 32968972 PMCID: PMC7652745 DOI: 10.1007/s13353-020-00585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, 50-363, Wrocław, Poland.,Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Nelson Nazzicari
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Piotr Plewiński
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Bielski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paolo Annicchiarico
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Ku YS, Contador CA, Ng MS, Yu J, Chung G, Lam HM. The Effects of Domestication on Secondary Metabolite Composition in Legumes. Front Genet 2020; 11:581357. [PMID: 33193705 PMCID: PMC7530298 DOI: 10.3389/fgene.2020.581357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Carolina A. Contador
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jeongjun Yu
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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23
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Abstract
Lupinus mutabilis is an important source of protein in different Andean countries, and its use in diets, particularly those of less wealthy individuals, has been observed for thousands of years. There is an increasing demand for protein crops suitable for Europe and this species is a potential candidate. Assessment of Lupinus mutabilis genetic material in European conditions started more than 40 years ago, with the characterization of a vast number of accessions from the Andean region. In this review, abiotic and biotic constraints to L. mutabilis cultivation in European soil and climatic conditions are discussed, and cultivation management practices are suggested. The beneficial interaction of L. mutabilis with Bradyrhizobium strains in the soil and various pollinator species is also discussed, and the effect of abiotic stresses on these interactions is highlighted. Prospects of alternative uses of L. mutabilis biomass in Northern Europe and opportunities for breeding strategies are discussed. In conclusion, the different approach to crop modeling for Southern and Northern European climatic conditions is highlighted.
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Xu W, Zhang Q, Yuan W, Xu F, Muhammad Aslam M, Miao R, Li Y, Wang Q, Li X, Zhang X, Zhang K, Xia T, Cheng F. The genome evolution and low-phosphorus adaptation in white lupin. Nat Commun 2020; 11:1069. [PMID: 32103018 PMCID: PMC7044338 DOI: 10.1038/s41467-020-14891-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/09/2020] [Indexed: 11/23/2022] Open
Abstract
White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils. Here, we assemble the genome of white lupin and find that it has evolved from a whole-genome triplication (WGT) event. We then decipher its diploid ancestral genome and reconstruct the three sub-genomes. Based on the results, we further reveal the sub-genome dominance and the genic expression of the different sub-genomes varying in relation to their transposable element (TE) density. The PUE genes in white lupin have been expanded through WGT as well as tandem and dispersed duplications. Furthermore, we characterize four main pathways for high PUE, which include carbon fixation, cluster root formation, soil-P remobilization, and cellular-P reuse. Among these, auxin modulation may be important for cluster root formation through involvement of potential genes LaABCG36s and LaABCG37s. These findings provide insights into the genome evolution and low-P adaptation of white lupin.
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Affiliation(s)
- Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Wei Yuan
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Mehtab Muhammad Aslam
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Rui Miao
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ying Li
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Qianwen Wang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Xing Li
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Tianyu Xia
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
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25
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Hufnagel B, Marques A, Soriano A, Marquès L, Divol F, Doumas P, Sallet E, Mancinotti D, Carrere S, Marande W, Arribat S, Keller J, Huneau C, Blein T, Aimé D, Laguerre M, Taylor J, Schubert V, Nelson M, Geu-Flores F, Crespi M, Gallardo K, Delaux PM, Salse J, Bergès H, Guyot R, Gouzy J, Péret B. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nat Commun 2020; 11:492. [PMID: 31980615 PMCID: PMC6981116 DOI: 10.1038/s41467-019-14197-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield. White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
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Affiliation(s)
- Bárbara Hufnagel
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - André Marques
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.,MPIPZ, Cologne, Germany
| | | | - Laurence Marquès
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Fanchon Divol
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Patrick Doumas
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | | | | | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Malika Laguerre
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | | | | | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | | | - Romain Guyot
- IRD, Montpellier, France INRAE / 13 Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Benjamin Péret
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.
