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Brhane H, Hammenhag C. Genetic diversity and population structure analysis of a diverse panel of pea ( Pisum sativum). Front Genet 2024; 15:1396888. [PMID: 38873115 PMCID: PMC11169732 DOI: 10.3389/fgene.2024.1396888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
Breeding resilient cultivars with increased tolerance to environmental stress and enhanced resistance to pests and diseases demands pre-breeding efforts that include understanding genetic diversity. This study aimed to evaluate the genetic diversity and population structure of 265 pea accessions. The diversity arrays technology (DArT) genotyping method was employed to identify single-nucleotide polymorphisms (SNPs) and silico markers. After stringent filtering, 6966 SNP and 8,454 silico markers were selected for diversity analysis. Genetic diversity was estimated by grouping accessions based on plant material type, geographic origin, growth habit, and seed color. Generally, diversity estimations obtained using SNPs were similar to those estimated using silico markers. The polymorphism information content (PIC) of the SNP markers ranged from 0.0 to 0.5, with a quarter of them displaying PIC values exceeding 0.4, making them highly informative. Analysis based on plant material type revealed narrow observed heterozygosity (Ho = 0.02-0.03) and expected heterozygosity (He = 0.26-0.31), with landrace accessions exhibiting the highest diversity. Geographic origin-based diversity analysis revealed Ho = 0.02-0.03 and He = 0.22 to 0.30, with European accessions showing the greatest diversity. Moreover, private alleles unique to landrace (4) and European (22) accessions were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance revealed a highly significant genetic differentiation among accession groups classified by seed color, growth habit, plant material types, and geographic origin (p < 0.01). Principal coordinate analysis and neighbor-joining cluster analysis revealed weak clustering of accessions at different grouping levels. This study underscores the significance of genetic diversity in pea collections, offering valuable insights for targeted breeding and conservation efforts. By leveraging genomic data and exploring untapped genetic resources, pea breeding programs can be fortified to ensure sustainable plant protein production and address future challenges in agriculture.
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Affiliation(s)
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Abdallah D, Ben Mustapha S, Balti I, Salhi-Hannachi A, Baraket G. Self-(in)compatibility in Tunisian apple accessions [Malus domestica. Borkh]: S-genotypes identification and pollen tube growth analysis. PLANTA 2024; 259:137. [PMID: 38683389 DOI: 10.1007/s00425-024-04418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
MAIN CONCLUSION Self-incompatibility studies have revealed a potential use of Tunisian apple resources for crop improvement and modern breeding programs and a likely correlation between the pollen tube growth and flowering period. Apples [Malus domestica. Borkh] exhibit an S-RNase-based gametophytic self-incompatibility (GSI) system. Four primer combinations were used to S-genotype eighteen Tunisian local apple accessions and twelve introduced accessions that served as references. Within the Tunisian local accessions, S2, S3, S7, and S28 S-alleles were the most frequent and were assigned to 14 S-genotypes; among them, S7S28, S3S7, S2S5, and S2S3 were the most abundant. PCA plot showed that population structuring was affected by the S-alleles frequencies and revealed a modern origin of the Tunisian varieties rather than being ancient ones. Nonetheless, the results obtained with 17 SSR markers showed a separate grouping of local Tunisian accessions that calls into question the hypothesis discussed. Pollination experiments showed that the pollen started to germinate within 24 h of pollination but 48 h after pollination in the "El Fessi" accession. The first pollen tubes arrived in the styles within 36 h of pollination in two early flowering accessions known as "Arbi" and "Bokri", and after 72 h of pollination in late flowering "El Fessi" and 48 h after pollination in remaining accessions. The first pollen tube arrests were observed in accessions "Arbi" and "Bokri" within 84 h of pollination, within 108 h of pollination in "El Fessi" and within 108 h of pollination in remaining accessions. In the apple accession called "Boutabgaya," the pollen tubes reached the base of the style within 120 h of pollination without being aborted. Nevertheless, the self-compatible nature of "Boutabgaya" needs more studies to be confirmed. However, our results revealed the malfunction of the female component of the GSI in this accession. To conclude, this work paved the path for further studies to enhance the insight (i) into the relation between the flowering period and the pollen tube growth, (ii) self-compatible nature of "Boutabgaya", and (iii) the origin of the Tunisian apple.
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Affiliation(s)
- Donia Abdallah
- Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.
| | - Sana Ben Mustapha
- Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Imen Balti
- Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Amel Salhi-Hannachi
- Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Ghada Baraket
- Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
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Plestenjak E, Meglič V, Sinkovič L, Pipan B. Factors Influencing the Emergence of Heterogeneous Populations of Common Bean ( Phaseolus vulgaris L.) and Their Potential for Intercropping. PLANTS (BASEL, SWITZERLAND) 2024; 13:1112. [PMID: 38674521 PMCID: PMC11055032 DOI: 10.3390/plants13081112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024]
Abstract
The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.
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Affiliation(s)
- Eva Plestenjak
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1001 Ljubljana, Slovenia
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
| | - Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
| | - Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia; (V.M.); (L.S.); (B.P.)
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Haber Z, Sharma D, Selvaraj KSV, Sade N. Is CRISPR/Cas9-based multi-trait enhancement of wheat forthcoming? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112021. [PMID: 38311249 DOI: 10.1016/j.plantsci.2024.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have been implemented in recent years in the genome editing of eukaryotes, including plants. The original system of knocking out a single gene by causing a double-strand break (DSB), followed by non-homologous end joining (NHEJ) or Homology-directed repair (HDR) has undergone many adaptations. These adaptations include employing CRISPR/Cas9 to upregulate gene expression or to cause specific small changes to the DNA sequence of the gene-of-interest. In plants, multiplexing, i.e., inducing multiple changes by CRISPR/Cas9, is extremely relevant due to the redundancy of many plant genes, and the time- and labor-consuming generation of stable transgenic plant lines via crossing. Here we discuss relevant examples of various traits, such as yield, biofortification, gluten content, abiotic stress tolerance, and biotic stress resistance, which have been successfully manipulated using CRISPR/Cas9 in plants. While existing studies have primarily focused on proving the impact of CRISPR/Cas9 on a single trait, there is a growing interest among researchers in creating a multi-stress tolerant wheat cultivar 'super wheat', to commercially and sustainably enhance wheat yields under climate change. Due to the complexity of the technical difficulties in generating multi-target CRISPR/Cas9 lines and of the interactions between stress responses, we propose enhancing already commercial local landraces with higher yield traits along with stress tolerances specific to the respective localities, instead of generating a general 'super wheat'. We hope this will serve as the sustainable solution to commercially enhancing crop yields under both stable and challenging environmental conditions.
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Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - K S Vijai Selvaraj
- Vegetable Research Station, Tamil Nadu Agricultural University, Palur 607102, Tamil Nadu, India
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.
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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Xue S, Wang H, Ma Y, Sun T, Wang Y, Meng F, Wang X, Yang Z, Zhang J, Du J, Li S, Li Z. Fine mapping of powdery mildew resistance gene PmXNM in a Chinese wheat landrace Xiaonanmai. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:35. [PMID: 38286845 DOI: 10.1007/s00122-024-04544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024]
Abstract
KEY MESSAGE Powdery mildew resistance gene PmXNM, originated from the Chinese wheat landrace Xiaonanmai, was delimited to a 300.7-kb interval enriched with resistance genes. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally devastating disease threatening the yield and quality of wheat worldwide. The use of broad-spectrum disease resistance genes from wheat landraces is an effective strategy to prevent this pathogen. Chinese wheat landrace Xiaonanmai (XNM) was immune to 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:4 progenies derived from the cross between XNM and Chinese Spring (CS) were used in this study. Genetic analysis revealed that powdery mildew resistance in XNM was controlled by a single dominant gene, temporarily designated PmXNM. Bulked segregant analysis and molecular mapping delimited PmXNM to the distal terminal region of chromosome 4AL flanked by markers caps213923 and kasp511718. The region carrying the PmXNM locus was approximately 300.7 kb and contained nine high-confidence genes according to the reference genome sequence of CS. Five of these genes, annotated as disease resistance RPP13-like proteins 1, were clustered in the target region. Haplotype analysis using the candidate gene-specific markers indicated that the majority of 267 common wheat accessions (75.3%) exhibited extensive gene losses at the PmXNM locus, as confirmed by aligning the targeted genome sequences of CS with those of other sequenced wheat cultivars. Seven candidate gene-specific markers have proven effective for marker-assisted introgression of PmXNM into modern elite cultivars.
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Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
| | - Huan Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Tiepeng Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yingxue Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Fan Meng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Xintian Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Zihan Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jieli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jinxuan Du
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Zhifang Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
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Sanchez D, Allier A, Ben Sadoun S, Mary-Huard T, Bauland C, Palaffre C, Lagardère B, Madur D, Combes V, Melkior S, Bettinger L, Murigneux A, Moreau L, Charcosset A. Assessing the potential of genetic resource introduction into elite germplasm: a collaborative multiparental population for flint maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:19. [PMID: 38214870 PMCID: PMC10786986 DOI: 10.1007/s00122-023-04509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/18/2023] [Indexed: 01/13/2024]
Abstract
KEY MESSAGE Implementing a collaborative pre-breeding multi-parental population efficiently identifies promising donor x elite pairs to enrich the flint maize elite germplasm. Genetic diversity is crucial for maintaining genetic gains and ensuring breeding programs' long-term success. In a closed breeding program, selection inevitably leads to a loss of genetic diversity. While managing diversity can delay this loss, introducing external sources of diversity is necessary to bring back favorable genetic variation. Genetic resources exhibit greater diversity than elite materials, but their lower performance levels hinder their use. This is the case for European flint maize, for which elite germplasm has incorporated only a limited portion of the diversity available in landraces. To enrich the diversity of this elite genetic pool, we established an original cooperative maize bridging population that involves crosses between private elite materials and diversity donors to create improved genotypes that will facilitate the incorporation of original favorable variations. Twenty donor × elite BC1S2 families were created and phenotyped for hybrid value for yield related traits. Crosses showed contrasted means and variances and therefore contrasted potential in terms of selection as measured by their usefulness criterion (UC). Average expected mean performance gain over the initial elite material was 5%. The most promising donor for each elite line was identified. Results also suggest that one more generation, i.e., 3 in total, of crossing to the elite is required to fully exploit the potential of a donor. Altogether, our results support the usefulness of incorporating genetic resources into elite flint maize. They call for further effort to create fixed diversity donors and identify those most suitable for each elite program.
