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

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, the...

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Published in:	International journal of molecular sciences Vol. 25; no. 10; p. 5217
Main Authors:	Chen, Zhiwei, Guo, Zhenzhu, Li, Luli, Halford, Nigel G, Guo, Guimei, Zhang, Shuwei, Zong, Yingjie, Liu, Shiseng, Liu, Chenghong, Zhou, Longhua
Format:	Journal Article
Language:	English
Published:	Switzerland MDPI AG 10-05-2024
Subjects:	Barley Biological diversity China Chromosomes Domestication Genes Genetic diversity Genetic Variation Genome, Plant genome-wide association studies (GWAS) Genome-Wide Association Study - methods Genomes Genomics Genotype genotyping-by-sequencing (GBS) Germplasm Grain Hordeum - genetics Hordeum vulgare L Kompetitive Allele Specific PCR (KASP) Morphology naked trait Phenotype Phylogenetics Phylogeny Polymorphism, Single Nucleotide Principal Component Analysis Proteins Quantitative Trait Loci Seed Bank Single nucleotide polymorphisms China Hordeum vulgare L genome-wide association studies (GWAS) genotyping-by-sequencing (GBS) naked trait Kompetitive Allele Specific PCR (KASP)
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Summary:	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 / 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1422-0067 1661-6596 1422-0067
DOI:	10.3390/ijms25105217