Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

Müller, Thomas; Schierscher-Viret, Beate; Fossati, Dario; Brabant, Cécile; Schori, A.; Keller, Beat; Krattinger, Simon G.

doi:10.1007/s00122-017-3010-5

Cited by 39 publications

(30 citation statements)

References 59 publications

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“…In diversity studies, wheat landraces usually cluster in a separate group from elite cultivars 20 (54,55,63,65) but some degree of mixture has also been found (39,62). Concerning the durum wheat materials examined here, the great genetic divergence between the bulk of the landraces and the reference set is remarkable ( Figure 4A).…”

Section: Relationship Between Landraces and Modern Cultivarsmentioning

confidence: 79%

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

Pascual

Ruiz

López-Fernández

et al. 2020

Preprint

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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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Section: Relationship Between Landraces and Modern Cultivarsmentioning

confidence: 79%

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

Pascual

Ruiz

López-Fernández

et al. 2020

Preprint

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“…This Vrn-A1 allele, which results in complete insensitivity to vernalization, is recognized as the spring-habit allele with the greatest effect among all such alleles described [61]. Even if the growth habit shows just a limited impact on genetic differentiation, spring and winter bread wheat accessions are frequently separated by discriminant analysis of principal components [62,63]. Two discrete groups regarding growth habit were not clearly defined in our PCoA, but the allelic variability of Vrn-A1 showed some relationship to population structure and a somewhat biased tendency along the second PCo axis (Fig.…”

Section: Bread Wheat Landracesmentioning

confidence: 99%

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Pascual

Ruíz²,

López-Fernández

et al. 2020

BMC Genomics

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Background: One of the main goals of the plant breeding in the twenty-first 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 10 K SNPs and 40 K 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 subsp. 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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“…Also, Wiśniewska and Kowalczyk [34] reported the susceptibility of Polish wheat to Fusarium infection. Polish wheat and spelt are characterized by high genetic variation [35][36][37]. However, genetic variability can lead to the emergence of both resistant and sensitive lines.…”

Section: Discussionmentioning

confidence: 99%

Trichothecene Genotypes Analysis of Fusarium Isolates from di-, tetra- and Hexaploid Wheat

2019

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New sources of resistance to fungal diseases, including FHB (Fusarium head blight), need to be identified. The results of research investigating ancient wheat species with desirable traits appear promising. The aim of this study was to determine the presence of Fusarium culmorum (W. G. Sm.) Sacc., F. graminearum Schwabe, F. poae (Peck) Wollenw, F. avenaceum (Fr.) Sacc. and F. langsethiae Torp & Nirenberg in the grain and glumes of diploid Triticum monococcum ssp. monococcum, tetraploid T. turgidum ssp. dicoccum, T. turgidum ssp. polonicum and T. turgidum ssp. durum, and hexaploid T. aestivum ssp. spelta and T. aestivum ssp. aestivum grown in north-eastern and south-eastern Poland and to analyze the trichothecene genotypes of the isolated strains. The results of this study also point to shifts in the genotype of Polish F. culmorum and F. graminearum populations from 3-ADON to NIV and 15-ADON to 3-ADON genotypes, respectively. Our findings indicate that selected einkorn lines could potentially be used as sources of genetic material for breeding new varieties resistant to FHB. The fungal genotypes should be closely screened in Poland and the neighboring countries to assess the effects of potential genotypes profile change on fungal virulence, toxin loading and host specificity.

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Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

Cited by 39 publications

References 59 publications

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

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

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Trichothecene Genotypes Analysis of Fusarium Isolates from di-, tetra- and Hexaploid Wheat

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