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Affiliation(s)
- Dimitri Sanchez
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Antoine Allier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Syngenta, 12 Chemin de L'Hobit, 31790, Saint-Sauveur, France
| | - Sarah Ben Sadoun
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris Saclay, 91120, Palaiseau, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Bernard Lagardère
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | | | | | - Alain Murigneux
- Limagrain Europe, 28 Route d'Ennezat, 63720, Chappes, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France.
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Basharat S, Ahmad F, Hameed M, Ahmad MSA, Asghar A, Fatima S, Ahmad KS, Shah SMR, Hashem A, Avila-Quezada GD, Abd_Allah EF, Abbas Z. Structural and Functional Strategies in Cenchrus Species to Combat Environmental Extremities Imposed by Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:203. [PMID: 38256756 PMCID: PMC10818359 DOI: 10.3390/plants13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024]
Abstract
Multiple abiotic stresses such as drought, salinity, heat, and cold stress prevailing in natural habitats affect plant growth and development. Different species modify their structural and functional traits to combat these abiotic stresses while growing in stressful environments. Cenchrus species, i.e., Cenchrus pennisetiformis, C. setiger, and C. prieurii are widely distributed grasses found growing all over the world. Samples from natural populations were collected from different ecological regions in the Punjab and Khyber Pakhtoonkhwa that were exposed to aridity, salinity, and cold, while one site was designated as normal control. In the present study, structural and functional modifications of three Cenchrus species under abiotic stresses were evaluated. It was expected that each Cenchrus species may evolve different strategies to cope with multiple abiotic stresses. All Cenchrus species responded differently whether growing in normal environment or stressful conditions. The most remarkable feature for survival in C. pennisetiformis under cold stress was increased inflorescence and increased stem and root lignification. C. prieurii showed better tolerance to saline and cold environments. C. setiger showed better development of leaf sheath anatomical traits. The structural and functional modifications in Cenchrus species such as development of mechanical tissues provided structural support, while dermal and parenchymatous tissues increased water storage capacity and minimized water loss. An increase in the concentration of organic osmolytes and ionic content aids turgor pressure maintenance and ionic content crucial for plant growth and development. It was concluded that structural and functional alterations in all Cenchrus species were very specific and critical for survival under different environmental stresses. The ecological fitness of these species relied on maintenance of growth and biomass production, and the development of mechanical, vascular, dermal and parenchyma tissues under stressful environmental conditions. Moreover, accumulation of beneficial ions (K+ and Ca2+) and organic osmolytes were critical in turgor maintenance, hence survival of Cenchrus spp.
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Affiliation(s)
- Sana Basharat
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (S.B.); (F.A.); (M.H.); (M.S.A.A.); (A.A.)
| | - Farooq Ahmad
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (S.B.); (F.A.); (M.H.); (M.S.A.A.); (A.A.)
| | - Mansoor Hameed
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (S.B.); (F.A.); (M.H.); (M.S.A.A.); (A.A.)
| | - Muhammad Sajid Aqeel Ahmad
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (S.B.); (F.A.); (M.H.); (M.S.A.A.); (A.A.)
| | - Ansa Asghar
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (S.B.); (F.A.); (M.H.); (M.S.A.A.); (A.A.)
| | - Sana Fatima
- Department of Botany, The Government Sadiq College Women University, Bahawalpur 63100, Pakistan;
| | - Khawaja Shafique Ahmad
- Department of Botany, University of Poonch Rawalakot, Rawalakot 12350, Azad Jammu and Kashmir, Pakistan;
| | - Syed Mohsan Raza Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54700, Pakistan;
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 1451, Saudi Arabia;
| | | | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia;
| | - Zaheer Abbas
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54700, Pakistan;
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Mukarumbwa P, Taruvinga A. Landrace and GM maize cultivars' selection choices among rural farming households in the Eastern Cape Province, South Africa. GM CROPS & FOOD 2023; 14:1-15. [PMID: 37210729 DOI: 10.1080/21645698.2023.2215146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Maize plays a significant role among rural farming households in South Africa. The study therefore estimated the drivers of maize cultivars' selection choices among rural farming households focusing on the commonly grown cultivars from the study area (Landrace and genetically modifies [GM] maize). A cross-sectional survey of 650 respondents randomly selected from Port St Johns and King Sabata Dalindyebo Local Municipalities of the Eastern Cape Province of South Africa were used. Descriptive results revealed that a significant number of the respondents from the study area (65%) were growing Landrace maize cultivars, followed by GM maize (31%), improved OPVs (3%) and conventional hybrids (1%). Multivariate Probit regression estimates show that GM maize cultivars' selection is positively influenced by the amount of rainfall (1% level), household size (5% level), education (1% level), size of arable land (10% level) and access to cell phones (5% level), whilst negatively influenced by the employment status (5%). Conversely, the selection of Landrace maize cultivars is negatively influenced by the of amount rainfall (1% level), education (1% level), income (10% level), access to cell phone (10% level) and radio (10% level) whilst positively influenced by the number of livestock (5% level). The study therefore argues that GM maize cultivars may be meaningfully promoted in high rainfall areas, focusing on arable land sizes and targeted awareness campaigns. The promotion of Landrace maize cultivars may be targeted in low rainfall areas in a mixed farming setting to enhance the complementarity of maize and livestock.
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Affiliation(s)
- Peter Mukarumbwa
- Department of Agricultural Economics and Extension, National University of Lesotho, Lesotho
| | - Amon Taruvinga
- Department of Agricultural Economics and Extension, National University of Lesotho, Lesotho
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Kamal NM, Gorafi YSA, Tomemori H, Kim JS, Elhadi GMI, Tsujimoto H. Genetic variation for grain nutritional profile and yield potential in sorghum and the possibility of selection for drought tolerance under irrigated conditions. BMC Genomics 2023; 24:515. [PMID: 37660014 PMCID: PMC10474746 DOI: 10.1186/s12864-023-09613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Increasing grain nutritional value in sorghum (Sorghum bicolor) is a paramount breeding objective, as is increasing drought resistance (DR), because sorghum is grown mainly in drought-prone areas. The genetic basis of grain nutritional traits remains largely unknown. Marker-assisted selection using significant loci identified through genome-wide association study (GWAS) shows potential for selecting desirable traits in crops. This study assessed natural variation available in sorghum accessions from around the globe to identify novel genes or genomic regions with potential for improving grain nutritional value, and to study associations between DR traits and grain weight and nutritional composition. RESULTS We dissected the genetic architecture of grain nutritional composition, protein content, thousand-kernel weight (TKW), and plant height (PH) in sorghum through GWAS of 163 unique African and Asian accessions under irrigated and post-flowering drought conditions. Several QTLs were detected. Some were significantly associated with DR, TKW, PH, protein, and Zn, Mn, and Ca contents. Genomic regions on chromosomes 1, 2, 4, 8, 9, and 10 were associated with TKW, nutritional, and DR traits; colocalization patterns of these markers indicate potential for simultaneous improvement of these traits. In African accessions, markers associated with TKW were mapped to six regions also associated with protein, Zn, Ca, Mn, Na, and DR, suggesting the potential for simultaneous selection for higher grain nutrition and TKW. Our results indicate that it may be possible to select for increased DR on the basis of grain nutrition and weight potential. CONCLUSIONS This study provides a valuable resource for selecting landraces for use in plant breeding programs and for identifying loci that may contribute to grain nutrition and weight with the hope of producing cultivars that combine improved yield traits, nutrition, and DR.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan.
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | - Hisashi Tomemori
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | | | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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11
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Marzario S, Sica R, Taranto F, Fania F, Esposito S, De Vita P, Gioia T, Logozzo G. Phenotypic evolution in durum wheat ( Triticum durum Desf.) based on SNPs, morphological traits, UPOV descriptors and kernel-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1206560. [PMID: 37701808 PMCID: PMC10493298 DOI: 10.3389/fpls.2023.1206560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 09/14/2023]
Abstract
Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.
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Affiliation(s)
- Stefania Marzario
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rita Sica
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | | | - Fabio Fania
- Department of Agriculture, Food, Natural Resources, and Engineering (DAFNE) - University of Foggia, Foggia, Italy
| | | | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
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Aung KM, Oo WH, Maung TZ, Min MH, Somsri A, Nam J, Kim KW, Nawade B, Lee CY, Chu SH, Park YJ. Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1225445. [PMID: 37560030 PMCID: PMC10407808 DOI: 10.3389/fpls.2023.1225445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.
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Affiliation(s)
- Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Win Htet Oo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Bhagwat Nawade
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea
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Spina A, Guarnaccia P, Canale M, Sanfilippo R, Bizzini M, Blangiforti S, Zingale S, Lo Piero AR, Allegra M, Sicilia A, Nicotra C, Anastasi U. Sicilian Rivet Wheat Landraces: Grain Characteristics and Technological Quality of Flour and Bread. PLANTS (BASEL, SWITZERLAND) 2023; 12:2641. [PMID: 37514255 PMCID: PMC10385672 DOI: 10.3390/plants12142641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
In recent years, the growth of tetraploid Sicilian wheat landraces has been arousing increasing interest. In this study, eighteen local genotypes of Triticum turgidum subsp. turgidum, belonging to the groups 'Bufala', 'Ciciredda', 'Bivona' and 'Paola', and two cultivars of Triticum turgidum subsp. durum (the old variety 'Bidì', and a more recent variety 'Simeto') were assessed for the characteristics of the grain and bread-making performance of their flours and doughs, as well as the quality of the loaves. The grain of the twenty genotypes came from a field trial conducted during 2018-2019 in south-eastern Sicily. The main commercial features of the grain (thousand kernel weight and hectolitre weight), including the defects (starchy, black pointed and shrunken kernels), were determined. The wholemeal flours and doughs obtained from the grain of each genotype were evaluated for the main technological quality (physico-chemical and rheological characteristics), and processed into loaves, whose main quality indices (volume, height, weight, moisture and porosity) were assessed. The results from such analyses allowed the authors to evaluate the genotypes' bread-making suitability. In particular, for the grain characteristics, hectolitre weight varied from 68.23 ('Bufala Rossa Lunga 01') to 77.43 ('Bidì 03') kg/hL, passing through the typical values for common and durum wheat. Among the grain defects, the black point defect was absent in all the grain samples, except for that of 'Bufala Nera Corta 01' (2%). Dry gluten content varied from 6.22 to 10.23 g/100 g, and sedimentation test values were low or medium-low, with values ranging from 22 to 35 mL. Amylase activity was low and highly variable among the genotypes, with the maximum value observed for 'Bufala Rossa Corta b01' (509 s). The doughs evidenced a poor quality for bread making with alveograph values of W ranging from 12 to 145 (10-4 × Joule) and thus the volume of the loaves varied from 346.25 cm3 of 'Bivona' and 'Ciciredda' to 415.00 cm3 of 'Bufala Rossa Lunga'. A Tandem Cluster Analysis was conducted on a set of all the response variables. The Hierarchical Cluster Analysis was initially run. A five-cluster solution identified three clusters further segmented and two single branches. Overall, the study highlighted the possibility of using some of these landraces alone for the production of traditional breads locally appreciated or together with other ingredients for the production of crumbly baked goods such as substitutes for bread and biscuits.
