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Genetic dissection of spike morphology in Australian barley panel: Insights from a multi-model GWAS and haplotype analysis
Journal article   Open access   Peer reviewed

Genetic dissection of spike morphology in Australian barley panel: Insights from a multi-model GWAS and haplotype analysis

Shunlin Zhang, Tianhua He, Yong Han, Gaofeng Zhou, Bettina Berger, Baojin Guo and Chengdao Li
Journal of Integrative Agriculture
2026
DOI: https://doi.org/10.1016/j.jia.2026.03.030
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CC BY-NC-ND V4.0,  Open Access

Abstract

barley breeding selection genome-wide association study haplotype analysis spike architecture
Barley (Hordeum vulgare L.) is a globally important cereal crop increasingly challenged by climate variability and shifting agronomic demands. Spike morphology is pivotal in determining yield potential, but its genetic underpinnings remain only partially understood. Here, we leveraged the OzBarley panel with 214 elite Australian barley accessions, integrating high-density markers (65,465 SNPs) with multi-environment phenotyping to dissect the genetic architecture of six spike traits: awn length (AL), grain number per spike (GNS), spike density (SD), spike length (SL), spikelet number per spike (SNS), and seed setting rate (SSR). Genome-wide association studies identified 27 stable quantitative trait loci (QTLs) distributed across six chromosomes, explaining up to 22.52% of phenotypic variance. High heritability estimates (49.02-93.54%) and strong inter-trait correlations (r=0.33-0.89, P<0.001) underscore the stable genetic control. Haplotype-based dissection prioritized two major loci: QAL.Murdoch.7H.1, and QGNS/SD/SNS.Murdoch.4H.1. A missense SNP (Lys372Asn) in HORVU.MOREX.r3.7HG0720710 was implicated in the suppression of awn length at QAL.Murdoch.7H.1, while a nonsynonymous mutation (Ala127Thr) in HORVU.MOREX.r3.4HG0336810 at QGNS/SD/SNS.Murdoch.4H.1 was associated with increased spikelet and grain number. Longitudinal analysis revealed directional selection for favourable haplotypes, QGNS/SD/SNS.Murdoch.4H.1-Hap002 and QAL.Murdoch.7H.1-Hap004, with frequencies increasing significantly in recent Australian cultivars. Conversely, unfavourable haplotypes introduced during the 1990s were later counter-selected, highlighting refined breeding strategies. Our findings offer critical insights into the genetic regulation of barley spike morphology, thereby linking genomic discoveries to breeding applications. The OzBarley panel serves as a valuable genomic resource for accelerating marker-assisted selection, facilitating the development of high-yielding barley cultivars tailored to meet future agricultural demands.

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