From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers

Rufo, Rubén; Álvaro, Fanny; Royo, C.; Soriano, José Miguel

doi:10.1371/journal.pone.0219867

Cited by 59 publications

(89 citation statements)

References 44 publications

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“…The highest average number of alleles was detected in the B genome, followed by the D genome and the A genome, using 17 SSR markers, as reported by Salem et al (2015) [36]. In the present study, we obtained 24,767 SNPs markers and observed the lowest frequency of SNPs in the D genomes, whereas the B genome contained the highest frequency of polymorphic markers, which is in agreement with the results of previous studies [1,19,28,32,37,38,[39][40][41]. Furthermore, the fewest SNP markers were located on chromosome 4D, whereas the highest number of SNP markers were located on chromosome 3B, as reported by Saintenac has the lowest number.…”

Section: Discussionsupporting

confidence: 92%

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Yang

Tan

et al. 2019

Preprint

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Background Availability of information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N.Results In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content ranged from 0.1 to 0.4, with an average of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was higher as indicated by the Shannon’s information index ( I ) = 0.512, diversity index ( h ) = 0.334, observed heterozygosity ( H o ) = 0.226, and unbiased diversity index (uh) = 0.338.Conclusion The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

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Section: Discussionsupporting

confidence: 92%

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Yang

Tan

et al. 2019

Preprint

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“…Among the MC chromosomes, 1B, 4B, and 6A showed the slowest decay both as physical and genetic distances. These results were partially confirmed in durum and bread wheat (Somers et al, 2007;Voss-Fels and Snowdon, 2016;Kidane et al, 2017;Rufo et al, 2019).…”

Section: Linkage Disequilibriummentioning

confidence: 56%

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

et al. 2020

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“…Only a small proportion of all the available PGR are used, and humans depend on a very limited number of crops, in particular wheat, rice and maize, for the largest part of their caloric intake (McCouch et al, 2013;Khoury et al, 2014). The development and expanding cultivation of modern crop cultivars has led to decreased genetic diversity within crops (Langridge et al, 2006;Feuillet et al, 2008;Rufo et al, 2019). This loss of genetic diversity could make adaptation of crops to changing environmental conditions more difficult.…”

Section: Introductionmentioning

confidence: 99%

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

Brink

Hintum

2020

Front. Plant Sci.

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Since the 1990s, the exchange of genetic resources has been increasingly regulated. The Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognize that countries have sovereign rights over their genetic resources and provide a framework for domestic legislations on Access and Benefit-Sharing (ABS). However, within the rules of these international agreements, countries can follow their own interpretations and establish their own rules and regulations, resulting in restricted access to genetic resources and limited benefit-sharing, effects that are contrary to the objectives of these agreements. Although the ITPGRFA's Multilateral System of Access and Benefit-Sharing provides opportunities for easier access to plant genetic resources for food and agriculture (PGRFA), plant genebanks face increasing complexity in their operation. Adding material to genebank collections has become more difficult, not only because collecting missions need to be negotiated with national and local authorities, but also because acquiring material from other collections is only possible if the origin of the material is properly documented and is done in compliance with regulations. Genebanks may only provide access to their own collections if the material that is to be released is distributed in compliance with a) the conditions under which the material was received and b) the national laws of the country where the genebank is located. The only way genebanks can deal with this new complexity, apart from ceasing to add or distribute material, is by setting up proper procedures to document the origin of every accession and the conditions for their use and further distribution. To prevent a further decrease in access to PGRFA, complexity must be fought. Applying the ITPGRFA's Standard Material Transfer Agreement (SMTA) only, even for material that does not fall under the ITPGRFA, would simplify matters. The scope of the ITPGRFA could be expanded to include all crops. Furthermore, certain ambiguities (e.g. regarding in situ material and wild species) could be resolved. Finally, compliance with the ITPGRFA should be improved and better monitored.

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From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers

Cited by 59 publications

References 44 publications

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

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