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Affiliation(s)
- Alfio Spina
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, Corso Savoia, 190, 95024 Acireale, Italy
| | - Paolo Guarnaccia
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123 Catania, Italy
| | - Michele Canale
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, Corso Savoia, 190, 95024 Acireale, Italy
| | - Rosalia Sanfilippo
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, Corso Savoia, 190, 95024 Acireale, Italy
| | - Michele Bizzini
- Stazione Consorziale Sperimentale di Granicoltura per la Sicilia, 95041 Caltagirone, Italy
| | - Sebastiano Blangiforti
- Stazione Consorziale Sperimentale di Granicoltura per la Sicilia, 95041 Caltagirone, Italy
| | - Silvia Zingale
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123 Catania, Italy
| | - Angela Roberta Lo Piero
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123 Catania, Italy
| | - Maria Allegra
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Corso Savoia, 190, 95024 Acireale, Italy
| | - Angelo Sicilia
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123 Catania, Italy
| | - Carmelo Nicotra
- Stazione Consorziale Sperimentale di Granicoltura per la Sicilia, 95041 Caltagirone, Italy
| | - Umberto Anastasi
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia 98, 95123 Catania, Italy
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14
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Patel A, Miles A, Strackhouse T, Cook L, Leng S, Patel S, Klinger K, Rudrabhatla S, Potlakayala SD. Methods of crop improvement and applications towards fortifying food security. Front Genome Ed 2023; 5:1171969. [PMID: 37484652 PMCID: PMC10361821 DOI: 10.3389/fgeed.2023.1171969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Agriculture has supported human life from the beginning of civilization, despite a plethora of biotic (pests, pathogens) and abiotic (drought, cold) stressors being exerted on the global food demand. In the past 50 years, the enhanced understanding of cellular and molecular mechanisms in plants has led to novel innovations in biotechnology, resulting in the introduction of desired genes/traits through plant genetic engineering. Targeted genome editing technologies such as Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have emerged as powerful tools for crop improvement. This new CRISPR technology is proving to be an efficient and straightforward process with low cost. It possesses applicability across most plant species, targets multiple genes, and is being used to engineer plant metabolic pathways to create resistance to pathogens and abiotic stressors. These novel genome editing (GE) technologies are poised to meet the UN's sustainable development goals of "zero hunger" and "good human health and wellbeing." These technologies could be more efficient in developing transgenic crops and aid in speeding up the regulatory approvals and risk assessments conducted by the US Departments of Agriculture (USDA), Food and Drug Administration (FDA), and Environmental Protection Agency (EPA).
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Affiliation(s)
- Aayushi Patel
- Penn State Harrisburg, Middletown, PA, United States
| | - Andrew Miles
- Penn State University Park, State College, University Park, PA, United States
| | | | - Logan Cook
- Penn State Harrisburg, Middletown, PA, United States
| | - Sining Leng
- Shanghai United Cell Biotechnology Co Ltd, Shanghai, China
| | - Shrina Patel
- Penn State Harrisburg, Middletown, PA, United States
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Korpetis E, Ninou E, Mylonas I, Ouzounidou G, Xynias IN, Mavromatis AG. Bread Wheat Landraces Adaptability to Low-Input Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2561. [PMID: 37447122 DOI: 10.3390/plants12132561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Bread wheat landraces were an important source of biodiversity used in agriculture before the widespread adoption of high-yielding commercial cultivars adapted to high inputs. Could future agriculture exploit these landraces in different cropping systems in organic or lower-input environments? A two-year field trial was conducted to evaluate grain yield, agronomic performance, and grain quality of bread wheat landraces under different cropping systems, including low-input/organic/conventional environments. Significant variability was found for almost all characteristics among landraces, which makes landraces valuable sources of genetic variation for breeding programs aimed at achieving high and consistent production as well as high-quality products in low-input/organic environments. Additionally, landraces play a crucial role in expanding the genetic diversity of cultivated bread wheat and mitigating biodiversity erosion, thereby enabling crops to better withstand the challenges of low-input/organic agriculture. The landrace "Xilokastro Lamias" had the highest yield among the landraces evaluated in the first growing season (2.65 t·ha-1) and one of the highest yields (2.52 t·ha-1) of all genotypes in the second growing season, which shows promising potential as a starting material in breeding programs targeting high and stable yields. GGE biplot analysis identified the landrace "Xilokastro Lamias", along with commercial cultivars "Yecora E" and "Panifor", as suitable candidates for direct use in low-input/organic wheat farming systems to achieve enhanced productivity. In the conventional environment (C2-IPGRB), commercial cultivars showed the highest values (3.09 to 3.41 ton·ha-1). Of the landraces, only the X4 showed a high GY (3.10 ton·ha-1) while the other landraces had ~33-85% lower yield. In the organic environment (O2-IPGRB), the highest productivity was found in the commercial cultivar X5 and the landrace X4. Commercial cultivars X8 and X7 showed ~68% reduction in GY in the organic environment compared to the conventional, while this reduction was half for the landraces. Finally, the reduction in grain yield between conventional and organic environments was observed to be 45% for commercial cultivars, while it was only half for landraces. This finding confirms the adaptability of landraces to organic agriculture.
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Affiliation(s)
- Evangelos Korpetis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA, 57001 Thessaloniki, Greece
| | - Elissavet Ninou
- Department of Agriculture, International Hellenic University, Sindos, 57400 Thessaloniki, Greece
| | - Ioannis Mylonas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA, 57001 Thessaloniki, Greece
| | - Georgia Ouzounidou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, S. Venizelou 1, Lycovrissi, 141 23 Attika, Greece
| | - Ioannis N Xynias
- School of Agricultural Technol. & Food Technol. and Nutrition, University of Western Macedonia, 53100 Florina, Greece
| | - Athanasios G Mavromatis
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Kalamartzis I, Papakaloudis P, Dordas C. Basil ( Ocimum basilicum) Landraces Can Be Used in a Water-Limited Environment. PLANTS (BASEL, SWITZERLAND) 2023; 12:2425. [PMID: 37446986 DOI: 10.3390/plants12132425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Basil (Ocimum basilicum L.) is a member of the Labiatae family and is one of the most widely consumed aromatic and medicinal plants in many countries due to its numerous properties and uses. The objective of the study was to determine whether landraces are better adapted to water-limited environments compared to commercial cultivars. Irrigation levels and genotypes affected plant height and leaf area index, with 25% and 33% higher values observed under complete irrigation, respectively. Additionally, limited water availability resulted in a 20% reduction in dry matter yield and a 21% reduction in essential oil yield over the three years in all of the genotypes tested, specifically in the lower irrigation treatment (d40), compared to the control treatment (d100). The landraces that performed the best under limited water supply were Athos white spike (AWS) and Gigas white spike (GWS), indicating their suitability for environments with limited water resources. The results demonstrate that there are landraces that can be utilized in dryland climates with appropriate water management, enabling water conservation and utilization of fields in water-scarce areas for irrigation purposes.
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Affiliation(s)
- Iakovos Kalamartzis
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paschalis Papakaloudis
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Dordas
- Laboratory of Agronomy, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Esmaeilzadeh-Salestani K, Tohidfar M, Ghanbari Moheb Seraj R, Khaleghdoust B, Keres I, Marawne H, Loit E. Transcriptome profiling of barley in response to mineral and organic fertilizers. BMC PLANT BIOLOGY 2023; 23:261. [PMID: 37193945 DOI: 10.1186/s12870-023-04263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen is very important for crop yield and quality. Crop producers face the challenge of reducing the use of mineral nitrogen while maintaining food security and other ecosystem services. The first step towards understanding the metabolic responses that could be used to improve nitrogen use efficiency is to identify the genes that are up- or downregulated under treatment with different forms and rates of nitrogen. We conducted a transcriptome analysis of barley (Hordeum vulgare L.) cv. Anni grown in a field experiment in 2019. The objective was to compare the effects of organic (cattle manure) and mineral nitrogen (NH4NO3; 0, 40, 80 kg N ha-1) fertilizers on gene activity at anthesis (BBCH60) and to associate the genes that were differentially expressed between treatment groups with metabolic pathways and biological functions. RESULTS The highest number of differentially expressed genes (8071) was found for the treatment with the highest mineral nitrogen rate. This number was 2.6 times higher than that for the group treated with a low nitrogen rate. The lowest number (500) was for the manure treatment group. Upregulated pathways in the mineral fertilizer treatment groups included biosynthesis of amino acids and ribosomal pathways. Downregulated pathways included starch and sucrose metabolism when mineral nitrogen was supplied at lower rates and carotenoid biosynthesis and phosphatidylinositol signaling at higher mineral nitrogen rates. The organic treatment group had the highest number of downregulated genes, with phenylpropanoid biosynthesis being the most significantly enriched pathway for these genes. Genes involved in starch and sucrose metabolism and plant-pathogen interaction pathways were enriched in the organic treatment group compared with the control treatment group receiving no nitrogen input. CONCLUSION These findings indicate stronger responses of genes to mineral fertilizers, probably because the slow and gradual decomposition of organic fertilizers means that less nitrogen is provided. These data contribute to our understanding of the genetic regulation of barley growth under field conditions. Identification of pathways affected by different nitrogen rates and forms under field conditions could help in the development of more sustainable cropping practices and guide breeders to create varieties with low nitrogen input requirements.
