Data_Sheet_1_Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (Hordeum Vulgare L.) in the Qinghai-Tibet Plateau.xlsx

Barley (Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3, and PpD-H2. EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.

大麦（*Hordeum vulgare* L.）是全球最重要的谷类作物之一。在青藏高原地区，六棱裸大麦在汉语中被称为“青稞”，藏语中称“nas”，其主产区为西藏。青藏高原复杂多变的生境为青稞的育种与适应性研究提供了独特的研究契机。然而，青稞诸多重要农艺性状的遗传架构仍未明确。抽穗期（Heading date, HD）、株高（Plant height, PH）与穗长（Spike length, SL）是大麦三类核心农艺性状。
本研究针对308份青稞种质资源开展分析，利用全基因组关联分析（Genome-Wide Association Study, GWAS）及结合特征向量分解的全基因组关联分析（EigenGWAS），对上述三个农艺性状的数量性状位点（Quantitative Trait Locus, QTL）与选择印记进行检测。所有供试种质均采用全新开发的专属靶向测序基因分型（targeted genotyping-by-sequencing, tGBS）技术完成基因型鉴定，最终获得14970个高质量单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）标记。
分析结果显示，栽培品种中的SNP数量高于地方品种，这表明西藏本地栽培品种及藏区栽培品种可能起源于不同区域的地方品种。本研究共鉴定得到与三个目标性状相关的62个QTL，已定位的QTL可较好地解释观测到的表型变异。我们共锚定114个已知功能基因，其中涵盖春化相关基因与光周期相关基因等。研究发现，83.87%的已鉴定QTL位于已注释大麦基因的非编码调控区域。其中48个QTL为本次研究首次报道，28个QTL具有多效性，另有3个QTL定位于已被深入解析的HvVRN1、HvVRN3及PpD-H2基因区域内。
EigenGWAS分析结果显示，多个与抽穗期相关的位点携带选择印记。本研究证实本次使用的青稞种质资源群体具有极高的遗传多样性，为解析适应性性状的遗传基础提供了良好的研究基础。本研究有助于加深对青稞复杂农艺性状的理解，并可推动青稞遗传改良的基因组辅助育种工作。