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Pre-harvest sprouting (PHS) induced by the absence of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterized TaABI4, an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed that TaABI4 has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP and potential PEST motifs. Putative cis-acting regulatory elements (CE1-like box, W-box, ABRE elements and RY elements) were identified in the TaABI4 promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling of TaABI4 indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation of TaABI4 in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15 and 20 DPA, respectively. Six expression quantitative trait loci (eQTL) of TaABI4 on chromosomes 2A, 2D, 3B and 4A were characterized based on the accumulated transcripts of TaABI4 in SHW-L1 and CM32-derived recombinant inbred lines. These QTLs explained 10.7 to 46.1% of the trait variation with 4.53–10.59 of LOD scores, which contain genes that may affect the expression of TaABI4.

MYB transcription factors (TFs) represents one of the largest TF families in plants. In this study, we performed genome-wide MYB-domain screening and identified a total of 997 MYBs in wheat (Triticum aestivum), among which 445 were 2-domain MYBs (R2R3-MYBs) that were clustered into 15 subgroups with varied conservation profiles. Homologous genes were highly conserved across the three subgenomes, with minor variations contributed by segmental duplications. Tandem and proximal gene duplications have contributed significantly to the expansion of the wheat Myb gene family. Furthermore, comprehensive transcriptome profiling of R2R3-Myb genes in 61 different tissue and time point samples revealed a clear pattern of temporal and spatial variations within six expression groups. The comprehensive genomic and transcriptional analyses provided valuable insights into the evolution and biological functions of R2R3-Myb genes in wheat. They would serve as a useful guide to further investigate the potential agronomic traits controlled by this large TF family.

Pre-harvest sprouting (PHS) induced by the decline of seed dormancy causes a severe reduction in crop yield and flour quality. In this study, we isolated and characterizedTaABI4,an ABA-responsive transcription factor that participates in regulating seed germination in wheat. Sequence analysis revealed thatTaABI4has three homologues, located on chromosomes 1A/1B/1D. TaABI4 contains a conserved AP2 domain, and AP2-associated, LRP, and potential PEST motifs. Putativecis-acting regulatory elements (CE1-like box, W-box, ABRE elements, and RY-elements) were identified in theTaABI4promoter region that showed high conservation in 17 wheat cultivars and wheat-related species. Expression profiling ofTaABI4indicated that it is a seed-specific gene accumulating during the middle stages of seed development. Transcript accumulation ofTaABI4in wheat cultivar Chuanmai 32 (CM32, PHS susceptible) was 5.07-fold and 1.39-fold higher than that in synthetic hexaploidy wheat SHW-L1 (PHS resistant) at 15DPA and 20DPA, respectively. Six expression quantitative trait loci (eQTL) ofTaABI4on chromosome 2A, 2D, 3B, and 4A were characterized based on the accumulated transcripts ofTaABI4in SHW-L1 and CM32 derived recombinant inbred lines. These QTLs explained from 10.7% to 46.1% of the trait variation with 4.53~10.59 of LOD scores, which contain genes that may affect the expression ofTaABI4.

A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection.

Key message A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Abstract Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.

The gene HvDEP1, on barley (Hordeum vulgare L.) chromosome 5H, encodes a γ-subunit of the heterotrimeric G-protein complex and was previously determined to be a candidate gene underlying a major quantitative trait locus for grain length. In the present study, we identified a 9 bp indel (insertion–deletion mutation) at position –84 bp from the start codon within a reported upstream open reading frame located in the 5′ UTR (untranslated region) and developed a diagnostic molecular marker. We also identified a 13 bp indel (–514 bp) in linkage disequilibrium that bridges an important regulatory motif. Using a doubled-haploid population and a barley diversity panel, we were able to show that the effects of these indels were environmentally stable and consistently delineated phenotypic groups based on grain length and 1000-grain weight. Genotypes represented by deletions at these two positions relative to the reference cv. Morex had consistently shorter grains, by 3.69–3.96%, and lower 1000-grain weight, by 2.38–4.21%, in a doubled-haploid population studied. Additionally, a diversity panel was tested but consistent differences were observed only for grain length, reinforcing literature indicating the importance of this gene for grain-length regulation. The frequency of the longer and heavier grained reference allele was higher in modern cultivars, suggesting that indirect selection for longer grain may have occurred through direct selection for grain yield via grain-weight improvement. These results indicate that grain length and 1000-grain weight in barley can be manipulated by targeting variation in gene promoters through marker-assisted selection.