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Affiliation(s)
- Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia.
| | - Masoud Tohidfar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Banafsheh Khaleghdoust
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Indrek Keres
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
| | - Hashem Marawne
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Evelin Loit
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R.Kreutzwaldi 1, 51014, Tartu, Estonia
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18
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Lazaridi E, Bebeli PJ. Evaluation of Cowpea Landraces under a Mediterranean Climate. PLANTS (BASEL, SWITZERLAND) 2023; 12:1947. [PMID: 37653864 PMCID: PMC10223609 DOI: 10.3390/plants12101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) yield is strongly influenced by environmental conditions. Average seed yield can decrease to a great extent when drought conditions occur, especially when they prevail during flowering and seed filling periods. Identifying genotypes presenting yield stability is one of the most important breeding goals. Local varieties or crop landraces are genetic resources that, despite exhibiting intermediate yield production capacity, present high yield stability in low-input cropping systems. The objective of this study was therefore to evaluate five selected cowpea landraces originated from different Greek islands under Mediterranean climatic conditions. A complete randomized block design with four replications was used during three consecutive cropping seasons. Many phenological and agronomic traits studied showed statistically significant genotype × experimental year interaction, while there was a strong experimental year effect. Among the landraces studied, local population VG23 from Kythira Island was the most productive under the experimental climatic and soil conditions, while local population VG2 from Lemnos Island was characterized by low seed productivity. Conclusively, our study showed that VG23 landrace is a promising genetic material to be used for seed yield improvement.
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Affiliation(s)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
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19
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Wang TC, Casadebaig P, Chen TW. More than 1000 genotypes are required to derive robust relationships between yield, yield stability and physiological parameters: a computational study on wheat crop. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:34. [PMID: 36897399 PMCID: PMC10006026 DOI: 10.1007/s00122-023-04264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
Using in silico experiment in crop model, we identified different physiological regulations of yield and yield stability, as well as quantify the genotype and environment numbers required for analysing yield stability convincingly. Identifying target traits for breeding stable and high-yielded cultivars simultaneously is difficult due to limited knowledge of physiological mechanisms behind yield stability. Besides, there is no consensus about the adequacy of a stability index (SI) and the minimal number of environments and genotypes required for evaluating yield stability. We studied this question using the crop model APSIM-Wheat to simulate 9100 virtual genotypes grown under 9000 environments. By analysing the simulated data, we showed that the shape of phenotype distributions affected the correlation between SI and mean yield and the genotypic superiority measure (Pi) was least affected among 11 SI. Pi was used as index to demonstrate that more than 150 environments were required to estimate yield stability of a genotype convincingly and more than 1000 genotypes were necessary to evaluate the contribution of a physiological parameter to yield stability. Network analyses suggested that a physiological parameter contributed preferentially to yield or Pi. For example, soil water absorption efficiency and potential grain filling rate explained better the variations in yield than in Pi; while light extinction coefficient and radiation use efficiency were more correlated with Pi than with yield. The high number of genotypes and environments required for studying Pi highlight the necessity and potential of in silico experiments to better understand the mechanisms behind yield stability.
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Affiliation(s)
- Tien-Cheng Wang
- Section of Intensive Plant Food Systems, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt Universität zu Berlin, Berlin, Germany.
- Institut für Gartenbauliche Produktionssysteme, Leibniz Universität Hannover, Hannover, Germany.
| | - Pierre Casadebaig
- INRAE, UMR AGIR, Université de Toulouse, 31320, Castanet-Tolosan, France
| | - Tsu-Wei Chen
- Section of Intensive Plant Food Systems, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt Universität zu Berlin, Berlin, Germany.
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20
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Mehmandar MN, Rasouli F, Giglou MT, Zahedi SM, Hassanpouraghdam MB, Aazami MA, Tajaragh RP, Ryant P, Mlcek J. Polyethylene Glycol and Sorbitol-Mediated In Vitro Screening for Drought Stress as an Efficient and Rapid Tool to Reach the Tolerant Cucumis melo L. Genotypes. PLANTS (BASEL, SWITZERLAND) 2023; 12:870. [PMID: 36840218 PMCID: PMC9967323 DOI: 10.3390/plants12040870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
An efficient method to instantly assess drought-tolerant plants after germination is using osmoregulation in tissue culture media. In this study, the responses of three Iranian melon genotypes to sorbitol (0.1, 0.2, and 0.4 M) or polyethylene glycol (PEG) (0.009, 0.012, and 0.015 M) were evaluated as drought stress simulators in MS medium. 'Girke' (GIR), 'Ghobadloo' (GHO), and 'Toghermezi' (TOG) were the genotypes. GIR is reputed as a drought-tolerant genotype in Iran. The PEG or sorbitol decreased the coleoptile length, fresh weight, and photosynthetic pigments content while enhancing proline and malondialdehyde (MDA) contents. Protein content and antioxidant enzyme activity were utterly dependent on genotype, osmotic regulators, and their concentration. Coleoptile length, root and shoot fresh weight, root dry weight, proline and MDA content, and guaiacol peroxidase (GPX) activity can be used as indicators for in vitro screening of Cucumis melo L. genotypes. The results showed that sorbitol mimics drought stress better than PEG. Overall, our findings suggest that in vitro screening could be an accurate, rapid, and reliable methodology for evaluating and identifying drought-tolerant genotypes.
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Affiliation(s)
- Maryam Nekoee Mehmandar
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh 5518779842, Iran
| | - Farzad Rasouli
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh 5518779842, Iran
| | - Mousa Torabi Giglou
- Department of Horticulture, Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran
| | - Seyed Morteza Zahedi
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh 5518779842, Iran
| | | | - Mohammad Ali Aazami
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh 5518779842, Iran
| | - Rana Panahi Tajaragh
- Department of Horticulture, Faculty of Agriculture, University of Maragheh, Maragheh 5518779842, Iran
| | - Pavel Ryant
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriScience, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jiri Mlcek
- Department of Food Analysis and Chemistry, Faculty of Technology, Tomas Bata University in Zlin, Vavreckova 5669, 760 01 Zlin, Czech Republic
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21
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Ramesh P, Juturu VN, Yugandhar P, Pedersen S, Hemasundar A, Yolcu S, Chandra Obul Reddy P, Chandra Mohan Reddy CV, Veerabramha Chari P, Mohan R, Chandra Sekhar A. Molecular genetics and phenotypic assessment of foxtail millet ( Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield-related traits. Front Genet 2023; 14:1052575. [PMID: 36760993 PMCID: PMC9905688 DOI: 10.3389/fgene.2023.1052575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv.) is highly valued for nutritional traits, stress tolerance and sustainability in resource-poor dryland agriculture. However, the low productivity of this crop in semi-arid regions of Southern India, is further threatened by climate stress. Landraces are valuable genetic resources, regionally adapted in form of novel alleles that are responsible for cope up the adverse conditions used by local farmers. In recent years, there is an erosion of genetic diversity. We have hypothesized that plant genetic resources collected from the semi-arid climatic zone would serve as a source of novel alleles for the development of climate resilience foxtail millet lines with enhanced yield. Keeping in view, there is an urgent need for conservation of genetic resources. To explore the genetic diversity, to identify superior genotypes and novel alleles, we collected a heterogeneous mixture of foxtail millet landraces from farmer fields. In an extensive multi-year study, we developed twenty genetically fixed foxtail millet landraces by single seed descent method. These landraces characterized along with four released cultivars with agro-morphological, physiological, yield and yield-related traits assessed genetic diversity and population structure. The landraces showed significant diversity in all the studied traits. We identified landraces S3G5, Red, Black and S1C1 that showed outstanding grain yield with earlier flowering, and maturity as compared to released cultivars. Diversity analysis using 67 simple sequence repeat microsatellite and other markers detected 127 alleles including 11 rare alleles, averaging 1.89 alleles per locus, expected heterozygosity of 0.26 and an average polymorphism information content of 0.23, collectively indicating a moderate genetic diversity in the landrace populations. Euclidean Ward's clustering, based on the molecular markers, principal coordinate analysis and structure analysis concordantly distinguished the genotypes into two to three sub-populations. A significant phenotypic and genotypic diversity observed in the landraces indicates a diverse gene pool that can be utilized for sustainable foxtail millet crop improvement.
