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

doi:10.1016/j.jia.2026.03.030

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Shunlin Zhang^1,², Tianhua He^1,², Yong Han³, Gaofeng Zhou^1,², Bettina Berger^4,⁵, Baojin Guo^1,^2,^6,⁷^#, Chengdao Li^1,^2,^3,⁸^#

¹Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia

²Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia

³ Department of Primary Industry and Regional Development, Government of Western Australia, 3-Baron-Hay Court, South Perth, WA 6151, Australia

⁴The Waite Research Institute and School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia

⁵ Australian Plant Phenomics Network, The University of Adelaide, Glen Osmond, SA 5064, Australia

⁶ State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

⁷Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China

⁸College of Agriculture, Shandong Agricultural University, Tai’an 271018, China

Highlights

1. Multi-model GWAS analysis of the OzBarley panel identified 27 stable QTLs for six spike traits.

2. Haplotype-based dissection revealed key loci affecting awn and spike fertility.

3. Favourable haplotypes were enriched in modern Australian barley cultivars.

Abstract
References

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摘要

大麦（Hordeum vulgare L.）是全球重要的禾谷类作物，正日益受到气候多变性和农业需求变化带来的挑战。穗部形态是决定产量潜力的关键因素，但其遗传基础尚未得到充分解析。本研究利用包含214个澳大利亚优良大麦种质资源的OzBarley群体，整合高密度标记（65,465个SNPs）和多环境表型数据，对六个穗部性状的遗传结构进行了解析，包括芒长（AL）、单穗粒数（GNS）、穗密度（SD）、穗长（SL）、单穗小穗数（SNS）和结实率（SSR）。全基因组关联分析鉴定出27个稳定的数量性状基因座（QTLs），分布于6条染色体上，可解释最高达22.52%的表型变异。高遗传力估计值（49.02%-93.54%）和性状间强相关性（r=0.33-0.89, P<0.001）表明这些性状受稳定的遗传调控。基于单倍型的分析重点解析了两个主效位点：QAL.Murdoch.7H.1和QGNS/SD/SNS.Murdoch.4H.1。在QAL.Murdoch.7H.1中，基因HORVU.MOREX.r3.7HG0720710的一个错义突变（Lys372Asn）与芒长抑制相关；而在QGNS/SD/SNS.Murdoch.4H.1中，基因HORVU.MOREX.r3.4HG0336810的非同义突变（Ala127Thr）与增加小穗数和粒数相关。纵向分析显示，优势单倍型QGNS/SD/SNS.Murdoch.4H.1-Hap002和QAL.Murdoch.7H.1-Hap004经历了定向选择，其在现代澳大利亚栽培品种中的频率显著上升。相反，20世纪90年代引入的不利单倍型在后续育种中被反向选择，凸显了育种策略的精细化。本研究为大麦穗部形态的遗传调控提供了关键见解，从而将基因组发现与育种应用联系起来。OzBarley群体可作为加速标记辅助选择的宝贵基因组资源，促进培育适应未来农业需求的高产大麦品种。

Abstract

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.

Keywords: barley spike architecture genome-wide association study haplotype analysis breeding selection

Online: 11 March 2026

Fund:

The OzBarley project was enabled by investment from the National Collaborative Research Infrastructure Strategy (NCRIS) through the Australian Research Data Commons (ARDC), the Australian Plant Phenomics Network (APPN) and Bioplatforms Australia (BPA). Additional investment for OzBarley, including field trials and travel support, was provided by the Grains Research and Development Corporation (GRDC) under the UOA2306-010RTX project.

About author: #Correspondence Baojin Guo, E-mail: Baojin.Guo@murdoch.edu.au); Chengdao Li, E-mail: c.li@murdoch.edu.au

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Shunlin Zhang, Tianhua He, Yong Han, Gaofeng Zhou, Bettina Berger, Baojin Guo, Chengdao Li. 2026. Genetic dissection of spike morphology in Australian barley panel: Insights from a multi-model GWAS and haplotype analysis. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.03.030

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