Shanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Rothamsted Research, Harpenden AL5 2JQ, UK.
Int J Mol Sci. 2024 May 10;25(10):5217. doi: 10.3390/ijms25105217.
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.
大麦是世界上最重要的谷物作物之一，其作为食物的价值不断被揭示，因此对大麦种质资源的研究和利用对全球粮食安全非常重要。尽管全球已经收集了大量的大麦种质资源样本，但它们的具体遗传组成并不清楚，在许多情况下，它们的起源甚至存在争议。本研究利用基因分型测序（GBS）技术对上海农业基因库的 183 份大麦种质资源样本进行了基因型分析，鉴定了 SNP 并估计了其遗传参数，进行了主成分分析（PCA），分析了样本的系统发育树和群体结构。此外，还对有壳/无壳粒性状进行了全基因组关联研究（GWAS），并利用关联 SNP 开发了 KASP 标记。结果表明，共鉴定出 181906 个 SNP，这些大麦种质资源样本可根据系统发育分析大致分为三类，这与行型和有壳/无壳粒的分类基本一致。群体结构分析表明，整个大麦群体可分为四个亚群（SPs），与之前的分类主要区别在于二棱和有壳基因型被细分为两个 SPs。有壳/无壳性状的 GWAS 分析表明，许多相关的位点与 / 位点无关，这表明可能有新的位点控制该性状。在第 7 号染色体上开发了一个与外显子型 SNP 相关的 KASP 标记。基于 KASP 检测的基因型与基于 SNP 的基因型一致，表明该基因可能与有壳/无壳性状相关。上述工作不仅为未来利用该大麦种质资源奠定了良好的基础，还为有壳/无壳性状提供了新的位点和候选基因。
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