QTL localisation of seed-related traits in Tibetan hulless barley based on a high-density single-nucleotide polymorphism genetic map

The effective use of high-quality and high-yielding germplasm resources is of great importance for the development of hulless barley varieties. Therefore, the search for such resources has long been a goal of the breeding community. In this study, a genotyping-by-sequencing (GBS) analysis was performed on an F2 (Nierumuzha × Kunlun 10) population. A high-density genetic map of hulless barley was constructed, which contained 1 475 efficient single-nucleotide polymorphism markers with 7 052 bin markers. The total length of the seven chromosomes was 1 139.4 cM, with an average marker distance of 0.59 cM. Based on this high-density linkage map, a total of 54 quantitative trait loci (QTLs) related to the seed traits were detected, including seed colour (SC), thousand kernel weight (TKW), seed average area (SAA), seed perimeter (SP), seed length (SL), seed width (SW), seed length/width (SLW), seed diameter (SD), and seed circular degree (SCD). These QTLs explained 3.32-35.73% (mean = 11.45%) of the phenotypic interpretation, including 24 main QTLs and 30 epistatic QTLs. A total of 24 candidate genes were identified within the QTL region, including one SC-associated transcription factor (ANT1), two TSW-related genes, a transcription factor (NAC021), a gene associated with the non-homologous end joining (NHEJ) pathway (ku70), three SAA-associated genes (LOL2, NAC021, TSK), two SL-associated genes (MADS21, MADS4), six SW-associated genes (FIP1, NAC021, DREB 1A, HVA22A, CYP78A6, SAUR71), five LW-related genes (NAM-B2, CRY1, LHY, CYP710A1, WRKY72), two SP-related genes (SKIP11, TCP18), two SD-related genes (NAC021, SKIP8), and three SCD-related genes (MYB1R1, RAX3, NAC100). These genes are involved in the regulation of the cell development, material transport, signal transduction, and plant morphogenesis and play an important role in the regulation of agronomic traits in hulless barley. The high-density genetic mapping and QTL identification of the seed traits in hulless barley provide a valuable genetic resource and the basis for further molecular marker-assisted selection and genomic studies.