Dataset Information

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

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.

SUBMITTER: Li Z

PROVIDER: S-EPMC7351530 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (<i>Hordeum Vulgare</i> L.) in the Qinghai-Tibet Plateau.

Li Zhiyong Z Lhundrup Namgyal N Guo Ganggang G Dol Kar K Chen Panpan P Gao Liyun L Chemi Wangmo W Zhang Jing J Wang Jiankang J Nyema Tashi T Dawa Dondrup D Li Huihui H

Frontiers in genetics 20200703

Barley (<i>Hordeum vulgare</i> 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. Hea ...[more]

PMID: 32719715

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Project description:Background Evaluation of the extent of genetic variation within and between the populations of crop genetic resources are of paramount importance in any breeding program. An experiment aimed at assessing the extent of variation among barley lines and the degree of association between hordein polypeptide and agronomic traits was hence executed. Methods Field experiment was conducted in six environments between 2017–2019 involving 19 barley lines. Hordein bands were separated using vertical Sodium Dodecyl Sulphate Poly- acrylamide Gel Electrophoresis (SDS-PAGE). Results The analysis of variance revealed significant variation among lines and wider range units were observed for the agronomic traits. The line (Acc# 16,811–6) was superior, producing the highest grain yield (2.97 ton ha−1) across environments, 3.6 ton ha−1 at Holleta, and 1.93 ton ha−1 at Chefedonsa. At Arsi Negelle a different line Acc# 17146–9 was the highest yielding (3.15ton ha−1). SDS-PAGE-based analysis of barley lines separated 12 hordein bands between C (four bands) and B (eight bands) subunits. Interestingly bands 52, 46a, and 46b were uniquely conserved in the four naked barley lines (Acc#16809–14,16956–11, 17240–3, 17244–19). A considerably high proportion of genetic diversity within the populations than among the populations could be a repercussion of high gene flow which substantiates the longstanding and dominant informal seed exchange system among the farmers. The significant positive association between grain yield and band 50 evocates the expression of this allele may code for higher grain yield. The negative association between days to maturity and band 52 perhaps stipulates earliness in barely lines upon the manifestation of the band. Band 52 and 60 appeared to be associated with more than one agronomic trait (days to maturity and thousand kernel weight; grain filling period and grain yield respectively) and could be the result of pleiotropic characteristics of the genes residing in these banding regions. Conclusion The barley lines exhibited substantial variation for hordein protein and agronomic traits. However, imparted the need for the implementation of decentralized breeding as a consequence of genotype-by-environment interaction. Significant hordein polypeptide and agronomic traits association advocated the utilization of hordein as a protein marker and perhaps consider them in the parental line selection. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-023-04117-x.

Project description:BackgroundFrost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.ResultsGWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.ConclusionsHaplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.

Dataset Information

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

Publications

Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley (<i>Hordeum Vulgare</i> L.) in the Qinghai-Tibet Plateau.

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