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Affiliation(s)
- Palakurthi Ramesh
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Vijaya Naresh Juturu
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Poli Yugandhar
- Plant Molecular Biology Laboratory, Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Sydney Pedersen
- Department of Biology, Mercyhurst University, Erie, PA, United States
| | - Alavilli Hemasundar
- Department of Bioresources Engineering, Sejong University, Seoul, South Korea
| | - Seher Yolcu
- Department of Life Sciences, Sogang University, Seoul, South Korea
| | - Puli Chandra Obul Reddy
- Plant Molecular Biology Laboratory, Department of Botany, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | | | - P. Veerabramha Chari
- Department of Biotechnology, Krishna University, Machilipatnam, Andhra Pradesh, India
| | - Rajinikanth Mohan
- Department of Biology, Mercyhurst University, Erie, PA, United States,*Correspondence: Akila Chandra Sekhar, , ; Rajinikanth Mohan,
| | - Akila Chandra Sekhar
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India,*Correspondence: Akila Chandra Sekhar, , ; Rajinikanth Mohan,
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22
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Fiore MC, Blangiforti S, Preiti G, Spina A, Bosi S, Marotti I, Mauceri A, Puccio G, Sunseri F, Mercati F. Elucidating the Genetic Relationships on the Original Old Sicilian Triticum Spp. Collection by SNP Genotyping. Int J Mol Sci 2022; 23:13378. [PMID: 36362168 PMCID: PMC9694989 DOI: 10.3390/ijms232113378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 07/30/2023] Open
Abstract
Several Triticum species spread in cultivation in Sicily and neighboring regions over the centuries, which led to the establishment of a large genetic diversity. Many ancient varieties were widely cultivated until the beginning of the last century before being replaced by modern varieties. Recently, they have been reintroduced in cultivation in Sicily. Here, the genetic diversity of 115 and 11 accessions from Sicily and Calabria, respectively, belonging to Triticum species was evaluated using a high-density SNP array. Einkorn, emmer, and spelta wheat genotypes were used as outgroups for species and subspecies; five modern varieties of durum and bread wheat were used as references. A principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) showed four distinct groups among Triticum species and T. turgidum subspecies. The population structure analysis distinguished five gene pools, among which three appeared private to the T. aestivum, T. turgidum subsp. Turgidum, and 'Timilia' group. The principal component analysis (PCA) displayed a bio-morphological trait relationship of a subset (110) of ancient wheat varieties and their wide variability within the T. turgidum subsp. durum subgroups. A discriminant analysis of principal components (DAPC) and phylogenetic analyses applied to the four durum wheat subgroups revealed that the improved varieties harbored a different gene pool compared to the most ancient varieties. The 'Russello' and 'Russello Ibleo' groups were distinguished; both displayed higher genetic variability compared to the 'Timilia' group accessions. This research represents a comprehensive approach to fingerprinting the old wheat Sicilian germplasm, which is useful in avoiding commercial fraud and sustaining the cultivation of landraces and ancient varieties.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, 90011 Bagheria, Italy
| | - Sebastiano Blangiforti
- Stazione Consorziale Sperimentale di Granicoltura per la Sicilia, Santo Pietro, 95041 Caltagirone, Italy
| | - Giovanni Preiti
- Department AGRARIA, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy
| | - Alfio Spina
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops, 190, 95024 Acireale, Italy
| | - Sara Bosi
- Department of Agricultural and Food Science, Alma Mater Studiorum, University of Bologna, Viale Fanin, 40127 Bologna, Italy
| | - Ilaria Marotti
- Department of Agricultural and Food Science, Alma Mater Studiorum, University of Bologna, Viale Fanin, 40127 Bologna, Italy
| | - Antonio Mauceri
- Department AGRARIA, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council (CNR) of Italy, Institute of Biosciences and Bioresources (IBBR), 90129 Palermo, Italy
| | - Francesco Sunseri
- Department AGRARIA, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy
| | - Francesco Mercati
- National Research Council (CNR) of Italy, Institute of Biosciences and Bioresources (IBBR), 90129 Palermo, Italy
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23
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Barnhart MH, Masalia RR, Mosley LJ, Burke JM. Phenotypic and transcriptomic responses of cultivated sunflower seedlings (Helianthus annuus L.) to four abiotic stresses. PLoS One 2022; 17:e0275462. [PMID: 36178944 PMCID: PMC9524668 DOI: 10.1371/journal.pone.0275462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/18/2022] [Indexed: 11/19/2022] Open
Abstract
Plants encounter and respond to numerous abiotic stresses during their lifetimes. These stresses are often related and could therefore elicit related responses. There are, however, relatively few detailed comparisons between multiple different stresses at the molecular level. Here, we investigated the phenotypic and transcriptomic response of cultivated sunflower (Helianthus annuus L.) seedlings to three water-related stresses (i.e., dry-down, an osmotic challenge, and salt stress), as well as a generalized low-nutrient stress. All four stresses negatively impacted seedling growth, with the nutrient stress having a more divergent response from control as compared to the water-related stresses. Phenotypic responses were consistent with expectations for growth in low-resource environments, including increased (i.e., less negative) carbon fractionation values and leaf C:N ratios, as well as increased belowground biomass allocation. The number of differentially expressed genes (DEGs) under stress was greater in leaf tissue, but roots exhibited a higher proportion of DEGs unique to individual stresses. Overall, the three water-related stresses had a more similar transcriptomic response to each other vs. nutrient stress, though this pattern was more pronounced in root vs. leaf tissue. In contrast to our DEG analyses, co-expression network analysis revealed that there was little indication of a shared response between the four stresses in despite the majority of DEGs being shared between multiple stresses. Importantly, osmotic stress, which is often used to simulate drought stress in experimental settings, had little transcriptomic resemblance to true water limitation (i.e., dry-down) in our study, calling into question its utility as a means for simulating drought.
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Affiliation(s)
- Max H. Barnhart
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Rishi R. Masalia
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - Liana J. Mosley
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
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24
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Guan J, Zhang J, Gong D, Zhang Z, Yu Y, Luo G, Somta P, Hu Z, Wang S, Yuan X, Zhang Y, Wang Y, Chen Y, Laosatit K, Chen X, Chen H, Sha A, Cheng X, Xie H, Wang L. Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding. Nat Commun 2022; 13:5707. [PMID: 36175442 PMCID: PMC9523027 DOI: 10.1038/s41467-022-33515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean. Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
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Affiliation(s)
- Jiantao Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jintao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Dan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengquan Zhang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Yu
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gaoling Luo
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Zheng Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaowen Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Yanlan Wang
- Crop Research Institute of Hunan Province, Changsha, China
| | - Yanhua Chen
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aihua Sha
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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25
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David S, Levin E, Fallik E, Alkalai-Tuvia S, Foolad MR, Lers A. Physiological genetic variation in tomato fruit chilling tolerance during postharvest storage. FRONTIERS IN PLANT SCIENCE 2022; 13:991983. [PMID: 36160961 PMCID: PMC9493348 DOI: 10.3389/fpls.2022.991983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
Storage at low temperatures is a common practice to prolong postharvest life of fruit and vegetables with a minimal negative impact on human/environmental health. Storage at low temperatures, however, can be restricted due to produce susceptibility to non-freezing chilling temperatures, when injuries such as physiological disorders and decays may result in unmarketable produce. We have investigated tomato fruit response to postharvest chilling stress in a recombinant inbred line (RIL) population developed from a cross between a chilling-sensitive cultivated tomato (Solanum lycopersicum L.) breeding line and a chilling-tolerant inbred accession of the tomato wild species S. pimpinellifolium L. Screening of the fruit of 148 RILs under cold storage (1.5°C) indicated presence of significant variations in chilling tolerance, manifested by varying degrees of fruit injury. Two extremely contrasting groups of RILs were identified, chilling-tolerant and chilling-sensitive RILs. The RILs in the two groups were further investigated under chilling stress conditions, and several physiological parameters, including weight loss, chlorophyll fluorescence parameters Fv/Fm, and Performance Index (PI), were determined to be efficient markers for identifying response to chilling stress in postharvest fruit. The Fv/Fm values reflected the physiological damages endured by the fruit after cold storage, and PI was a sensitive marker for early changes in photosystem II function. These two parameters were early indicators of chilling response before occurrence of visible chilling injuries. Antioxidant activities and ascorbic acid content were significantly higher in the chilling-tolerant than the chilling-sensitive lines. Further, the expression of C-repeat/DREB binding factors (CBFs) genes swiftly changed within 1-hr of fruit exposure to the chilling temperature, and the SlCBF1 transcript level was generally higher in the chilling-tolerant than chilling-sensitive lines after 2-hr exposure to the low temperature. This research demonstrates the presence of potential genetic variation in fruit chilling tolerance in the tomato RIL population. Further investigation of the RIL population is underway to better understand the genetic, physiological, and biochemical mechanisms involved in postharvest fruit chilling tolerance in tomato.
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Affiliation(s)
- Sivan David
- Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion, Israel
- Robert H. Smith Faculty of Agriculture Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Elena Levin
- Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion, Israel
| | - Elazar Fallik
- Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion, Israel
| | - Sharon Alkalai-Tuvia
- Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion, Israel
| | - Majid R. Foolad
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Amnon Lers
- Department of Postharvest Science, Volcani Institute, Agricultural Research Organization, Rishon LeZion, Israel
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26
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Coast O, Posch BC, Rognoni BG, Bramley H, Gaju O, Mackenzie J, Pickles C, Kelly AM, Lu M, Ruan YL, Trethowan R, Atkin OK. Wheat photosystem II heat tolerance: evidence for genotype-by-environment interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1368-1382. [PMID: 35781899 DOI: 10.1111/tpj.15894] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
High temperature stress inhibits photosynthesis and threatens wheat production. One measure of photosynthetic heat tolerance is Tcrit - the critical temperature at which incipient damage to photosystem II (PSII) occurs. This trait could be improved in wheat by exploiting genetic variation and genotype-by-environment interactions (GEI). Flag leaf Tcrit of 54 wheat genotypes was evaluated in 12 thermal environments over 3 years in Australia, and analysed using linear mixed models to assess GEI effects. Nine of the 12 environments had significant genetic effects and highly variable broad-sense heritability (H2 ranged from 0.15 to 0.75). Tcrit GEI was variable, with 55.6% of the genetic variance across environments accounted for by the factor analytic model. Mean daily growth temperature in the month preceding anthesis was the most influential environmental driver of Tcrit GEI, suggesting biochemical, physiological and structural adjustments to temperature requiring different durations to manifest. These changes help protect or repair PSII upon exposure to heat stress, and may improve carbon assimilation under high temperature. To support breeding efforts to improve wheat performance under high temperature, we identified genotypes superior to commercial cultivars commonly grown by farmers, and demonstrated potential for developing genotypes with greater photosynthetic heat tolerance.
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Affiliation(s)
- Onoriode Coast
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
- School of Environmental and Rural Sciences, Faculty of Science Agriculture Business and Law, University of New England, Armidale, NSW, 2351, Australia
| | - Bradley C Posch
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bethany G Rognoni
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Lincoln Institute of Agri-Food Technology, University of Lincoln, Riseholme Park, Lincoln, Lincolnshire, LN2 2LG, UK
| | - John Mackenzie
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Claire Pickles
- Birchip Cropping Group, 73 Cumming Avenue, Birchip, VIC, 3483, Australia
| | - Alison M Kelly
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD, 4350, Australia
| | - Meiqin Lu
- Australian Grain Technologies, 12656 Newell Highway, Narrabri, NSW, 2390, Australia
| | - Yong-Ling Ruan
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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27
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Cortés AJ, López-Hernández F, Blair MW. Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives. Front Genet 2022; 13:910386. [PMID: 35991553 PMCID: PMC9389289 DOI: 10.3389/fgene.2022.910386] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. “I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.
