Multiple phytohormones, including gibberellin (GA), abscisic acid (ABA), and indole-3-acetic acid (IAA), regulate seed germination. In this study, a barley aldehyde oxidase 1 (HvAO1) gene was identified, which is located near the SD2 (seed dormancy 2) region at the telomeric end of chromosome 5H. A doubled-haploid population (AC Metcalfe/Baudin) was used to characterize HvAO1 and validated its association with seed germination and malting quality. Aldehyde oxidase is predicted to catalyse the oxidation of various aldehydes, such as indoleacetaldehyde and abscisic aldehyde, into IAA and ABA, which is the final step of IAA/ABA biogenesis. This process influences the final IAA/ABA concentration in the seed, affecting the seed dormancy. Sequence analysis revealed substantial variations in the HvAO1 promoter regions between AC Metcalfe and Baudin. The combining seed germination tests, genetic variation analysis, gene expression, and phytohormone measurements showed that Baudin, which displays strong seed dormancy, has a specific sequence variation in the promoter region of the HvAO1 gene. This variation is associated with a higher expression level of the HvAO1 gene and an increased level of ABA than those in AC Metcalfe, which shows weak dormancy and lacks this sequence variation. In addition to its strong effect on the SD2 gene, HvAO1 shows excellent potential to fine-tune malting quality and seed dormancy, as evidenced by genotyping with HvAO1-specific markers, dormancy phenotypes, and malting quality. Our findings provide a new strategy for introducing favourable HvAO1 alleles to achieve the desired level of seed dormancy and high malting quality in barley.

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

Salinity causes a detrimental impact on plant growth, particularly when the stress occurs during germination and early development stages. Barley is one of the most salt-tolerant crops; previously we mapped two quantitative trait loci (QTL) for salinity tolerance during germination on the short arm of chromosome 2H using a CM72/Gairdner doubled haploid (DH) population. Here, we narrowed down the major QTL to a region of 0.341 or 0.439 Mb containing 9 or 24 candidate genes belonging to 6 or 20 functional gene families according to barley reference genomes v1 and v3 respectively, using two DH populations of CM72/Gairdner and Skiff/CM72, F₂ and F₃ generations of CM72/Gairdner/*Spartacus CL. Two Receptor-like kinase 4 (RLPK4) v1 or Receptor-like kinase (RLK) v3 could be the candidates for enhanced germination under salinity stress because of their upregulated expression in salt-tolerant variety CM72. Besides, several insertion/deletion polymorphisms were identified within the 3rd exon of the genes between CM72 and Gairdner. The sequence variations resulted in shifted functional protein domains, which may be associated with differences in salinity tolerance. Two molecular markers were designed for selecting the locus with receptor-like protein kinase 4, and one was inside HORVU2Hr1G111760.1 or HORVU.MOREX.r3.2HG0202810.1. The diagnostic markers will allow for pyramiding of 2H locus in barley varieties and facilitate genetic improvement for saline soils. Further, validation of the genes to elucidate the mechanisms involved in enhancing salinity tolerance at germination and designing RLPK4 specific markers is proposed. For this publication, all the analysis was based on barley reference genome of 2017 (v1), and it was used throughout for consistence. However, the positions of the markers and genes identified were updated according to new genome (v3) for reference.

Grain kernel discoloration (KD) in cereal crops leads to down-grading grain quality and substantial economic losses worldwide. Breeding KD tolerant varieties requires a clear understanding of the genetic basis underlying this trait. Here, we generated a high-density single nucleotide polymorphisms (SNPs) map for a diverse barley germplasm and collected trait data from two independent field trials for five KD related traits: grain brightness (TL), redness (Ta), yellowness (Tb), black point impact (Tbpi), and total black point in percentage (Tbpt). Although grain brightness and black point is genetically correlated, the grain brightness traits (TL, Ta, and Tb) have significantly higher heritability than that of the black point traits (Tbpt and Tbpi), suggesting black point traits may be more susceptible to environmental influence. Using genome-wide association studies (GWAS), we identified a total of 37 quantitative trait loci (QTL), including two major QTL hotspots on chromosomes 4H and 7H, respectively. The two QTL hotspots are associated with all five KD traits. Further genetic linkage and gene transcription analyses identified candidate genes for the grain KD, including several genes in the flavonoid pathway and plant peroxidase. Our study provides valuable insights into the genetic basis for the grain KD in barley and would greatly facilitate future breeding programs for improving grain KD resistance.

Crop genetic improvements catalysed population growth, which in turn has increased the pressure for food security. We need to produce 70% more food to meet the demands of 9.5 billion people by 2050. Climate changes have posed challenges for global food supply, while the narrow genetic base of elite crop cultivars has further limited our capacity to increase genetic gain through conventional breeding. The effective utilization of genetic resources in germplasm collections for crop improvement is crucial to increasing genetic gain to address challenges in the global food supply. Genomic selection (GS) uses genome-wide markers and phenotype information from observed populations to establish associations, followed by genome-wide markers to predict phenotypic values in test populations. Characterizing an extensive germplasm collection can serve a dual purpose in GS, as a reference population for predicting model, and mining desirable genetic variants for incorporation into elite cultivars. New technologies, such as high-throughput genotyping and phenotyping, machine learning, and gene editing, have great potential to contribute to genome-assisted breeding. Breeding programmes integrating germplasm characterization, GS and emerging technologies offer promise for accelerating the development of cultivars with improved yield and enhanced resistance and tolerance to biotic and abiotic stresses. Finally, scientifically informed regulations on new breeding technologies, and increased sharing of genetic resources, genomic data, and bioinformatics expertise between developed and developing economies will be the key to meeting the challenges of the rapidly changing climate and increased demand for food.