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Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank

文献类型： 外文期刊

作者： Chen, Zhiwei 1 ; Guo, Zhenzhu 1 ; Li, Luli 1 ; Halford, Nigel G. 2 ; Guo, Guimei 1 ; Zhang, Shuwei 1 ; Zong, Yingjie 1 ; Liu, Shiseng 1 ; Liu, Chenghong 1 ; Zhou, Longhua 1 ;

作者机构： 1.Shanghai Acad Agr Sci, Shanghai Key Lab Agr Genet & Breeding 21DZ2271900, Shanghai Agr Biosafety Evaluat & Testing Profess T, Biotechnol Res Inst,Key Lab Safety Assessment Envi, Shanghai 201106, Peoples R China

2.Rothamsted Res, Harpenden AL5 2JQ, England

关键词： Hordeum vulgare L.; naked trait; genotyping-by-sequencing (GBS); genome-wide association studies (GWAS); Kompetitive Allele Specific PCR (KASP)

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：5.6； 五年影响因子：6.2 ）

ISSN： 1661-6596

年卷期： 2024 年 25 卷 10 期

页码：

收录情况： SCI

摘要： Barley is one of the most important cereal crops in the world, and its value as a food is constantly being revealed, so the research into and the use of barley germplasm are very important for global food security. Although a large number of barley germplasm samples have been collected globally, their specific genetic compositions are not well understood, and in many cases their origins are even disputed. In this study, 183 barley germplasm samples from the Shanghai Agricultural Gene Bank were genotyped using genotyping-by-sequencing (GBS) technology, SNPs were identified and their genetic parameters were estimated, principal component analysis (PCA) was preformed, and the phylogenetic tree and population structure of the samples were also analyzed. In addition, a genome-wide association study (GWAS) was carried out for the hulled/naked grain trait, and a KASP marker was developed using an associated SNP. The results showed that a total of 181,906 SNPs were identified, and these barley germplasm samples could be roughly divided into three categories according to the phylogenetic analysis, which was generally consistent with the classification of the traits of row type and hulled/naked grain. Population structure analysis showed that the whole barley population could be divided into four sub-populations (SPs), the main difference from previous classifications being that the two-rowed and the hulled genotypes were sub-divided into two SPs. The GWAS analysis of the hulled/naked trait showed that many associated loci were unrelated to the Nud/nud locus, indicating that there might be new loci controlling the trait. A KASP marker was developed for one exon-type SNP on chromosome 7. Genotyping based on the KASP assay was consistent with that based on SNPs, indicating that the gene of this locus might be associated with the hulled/naked trait. The above work not only lays a good foundation for the future utilization of this barley germplasm population but it provides new loci and candidate genes for the hulled/naked trait.

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