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Affiliation(s)
- Andrés J. Cortés
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
| | - Felipe López-Hernández
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Matthew W. Blair
- Department of Agricultural & Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
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Malhotra N, Sharma P, Sood H, Chandora R, Arya M, Rana JC, Singh M. Agro-Morphological Characterization and Nutritional Profiling of Traditional Himalayan Crop Landraces for Their Promotion Toward Mainstream Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:898220. [PMID: 35812955 PMCID: PMC9258745 DOI: 10.3389/fpls.2022.898220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The northwest Indian Himalayas are often regarded as a biological hotspot for the presence of rich agro-biodiversity harboring locally adapted traditional crop landraces facing utter neglect owing to modern agricultural systems promoting high-yielding varieties. Addressing this challenge requires extricating the potential of such cultivars in terms of agro-morphological and nutritional attributes. In this study, 29 traditional crop landraces of maize (11), paddy (07), finger millet (03), buckwheat (05), and naked barley (03) were characterized and evaluated for target traits of interest. In maize, Chitkanu emerged as an early maturing landrace (107 days) with high concentrations of zinc (Zn), iron (Fe), and potassium (K), and Safed makki showed the highest 100-seed weight (28.20 g). Similarly, Bamkua dhan exhibited high concentrations of K and phosphorus (P), and Lamgudi dhan showed a high protein content (14.86 g/100 g) among paddy landraces. Ogla-I and Phapra-I showed high contents of protein (14.80 g/100 g) and flavonoids (20.50 mg/g) among buckwheat landraces, respectively, followed by Nei-I, which exhibited the highest protein content (15.66 g/100 g) among naked barley landraces. Most of the target traits varied significantly (p < 0.05) among evaluated samples, except those associated with finger millet landraces. The grouping pattern obtained by principal component analysis (PCA) and multidimensional scaling (MDS) was congruent with the geographical relationship among the crop landraces. This study led to the identification of elite crop landraces having useful variations that could be exploited in plant breeding programs and biofortification strategies for future crop improvement. Our endeavor would aid in conserving the depleting Himalayan agro-biodiversity and promoting versatile traditional crops toward mainstream agriculture vis-à-vis future nutritional security.
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Affiliation(s)
- Nikhil Malhotra
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
| | - Paras Sharma
- Indian Council of Medical Research (ICMR)-National Institute of Nutrition, Hyderabad, India
| | - Hemant Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, India
| | - Rahul Chandora
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
| | - Mamta Arya
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Bhowali, India
| | - Jai Chand Rana
- Alliance of Bioversity International and CIAT, New Delhi, India
| | - Mohar Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources Regional Station, Shimla, India
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29
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Tomás D, Viegas W, Silva M. Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:842599. [PMID: 35783979 PMCID: PMC9248373 DOI: 10.3389/fpls.2022.842599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
High temperature (HT) events have negative impact on wheat grains yield and quality. Transcriptome profiles of wheat developing grains of commercial genotypes (Antequera and Bancal) and landraces (Ardito and Magueija) submitted to heatwave-like treatments during grain filling were evaluated. Landraces showed significantly more differentially expressed genes (DEGs) and presented more similar responses than commercial genotypes. DEGs were more associated with transcription and RNA and protein synthesis in Antequera and with metabolism alterations in Bancal and landraces. Landraces upregulated genes encoding proteins already described as HT responsive, like heat shock proteins and cupins. Apart from the genes encoding HSP, two other genes were upregulated in all genotypes, one encoding for Adenylate kinase, essential for the cellular homeostasis, and the other for ferritin, recently related with increased tolerance to several abiotic stress in Arabidopsis. Moreover, a NAC transcription factor involved in plant development, known to be a negative regulator of starch synthesis and grain yield, was found to be upregulated in both commercial varieties and downregulated in Magueija landrace. The detected diversity of molecular processes involved in heat response of commercial and traditional genotypes contribute to understand the importance of genetic diversity and relevant pathways to cope with these extreme events.
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30
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Cope JE, Norton GJ, George TS, Newton AC. Evaluating Variation in Germination and Growth of Landraces of Barley ( Hordeum vulgare L.) Under Salinity Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:863069. [PMID: 35783948 PMCID: PMC9245355 DOI: 10.3389/fpls.2022.863069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Ongoing climate change is resulting in increasing areas of salinity affected soils, rising saline groundwater and droughts resulting in irrigation with brackish water. This leads to increased salinity stress in crops that are already grown on marginal agricultural lands, such as barley. Tolerance to salinity stress is limited in the elite barley cultivar pools, but landraces of barley hold potential sources of tolerance due to their continuous selection on marginal lands. This study analyzed 140 heritage cultivars and landrace lines of barley, including 37 Scottish Bere lines that were selected from coastal regions, to screen for tolerance to salinity stress. Tolerance to salinity stress was screened by looking at the germination speed and the early root growth during germination, and the pre-maturity biomass accumulation during early growth stages. Results showed that most lines increased germination time, and decreased shoot biomass and early root growth with greater salinity stress. Elite cultivars showed increased response to the salinity, compared to the landrace lines. Individual Bere and landrace lines showed little to no effect of increased salinity in one or more experiments, one line showed high salinity tolerance in all experiments-Bere 49 A 27 Shetland. A Genome Wide Association Screening identified a number of genomic regions associated with increased tolerance to salinity stress. Two chromosomal regions were found, one associated with shoot biomass on 5HL, and another associated with early root growth, in each of the salinities, on 3HS. Within these regions a number of promising candidate genes were identified. Further analysis of these new regions and candidate genes should be undertaken, along with field trials, to identify targets for future breeding for salinity tolerance.
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Affiliation(s)
- Jonathan E. Cope
- The James Hutton Institute, Dundee, United Kingdom
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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31
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Melandri G, Monteverde E, Riewe D, AbdElgawad H, McCouch SR, Bouwmeester H. Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought. PLANT PHYSIOLOGY 2022; 189:1139-1152. [PMID: 35166848 PMCID: PMC9157150 DOI: 10.1093/plphys/kiac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/17/2022] [Indexed: 05/13/2023]
Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Eliana Monteverde
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
- Departamento de Biología Vegetal, Facultad de Agronomía, Laboratorio de Evolución y Domesticación de las Plantas, Universidad de La República, Montevideo, Uruguay
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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32
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Long W, Luo L, Luo L, Xu W, Li Y, Cai Y, Xie H. Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2. FRONTIERS IN PLANT SCIENCE 2022; 13:857435. [PMID: 35548287 PMCID: PMC9083905 DOI: 10.3389/fpls.2022.857435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion-deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.
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Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice. Metabolites 2022; 12:metabo12050384. [PMID: 35629888 PMCID: PMC9142891 DOI: 10.3390/metabo12050384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Rice (Oryza sativa L.) is one of the most globally important crops, nutritionally and economically. Therefore, analyzing the genetic basis of its nutritional quality is a paramount prerequisite for cultivating new varieties with increased nutritional health. To systematically compare the nutritional quality differences between landraces and cultivated rice, and to mine key genes that determine the specific nutritional traits of landraces, a seed metabolome database of 985 nutritional metabolites covering amino acids, flavonoids, anthocyanins, and vitamins by a widely targeted metabolomic approach with 114 rice varieties (35 landraces and 79 cultivars) was established. To further reveal the molecular mechanism of the metabolic differences in landrace and cultivated rice seeds, four cultivars and six landrace seeds were selected for transcriptome and metabolome analysis during germination, respectively. The integrated analysis compared the metabolic profiles and transcriptomes of different types of rice, identifying 358 differentially accumulated metabolites (DAMs) and 1982 differentially expressed genes (DEGs), establishing a metabolite–gene correlation network. A PCA revealed anthocyanins, flavonoids, and lipids as the central differential nutritional metabolites between landraces and cultivated rice. The metabolite–gene correlation network was used to screen out 20 candidate genes postulated to be involved in the structural modification of anthocyanins. Five glycosyltransferases were verified to catalyze the glycosylation of anthocyanins by in vitro enzyme activity experiments. At the same time, the different mechanisms of the anthocyanin synthesis pathway and structural diversity in landrace and cultivated rice were systematically analyzed, providing new insights for the improvement and utilization of the nutritional quality of rice landrace varieties.
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34
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Janzen GM, Aguilar‐Rangel MR, Cíntora‐Martínez C, Blöcher‐Juárez KA, González‐Segovia E, Studer AJ, Runcie DE, Flint‐Garcia SA, Rellán‐Álvarez R, Sawers RJH, Hufford MB. Demonstration of local adaptation in maize landraces by reciprocal transplantation. Evol Appl 2022; 15:817-837. [PMID: 35603032 PMCID: PMC9108319 DOI: 10.1111/eva.13372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022] Open
Abstract
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland‐adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (QST) was greater than neutral allele frequency differentiation (FST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces’ native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland‐adaptive. These results give substance to the long‐held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.
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Affiliation(s)
- Garrett M. Janzen
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa USA 50011
- Department of Plant Biology University of Georgia Athens Georgia USA 30602
| | | | | | | | - Eric González‐Segovia
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
| | - Anthony J. Studer
- Department of Crop Sciences University of Illinois Urbana‐Champaign 1201 West Gregory Drive Urbana Illinois USA 61801
| | - Daniel E. Runcie
- Department of Plant Sciences University of California‐Davis 278 Robbins Berkeley California USA 95616
| | - Sherry A. Flint‐Garcia
- Agricultural Research Service United States Department of Agriculture Columbia Missouri 65211 USA
- University of Missouri 301 Curtis Hall Columbia Missouri USA 65211
| | - Rubén Rellán‐Álvarez
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
- Present address: Molecular and Structural Biochemistry North Carolina State University 128 Polk Hall Raleigh North Carolina USA 27695‐7622
| | - Ruairidh J. H. Sawers
- Langebio, Cinvestav, Km 9.6 Libramiento Norte Carretera Len Irapuato, Guanajuato Mexico 36821
- Department of Plant Science Pennsylvania State University University Park Pennsylvania USA 16802
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa USA 50011
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35
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Fine-scale genetic structure of the rice landrace population in Japan. Mol Genet Genomics 2022; 297:711-718. [PMID: 35290520 DOI: 10.1007/s00438-022-01880-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Rice cultivation was introduced into Japan 3000 years ago and has expanded across the country and encompasses a wide variety of environmental conditions. Here, we elucidated the differentiation of the genetic population structure of 1037 rice landraces across Japan. Using 4451 polymorphisms derived from genome-wide analysis of double-digest restriction-site-associated DNA analysis, population genomics including ADMIXTURE and principal component analysis was carried out. These landraces were classified into nine subpopulations based on geographical origin. Massive-scale genotyping and diversity analysis demonstrated that the differentiation of genetic population structure in rice landraces across Japan might consist of two phases, namely western to eastern and southern to northern phases. The differentiation of genetic population structure was detected only in landraces from three geographical regions, Hokuriku, Tohoku, and Hokkaido, as the southern to northern phase. Conversely, differentiation was not observed in landraces from six geographical regions, Kyushu, Shikoku, Chugoku, Kinki, Tokai, and Kanto, as the western to eastern phase. The genetic population structure may have facilitated the expansion of genetic diversity among local regions.
