Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

10.21203/rs.2.9775/v3 ◽

2020 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genome Wide Association Studies ◽

Reference Set ◽

Genome Wide ◽

Wheat Landraces

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Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

10.21203/rs.2.9775/v2 ◽

2019 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Genome Wide Association Studies ◽

Reference Set ◽

Genome Wide ◽

Wheat Landraces

Abstract Background One of the main goals of the plant breeding in the 21 st century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10K SNPs and 40K high-quality DArT markers, which were mapped against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsps. durum , turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

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Genomic Analysis of Spanish Wheat Landraces Reveals Their Huge Potential for Breeding

10.21203/rs.2.9775/v1 ◽

2019 ◽

Author(s):

Laura Pascual ◽

Magdalena Ruiz ◽

Matilde López-Fernández ◽

Helena Pérez-Peña ◽

Elena Benavente ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Durum Wheat ◽

Bread Wheat ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Geographic Origin ◽

Local Conditions ◽

Reference Set ◽

Wheat Landraces

Abstract Background One of the main goals for the XXI century breeding is the development of crop cultivars that can maintain current yields under unfavorable environments. Landraces that have been grown under varied local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a wide collection of wheat landraces. These accessions, locally adapted to a really wide diversity of eco-climatic conditions, represent a highly valuable material for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results DArTseq GBS approach generated 10K SNPs and 40K DArT high-quality markers that were mapped against the currently available bread wheat reference genome. The markers with known location were distributed in all the chromosomes, having a relatively well-balanced genome-wide coverage. The genetic analysis showed that Spanish wheat landraces are clustered in different groups, thus representing genetic pools capable to provide different allelic variation. The subspecies had a major impact on the population structure of durum wheat landraces, identifying three different clusters that corresponded to subsps. durum, turgidum and dicoccon. The population structure of bread wheat landraces was more biased by geographic origin. Conclusions The results showed a wider genetic diversity in landraces when compared to a reference set that included commercial varieties, and a higher divergence between landraces and the reference set in durum wheat than in bread wheat. Some genomic regions with patterns of variation that differ between landraces and reference varieties could be detected, pointing out loci under selection during crop improvement that could help to target breeding efforts. The results obtained from this work will be highly valuable for future GWAS analysis.

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Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

Plant Genetic Resources ◽

10.1017/s147926212100006x ◽

2021 ◽

pp. 1-10

Author(s):

Karthika Rajendran ◽

Clarice J. Coyne ◽

Ping Zheng ◽

Gopesh Saha ◽

Dorrie Main ◽

...

Keyword(s):

Genetic Diversity ◽

Lens Culinaris ◽

Agronomic Traits ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Principal Component ◽

Genotyping By Sequencing ◽

Phenotypic Data ◽

Reference Set ◽

Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

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Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽

10.3390/genes11111298 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1298

Author(s):

Caléo Panhoca de Almeida ◽

Jean Fausto de Carvalho Paulino ◽

Sérgio Augusto Morais Carbonell ◽

Alisson Fernando Chiorato ◽

Qijian Song ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Common Bean ◽

Gene Diversity ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

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The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

Horticulture Research ◽

10.1038/s41438-018-0080-8 ◽

2018 ◽

Vol 5 (1) ◽

Cited By ~ 20

Author(s):

Xin Wang ◽

Kan Bao ◽

Umesh K. Reddy ◽

Yang Bai ◽

Sue A. Hammar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Cucumis Sativus ◽

Core Collection ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Collection Development ◽

Cucumis Sativus L ◽

Genome Wide

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Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Genes ◽

10.3390/genes12030340 ◽

2021 ◽

Vol 12 (3) ◽

pp. 340

Author(s):

Muhammad Massub Tehseen ◽

Deniz Istipliler ◽

Zakaria Kehel ◽

Carolina P. Sansaloni ◽

Marta da Silva Lopes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Bread Wheat ◽

Structure Analysis ◽

Geographic Origin ◽

Climatic Conditions ◽

Population Structure Analysis ◽

North Eastern ◽

Wheat Landraces

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

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Genetic diversity of Ethiopian durum wheat landraces

PLoS ONE ◽

10.1371/journal.pone.0247016 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0247016

Author(s):

Kefyalew Negisho ◽

Surafel Shibru ◽

Klaus Pillen ◽

Frank Ordon ◽

Gwendolin Wehner

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Genetic Differentiation ◽

Durum Wheat ◽

Total Variation ◽

Population Structure Analysis ◽

Wheat Landraces ◽

Wheat Lines ◽

Durum Wheat Landraces

Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.

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Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity

Plants ◽

10.3390/plants10020211 ◽

2021 ◽

Vol 10 (2) ◽

pp. 211

Author(s):

Mazin Mahjoob Mohamed Mahjoob ◽

Yasir Serag Alnor Gorafi ◽

Nasrein Mohamed Kamal ◽

Yuji Yamasaki ◽

Izzat Sidahmed Ali Tahir ◽

...

Keyword(s):

Genetic Diversity ◽

Bread Wheat ◽

Association Studies ◽

Aegilops Tauschii ◽

Genome Wide Association ◽

Physiological Traits ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Wide Range ◽

Or Genes

Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker–trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.

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