Abstract
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.
Highlights
Barley (Hordeum vulgare L.) was domesticated in Israel and Jordan in the southern part of the Fertile Crescent approximately 10,000 years ago (Badr et al, 2000)
We identified several genetic loci associated with spike length (SL), plant height (PH), and Heading date (HD) in qingke barley from the Qinghai-Tibet Plateau using 14,970 single nucleotide polymorphisms (SNPs) in a tGBS genotyping assay
The number of SNPs was higher in the varieties than in the landraces, indicating that the varieties grown in Tibet and the varieties from around the Tibetan area may be derived from the different landraces grown in the different regions
Summary
Barley (Hordeum vulgare L.) was domesticated in Israel and Jordan in the southern part of the Fertile Crescent approximately 10,000 years ago (Badr et al, 2000). Barley is mainly used for food, fodder, alcoholic beverage ingredient, and is generally considered to be a healthful food (Blake et al, 2010; Collins et al, 2010). In the Qinghai-Tibet plateau, Tibetans use qingke barley to make wine and for consumption (Tashi et al, 2013). As the main food of Tibetans, qingke barley has been grown on the QinghaiTibet Plateau for at least 3,500 years, most probably following its introduction via northern Pakistan, India and Nepal (Zeng et al, 2018). Tibetans have a rich spiritual and cultural connection to qingke barley on the Qinghai-Tibet Plateau due to its wide range of medicinal and nutritional uses. Analysis of the genetic diversity present in cultivated varieties of qingke barley is especially important
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