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36
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Perez-Limón S, Li M, Cintora-Martinez GC, Aguilar-Rangel MR, Salazar-Vidal MN, González-Segovia E, Blöcher-Juárez K, Guerrero-Zavala A, Barrales-Gamez B, Carcaño-Macias J, Costich DE, Nieto-Sotelo J, Martinez de la Vega O, Simpson J, Hufford MB, Ross-Ibarra J, Flint-Garcia S, Diaz-Garcia L, Rellán-Álvarez R, Sawers RJH. A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize. G3 (BETHESDA, MD.) 2022; 12:jkab447. [PMID: 35100386 PMCID: PMC8896015 DOI: 10.1093/g3journal/jkab447] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/16/2021] [Indexed: 01/31/2023]
Abstract
Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
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Affiliation(s)
- Sergio Perez-Limón
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
| | - Meng Li
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
| | - G Carolina Cintora-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - M Rocio Aguilar-Rangel
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - M Nancy Salazar-Vidal
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Evolution and Ecology, UC Davis, CA 95616 USA
| | - Eric González-Segovia
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Karla Blöcher-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Alejandro Guerrero-Zavala
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Benjamin Barrales-Gamez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Jessica Carcaño-Macias
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Denise E Costich
- International Center for Maize and Wheat Improvement (CIMMyT), De México 56237, México
| | - Jorge Nieto-Sotelo
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Octavio Martinez de la Vega
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - June Simpson
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, UC Davis, CA 95616 USA
- Center for Population Biology, and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture, Agricultural Research Service Plant Genetics Research Unit, Columbia, MO 65211, USA
| | - Luis Diaz-Garcia
- Campo Experimental Pabellón-INIFAP. Carretera Aguascalientes-Zacatecas, Aguascalientes, CP 20660, México
| | - Rubén Rellán-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruairidh J H Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
- Department of Plant Science, The Pennsylvania State University, State College, PA 16802, USA
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Kumar S, Kaushik RA, Jain D, Saini VP, Babu SR, Choudhary R, Ercisli S. Genetic diversity among local mango (Mangifera indica L.) germplasm using morphological, biochemical and chloroplast DNA barcodes analyses. Mol Biol Rep 2022; 49:3491-3501. [PMID: 35076854 DOI: 10.1007/s11033-022-07186-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND In this study, the genetic diversity of local mango (Mangifera indica L.) germplasm including 14 genotypes were evaluated by using morphological, biochemical markers and DNA barcoding technique. Morphological characterization is the first step towards utilizing these germplasm in crop improvement studies. The advanced chloroplast based DNA barcode method can be utilized to assess the genetic diversity and phylogenetic structure in such populations. METHODS The study was carried out during 2018-2019 years to evaluate local mango germplasm including 14 diverse genotypes based on a number of morphological and biochemical traits and chloroplast DNA barcoding as well. The experiment was laid out in one way ANOVA design with fourteen germplasm indicated with indigenous collection number. RESULTS Among local mango germplasm, IC 589756 was found to be the most promising with respect to high magnitudes of fruit length, fruit width, fruit weight, pulp weight, soluble solid content (SSC)/Acidity ratio, pH and low acidity followed by IC 589746 exhibiting the highest pulp percentage and SSC accompanied with lowest stone weight and stone percent as compared to the other genotypes. Further, the dendrogram and cluster analyses based on sequencing of chloroplast marker i.e., trnH- psbA and trnCD depicted the relationship among mango genotypes and clearly clustered them into two main clusters at a similarity coefficient 0.035 and 0.150, respectively. The first cluster includes only one genotype and cluster-II contains 13 genotypes. CONCLUSIONS Particularly results revealed that DNA barcoding of local mango germplasm can assist not only in molecular identification but also help in elucidation of their phylogenetic relationship and thus important in maintaining biodiversity inventories.
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Affiliation(s)
- Sanjay Kumar
- Department of Horticulture, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, 313001, India
| | - Ram Avtar Kaushik
- Department of Horticulture, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, 313001, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, 313001, India.
| | - Ved Prakash Saini
- College of Fisheries, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, 313001, India
| | - S Ramesh Babu
- Department of Entomology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, 313001, India
| | - Ravish Choudhary
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey
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38
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Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
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Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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Würschum T, Weiß TM, Renner J, Friedrich Utz H, Gierl A, Jonczyk R, Römisch-Margl L, Schipprack W, Schön CC, Schrag TA, Leiser WL, Melchinger AE. High-resolution association mapping with libraries of immortalized lines from ancestral landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:243-256. [PMID: 34668978 PMCID: PMC8741726 DOI: 10.1007/s00122-021-03963-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
Association mapping with immortalized lines of landraces offers several advantages including a high mapping resolution, as demonstrated here in maize by identifying the causal variants underlying QTL for oil content and the metabolite allantoin. Landraces are traditional varieties of crops that present a valuable yet largely untapped reservoir of genetic variation to meet future challenges of agriculture. Here, we performed association mapping in a panel comprising 358 immortalized maize lines from six European Flint landraces. Linkage disequilibrium decayed much faster in the landraces than in the elite lines included for comparison, permitting a high mapping resolution. We demonstrate this by fine-mapping a quantitative trait locus (QTL) for oil content down to the phenylalanine insertion F469 in DGAT1-2 as the causal variant. For the metabolite allantoin, related to abiotic stress response, we identified promoter polymorphisms and differential expression of an allantoinase as putative cause of variation. Our results demonstrate the power of this approach to dissect QTL potentially down to the causal variants, toward the utilization of natural or engineered alleles in breeding. Moreover, we provide guidelines for studies using ancestral landraces for crop genetic research and breeding.
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Affiliation(s)
- Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Thea M Weiß
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Juliane Renner
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - H Friedrich Utz
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Alfons Gierl
- Genetics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354, Freising, Germany
| | - Rafal Jonczyk
- Genetics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354, Freising, Germany
| | - Lilla Römisch-Margl
- Genetics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354, Freising, Germany
| | - Wolfgang Schipprack
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Tobias A Schrag
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
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Chakraborty D. Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms. Methods Mol Biol 2022; 2512:269-279. [PMID: 35818011 DOI: 10.1007/978-1-0716-2429-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the current context of global climate change trends, threat to food and nutrition security, collection, conservation and management, and characterization and evaluation of crop germplasms especially traditional landraces are gaining momentum more than ever before. Aromatic rice is an elite category of cultivated rice having huge sociocultural heritage value, fetching premium prices globally. Hence, its identification, in situ conservation, and appropriate characterization are likely to augment reliability of this distinctive category of rice, and rice commodity chain actors. badh2.1 is recognised as the major allele responsible for rice 2-acetyl-1-pyrroline aroma production in a vast number of aromatic rice globally. However, most of the previous works on the genetics and biochemical pathways of aroma expression in rice have encompassed mainly Basmati, Sadri, Della, Jasmine, and a few modern hybrids. But apart from these spotlighted varieties, a myriad of indigenous, aromatic rice germplasms exists. Allele-specific amplification, a low-cost, accurate method invented by Bradbury et al. 2005, can be utilized successfully for discriminating the rarely explored aromatic and nonaromatic rice as described.
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Affiliation(s)
- Debarati Chakraborty
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India.
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41
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Canales FJ, Montilla-Bascón G, Gallego-Sánchez LM, Flores F, Rispail N, Prats E. Deciphering Main Climate and Edaphic Components Driving Oat Adaptation to Mediterranean Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:780562. [PMID: 34899808 PMCID: PMC8662754 DOI: 10.3389/fpls.2021.780562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/25/2021] [Indexed: 06/14/2023]
Abstract
Oat, Avena sativa, is an important crop traditionally grown in cool-temperate regions. However, its cultivated area in the Mediterranean rim steadily increased during the last 20 years due to its good adaptation to a wide range of soils. Nevertheless, under Mediterranean cultivation conditions, oats have to face high temperatures and drought episodes that reduce its yield as compared with northern regions. Therefore, oat crop needs to be improved for adaptation to Mediterranean environments. In this work, we investigated the influence of climatic and edaphic variables on a collection of 709 Mediterranean landraces and cultivars growing under Mediterranean conditions. We performed genotype-environment interaction analysis using heritability-adjusted genotype plus genotype-environment biplot analyses to determine the best performing accessions. Further, their local adaptation to different environmental variables and the partial contribution of climate and edaphic factors to the different agronomic traits was determined through canonical correspondence, redundancy analysis, and variation partitioning. Here, we show that northern bred elite cultivars were not among the best performing accessions in Mediterranean environments, with several landraces outyielding these. While all the best performing cultivars had early flowering, this was not the case for all the best performing landraces, which showed different patterns of adaption to Mediterranean agroclimatic conditions. Thus, higher yielding landraces showed adaptation to moderate to low levels of rain during pre- and post-flowering periods and moderate to high temperature and radiation during post-flowering period. This analysis also highlights landraces adapted to more extreme environmental conditions. The study allowed the selection of oat genotypes adapted to different climate and edaphic factors, reducing undesired effect of environmental variables on agronomic traits and highlights the usefulness of variation partitioning for selecting genotypes adapted to specific climate and edaphic conditions.
