Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Abstract

Summary Barley ( Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana . Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

A global barley panel revealing genomic signatures of breeding in modern cultivars

“…Furthermore, a total of 246 MTAs were considered to be ‘stable’, 76 MTAs were considered to be ‘consistent’, and 73 MTAs were considered to be ‘robust’ (S13 File). More than 30% of the significant MTAs were also detected in our previous study [10], in which a GWAS was performed using 4,600 SNPs (in comparison to the 33,486 SNPs used in the present study) obtained from target enrichment sequencing data for phenology genes combined with field trial data from 2015 and 2016. Here, novel and highly significant MTAs were located within the genes HORVU5Hr1G096560 (disease resistance protein), HORVU5Hr1G095040 (beta glucosidase C), and HORVU5Hr1G104240 (zinc finger A20 and AN1 domain-containing stress-associated protein 6) on chromosome 5H (S13 File).…”

“…To examine the origins and patterns of genetic diversity within the currently available barley cultivar gene pool, we assembled a global panel of 632 genotypes to represent barley genotypes from major global barley breeding programmes, including both historical cultivars and modern cultivars from 43 countries (S1 Fig, S1 File). The panel of 632 genotypes geographically diverse barley cultivars was genotyped using target capture [10, 11], low-coverage whole-genome sequencing (WGS), and genotyping-by-sequencing (GBS) by Diversity Arrays Technology (DArTseq). In total, 15,328 single-nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) were detected via low-coverage WGS, 4,260 SNPs via target-enrichment sequencing, and 18,551 SNPs via DArTseq were distributed across 5,171 barley genes.…”

“…Across all field trials, we identified 1,132 significant unique marker-trait associations (MTAs) (false discovery rate [FDR] of P < 0.05) for flowering time located within 327 unique genes with functional annotations, each explaining up to 18.7% of the phenotypic variation (S13 File, S18 Figure). These regions include known phenology-related genes, such as HvPPD-H1 , PHYTOCHROME C ( HvPhyC ), PROTEIN KINASE 2A ( HvCK2A ), HvADA2, PHYTOCHROME-ASSOCIATED PROTEIN 2 ( HvPAP2 ), and VERNALIZATION H1 ( HvVRN-H1 ) [4,10–12]. Furthermore, a total of 246 MTAs were considered to be ‘stable’, 76 MTAs were considered to be ‘consistent’, and 73 MTAs were considered to be ‘robust’ (S13 File).…”

“…Notably, we also detected novel associations with candidate phenology-related genes that were not included in the previous target-enrichment sequencing study [10] but that have annotations linking them to roles in flowering time regulation, including CCT and PRR motifs characteristic of key phenology genes such as HvCO1 , HvVRN-H2 , and HvPPD-H1 [4]. These genes included HORVU1Hr1G011030 and HORVU5Hr1G125620 (both annotated as COP1-interacting protein-related), HORVU2Hr1G055130 and HORVU7Hr1G044380 (both annotated as CONSTANS, CO-like, and TOC1 [CCT] motif family protein, and HORVU3Hr1G092330 and HORVU6Hr1G008870 (both annotated as pentatricopeptide repeat-containing protein).…”

“…Population genetic studies have examined a variety of aspects of barley genetic variation on a global scale, and have identified a striking degree of variability in traits related to flowering time, grain yield, and tolerance to abiotic and biotic factors [10–14]. This suggests that current barley germplasm resources might be harnessed to meet future challenges imposed by climate change.…”