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26
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Rychel-Bielska S, Plewiński P, Kozak B, Galek R, Ksia Żkiewicz M. Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin ( Lupinus angustifolius L.). FRONTIERS IN PLANT SCIENCE 2020; 11:572135. [PMID: 33193508 DOI: 10.3389/fpls.2020.572135/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/24/2020] [Indexed: 05/18/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a moderate-yielding legume crop known for its high grain protein content and contribution to soil improvement. It is cultivated under photoperiods ranging from 9 to 17 h, as a spring-sown (in colder locations) or as an autumn-sown crop (in warmer regions). Wild populations require a prolonged cold period, called vernalization, to induce flowering. The key achievement of L. angustifolius domestication was the discovery of two natural mutations (named Ku and Jul) conferring vernalization independence. These mutations are overlapping deletion variants in the promoter of LanFTc1, a homolog of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene. The third deletion, named here as Pal, was recently found in primitive germplasm. In this study, we genotyped L. angustifolius germplasm that differs in domestication status and geographical origin for LanFTc1 alleles, which we then phenotyped to establish flowering time and vernalization responsiveness. The Ku and Jul lines were vernalization-independent and early flowering, wild (ku) lines were vernalization-dependent and late flowering, whereas the Pal line conferred intermediate phenotype. Three lines representing ku, Pal, and Ku alleles were subjected to gene expression surveys under 8- and 16-h photoperiods. FT homologs (LanFTa1, LanFTa2, LanFTc1, and LanFTc2) and some genes selected by recent expression quantitative trait loci mapping were analyzed. Expression profiles of LanFTc1 and LanAGL8 (AGAMOUS-like 8) matched observed differences in flowering time between genotypes, highlighted by high induction after vernalization in the ku line. Moreover, these genes revealed altered circadian clock control in Pal line under short days. LanFD (FD) and LanCRLK1 (CALCIUM/CALMODULIN-REGULATED RECEPTOR-LIKE KINASE 1) were negatively responsive to vernalization in Ku and Pal lines but positively responsive or variable in ku, whereas LanUGT85A2 (UDP-GLUCOSYL TRANSFERASE 85A2) was significantly suppressed by vernalization in all lines. Such a pattern suggests the opposite regulation of these gene pairs in the vernalization pathway. LanCRLK1 and LanUGT85A2 are homologs of A. thaliana genes involved in the FLOWERING LOCUS C (FLC) vernalization pathway. Lupins, like many other legumes, do not have any FLC homologs. Therefore, candidate genes surveyed in this study, namely LanFTc1, LanAGL8, LanCRLK1, and LanUGT85A2, may constitute anchors for further elucidation of molecular components contributing to vernalization response in legumes.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Michał Ksia Żkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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27
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Książkiewicz M, Yang H. Molecular Marker Resources Supporting the Australian Lupin Breeding Program. COMPENDIUM OF PLANT GENOMES 2020. [DOI: 10.1007/978-3-030-21270-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Plewiński P, Książkiewicz M, Rychel-Bielska S, Rudy E, Wolko B. Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2019; 20:ijms20225670. [PMID: 31726789 PMCID: PMC6888189 DOI: 10.3390/ijms20225670] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 12/12/2022] Open
Abstract
The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.
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29
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Iqbal MM, Huynh M, Udall JA, Kilian A, Adhikari KN, Berger JD, Erskine W, Nelson MN. The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop. BMC Genet 2019; 20:68. [PMID: 31412771 PMCID: PMC6694670 DOI: 10.1186/s12863-019-0767-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. RESULTS We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. CONCLUSION These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.
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Affiliation(s)
- Muhammad Munir Iqbal
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Mark Huynh
- The College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, 2881 F&B Rd., College Station, TX, 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, Australia
| | - Kedar N Adhikari
- School of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of Sydney, Narrabri, NSW, Australia
| | | | - William Erskine
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Matthew N Nelson
- Agriculture and Food, CSIRO, Floreat, WA, Australia
- The UWA Institute of Agriculture, Perth, WA, Australia
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30
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Rychel S, Książkiewicz M. Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.). J Appl Genet 2019; 60:269-281. [PMID: 31410824 PMCID: PMC6803572 DOI: 10.1007/s13353-019-00508-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
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Affiliation(s)
- Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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31
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Susek K, Bielski W, Czyż KB, Hasterok R, Jackson SA, Wolko B, Naganowska B. Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution. Genes (Basel) 2019; 10:genes10040259. [PMID: 30939837 PMCID: PMC6523792 DOI: 10.3390/genes10040259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.
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Affiliation(s)
- Karolina Susek
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, 40-032 Katowice, Poland.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
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32
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Abraham EM, Ganopoulos I, Madesis P, Mavromatis A, Mylona P, Nianiou-Obeidat I, Parissi Z, Polidoros A, Tani E, Vlachostergios D. The Use of Lupin as a Source of Protein in Animal Feeding: Genomic Tools and Breeding Approaches. Int J Mol Sci 2019; 20:ijms20040851. [PMID: 30781397 PMCID: PMC6413129 DOI: 10.3390/ijms20040851] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 12/05/2022] Open
Abstract
Livestock production in the European Union EU is highly dependent on imported soybean, exposing the livestock farming system to risks related to the global trade of soybean. Lupin species could be a realistic sustainable alternative source of protein for animal feeding. Lupinus is a very diverse genus with many species. However, only four of them—namely, L. albus, L. angustifolius, L. luteus and L. mutabilis—are cultivated. Their use in livestock farming systems has many advantages in relation to economic and environmental impact. Generally, lupin grains are characterized by high protein content, while their oil content is relatively low but of high quality. On the other hand, the presence of quinolizidine alkaloids and their specific carbohydrate composition are the main antinutritional factors that prevent their use in animal feeding. This research is mainly related to L. albus and to L. angustifolius, and to a lesser extent, to L. lauteus and L. mutabilis. The breeding efforts are mostly focused on yield stabilization, resistance to biotic and abiotic stresses, biochemical structure associated with seed quality and late maturing. Progress is made in improving lupin with respect to the seed quality, as well as the tolerance to biotic and abiotic stress. It has to be noted that modern cultivars, mostly of L. albus and L. angustifolius, contain low levels of alkaloids. However, for future breeding efforts, the implementation of marker-assisted selection and the available genomic tools is of great importance.
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Affiliation(s)
- Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | | | - Athanasios Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Photini Mylona
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, 57001 Thessaloniki, Greece.
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Zoi Parissi
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Alexios Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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