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Affiliation(s)
| | | | | | | | | | - Elena Prats
- CSIC, Institute of Sustainable Agriculture, Córdoba, Spain
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42
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Komarnytsky S, Retchin S, Vong CI, Lila MA. Gains and Losses of Agricultural Food Production: Implications for the Twenty-First Century. Annu Rev Food Sci Technol 2021; 13:239-261. [PMID: 34813357 DOI: 10.1146/annurev-food-082421-114831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The world food supply depends on a diminishing list of plant crops and animal livestock to not only feed the ever-growing human population but also improve its nutritional state and lower the disease burden. Over the past century or so, technological advances in agricultural and food processing have helped reduce hunger and poverty but have not adequately addressed sustainability targets. This has led to an erosion of agricultural biodiversity and balanced diets and contributed to climate change and rising rates of chronic metabolic diseases. Modern food supply chains have progressively lost dietary fiber, complex carbohydrates, micronutrients, and several classes of phytochemicals with high bioactivity and nutritional relevance. This review introduces the concept of agricultural food systems losses and focuses on improved sources of agricultural diversity, proteins with enhanced resilience, and novel monitoring, processing, and distribution technologies that are poised to improve food security, reduce food loss and waste, and improve health profiles in the near future. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Slavko Komarnytsky
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Sophia Retchin
- Kenan-Flagler Business School, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chi In Vong
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
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Rubiales D, Annicchiarico P, Vaz Patto MC, Julier B. Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:782574. [PMID: 34868184 PMCID: PMC8637196 DOI: 10.3389/fpls.2021.782574] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.
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Affiliation(s)
- Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | | | - Bernadette Julier
- Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), URP3F, Lusignan, France
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Hanif U, Alipour H, Gul A, Jing L, Darvishzadeh R, Amir R, Munir F, Ilyas MK, Ghafoor A, Siddiqui SU, St Amand P, Bernado A, Bai G, Sonder K, Rasheed A, He Z, Li H. Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study. THE PLANT GENOME 2021; 14:e20096. [PMID: 34275212 DOI: 10.1002/tpg2.20096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/31/2021] [Indexed: 05/21/2023]
Abstract
Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.
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Affiliation(s)
- Uzma Hanif
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Hadi Alipour
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Li Jing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Reza Darvishzadeh
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Rabia Amir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Sadar Uddin Siddiqui
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Paul St Amand
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernado
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Kai Sonder
- International Wheat and Maize Improvement Center (CIMMYT), Texcoco, Mexico
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
- Dep. of Plant Sciences, Quaid-i-Azam Univ., Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
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Li J, Feng S, Qu Y, Gong X, Luo Y, Yang Q, Zhang Y, Dang K, Gao X, Feng B. Identifying the primary meteorological factors affecting the growth and development of Tartary buckwheat and a comprehensive landrace evaluation using a multi-environment phenotypic investigation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:6104-6116. [PMID: 33908040 DOI: 10.1002/jsfa.11267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/09/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is a traditional edible and medicinal crop and has been praised as one of the green foods for humans in the 21st century. However, its production and promotion are restricted by the low yields of current varieties. The interaction of genotype and environment could lead to inconsistent phenotypic performance of genotypes across different environments. Climate change has intensified these effects and poses a substantial threat to crop production. RESULTS In the present study, the effects of meteorological factors on the phenotypic traits of 200 Tartary buckwheat landraces across four macro-environments were investigated. Overall, the phenotypic performance of these Tartary buckwheat landraces was markedly varied across the different environments. Also, the average daily temperature and precipitation had relatively higher impacts on phenotypic performance. The results also revealed the negative impacts of relative humidity on the yield-related traits. Twenty-five Tartary buckwheat landraces were ultimately identified as having good overall phenotypic performance and high yield stability. CONCLUSION Understanding the impacts of meteorological factors on the phenotypic performance of crops can guide appropriate measures and facilitate germplasm selection for yield enhancement in the context of climate change. The landraces selected comprehensively in this study could be used as parents or intermediate materials for breeding high-quality Tartary buckwheat varieties in the future. The methods used could also be extended to other crops for breeding and germplasm innovation. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Shan Feng
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an, China
| | - Yang Qu
- Institute of Minor Grain Crops Research, Baoji Academy of Agricultural Sciences, Qishan, China
| | - Xiangwei Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Yan Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Yuchuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Ke Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A & F University, Yangling, China
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State of Crop Landraces in Arcadia (Greece) and In-Situ Conservation Potential. DIVERSITY 2021. [DOI: 10.3390/d13110558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genetic erosion of landraces is increasing worldwide, however there are still regions rich in landrace biodiversity, such as islands and mountainous isolated areas. Defining the reasons of landrace abandonment in these areas, as well as collecting and preserving landraces, is of outmost importance. In this context, the Agricultural University of Athens organized missions in 53 villages of Arcadia, a prefecture rich in floral biodiversity and variable climatic conditions and topography. The aim was to collect samples of the on-farm (in-situ) conserved annual crop landraces and record the location of perennial crop local varieties. Since traditional knowledge and practices have been playing a vital role in the survival of landraces and local varieties, information was obtained through personal interviews with locals using semi-structured questionnaires. Even though the number of accessions collected from Arcadia has been reduced (141 samples) compared to previous collections and genetic erosion is advancing dramatically for cereals and pulses, a significant number of landraces is still cultivated by the locals. The reasons of landrace abandonment were other sources of occupation than agriculture, such as public service jobs, mechanization, and commercialization of agriculture. Gastronomic and agro-tourism along with European Union trademarks and policies can support locals in landrace/local varieties in-situ conservation.
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Guevara-Escudero M, Osorio AN, Cortés AJ. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102022. [PMID: 34685832 PMCID: PMC8541610 DOI: 10.3390/plants10102022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 05/18/2023]
Abstract
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.
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Affiliation(s)
- Melisa Guevara-Escudero
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Angy N. Osorio
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Andrés J. Cortés
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
- Main Address: Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia
- Correspondence:
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The Jacalin-Related Lectin HvHorcH Is Involved in the Physiological Response of Barley Roots to Salt Stress. Int J Mol Sci 2021; 22:ijms221910248. [PMID: 34638593 PMCID: PMC8549704 DOI: 10.3390/ijms221910248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
Salt stress tolerance of crop plants is a trait with increasing value for future food production. In an attempt to identify proteins that participate in the salt stress response of barley, we have used a cDNA library from salt-stressed seedling roots of the relatively salt-stress-tolerant cv. Morex for the transfection of a salt-stress-sensitive yeast strain (Saccharomyces cerevisiae YSH818 Δhog1 mutant). From the retrieved cDNA sequences conferring salt tolerance to the yeast mutant, eleven contained the coding sequence of a jacalin-related lectin (JRL) that shows homology to the previously identified JRL horcolin from barley coleoptiles that we therefore named the gene HvHorcH. The detection of HvHorcH protein in root extracellular fluid suggests a secretion under stress conditions. Furthermore, HvHorcH exhibited specificity towards mannose. Protein abundance of HvHorcH in roots of salt-sensitive or salt-tolerant barley cultivars were not trait-specific to salinity treatment, but protein levels increased in response to the treatment, particularly in the root tip. Expression of HvHorcH in Arabidopsis thaliana root tips increased salt tolerance. Hence, we conclude that this protein is involved in the adaptation of plants to salinity.
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Local Melon and Watermelon Crop Populations to Moderate Yield Responses to Climate Change in North Africa. CLIMATE 2021. [DOI: 10.3390/cli9080129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Climate change is having a tremendous influence on world food production, with arid, semi-arid, and dry sub-humid areas especially susceptible. In these areas, locally adapted crop varieties or landraces can be used to mitigate the influence of climate change on current and future food security challenges. The high genetic diversity within these populations allows for crops to adapt to changing environments or other stresses that influence growth and productivity. Thus, local Moroccan melon (Cucumis melo) and watermelon (Citrullus lanatus) landraces were compared to pure-line varieties in southwestern Morocco to identify their adaptability and possible ability to mitigate current and future climate change. Results indicated that the melon and watermelon landraces evaluated most likely could help mitigate yield losses from climate change in this area of Morocco. ‘AitOulyad’, a local muskmelon type, and ‘Rasmouka Ananas’ were both outstanding melon landraces with high plant vigor and yields. For watermelon, ‘AitOulyad’ had extremely high yields but had high numbers of seed in the flesh, while ‘Rasmouka’ had a lower yield, fewer seeds in the flesh, and a higher fruit consistency. This research indicates that melon and watermelon landraces in this area of southwestern Morocco with a semi-arid to arid climate will continue to play a major role in crop adaptation to maintain high productivity under a rapidly changing environment.
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Xue S, Lu M, Hu S, Xu H, Ma Y, Lu N, Bai S, Gu A, Wan H, Li S. Characterization of PmHHXM, a New Broad-Spectrum Powdery Mildew Resistance Gene in Chinese Wheat Landrace Honghuaxiaomai. PLANT DISEASE 2021; 105:2089-2096. [PMID: 33417497 DOI: 10.1094/pdis-10-20-2296-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Powdery mildew, caused by fungal pathogen Blumeria graminis f. sp. tritici, is an agronomically important and widespread wheat disease causing severe yield losses. Deployment of broad-spectrum disease resistance genes is the preferred strategy to prevent this pathogen. Chinese wheat landrace Honghuaxiaomai (HHXM) was resistant to all 23 tested B. graminis f. sp. tritici isolates at the seedling stage. The F1, F2, and F2:3 progenies derived from the cross HHXM × Yangmai 158 were used in this study, and genetic analysis revealed that a single dominant gene, designated PmHHXM, conferred resistance to B. graminis f. sp. tritici isolate E09. Bulked segregant analysis and molecular mapping initially located PmHHXM to the distal region of chromosome 4AL. To fine map PmHHXM, we identified two critical recombinants from 592 F2 plants and delimited PmHHXM to a 0.18-cM Xkasp475200 to Xhnu552 interval covering 1.77 Mb, in which a number of disease resistance-related gene clusters were annotated. Comparative mapping of this interval revealed a perturbed synteny among Triticeae species. This study reports the new powdery mildew resistance gene PmHHXM, which seems different from three known quantitative trait loci/genes identified on chromosome 4AL and has significant values for further genetic improvement. Analysis of the polymorphisms of 13 cosegregating markers between HHXM and 170 modern wheat cultivars indicates that Xhnu227 and Xsts478700 developed here are ideal for marker-assisted introgression of this locus in wheat breeding.
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Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Mingxue Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Shanshan Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Hongxing Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Nan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Aoyang Gu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Areas), Chengdu 610066, Sichuan, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, Henan, China
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