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Key message <p>GWAS of 17 spike traits in 246 wheat varieties identifies three novel QTLs, 70 candidate genes, and seven validated KASP markers for spike architecture.</p> Abstract <p>Spike morphology is a critical determinant of wheat yield, influencing grain formation and photoassimilate partitioning. To dissect its genetic basis, we conducted a genome-wide association study (GWAS) on 17 spike-related traits. A natural population comprising 246 wheat varieties was evaluated in five field environments over two growing seasons. Genotyping was performed using a 60&#xa0;K SNP array, yielding 36,591 high-quality markers (36,554 SNPs and 37 InDels) for analysis. GWAS identified 1,246 significant markers, including 139 with pleiotropic effects (associated with ≥ 2 traits) and 26 that were stable across multiple environments (traits detected in ≥ 3 environments). These stable markers delineated 16 quantitative trait loci (QTLs) for eight key traits, such as spike length, grain dimensions, and spikelet density. Among these, we discovered three novel QTLs: one for spike length and two for total spikelet number per spike. Gene annotation within the QTL intervals yielded 98 candidate genes. Subsequent expression analysis refined this set to 70 high-confidence candidates, five of which are known wheat genes with potential novel roles in spike development. To facilitate breeding, we developed seven Kompetitive Allele-Specific PCR (KASP) markers and subsequently validated them in an independent cohort: five for spike length and two for spikelet density. This study provides novel genetic insights and practical molecular tools, facilitating marker-assisted selection for improved wheat spike architecture and yield.</p>

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Genome-wide association study of spike-related traits in common wheat

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月2日

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  • Maosen Niu,
  • Longteng Ma,
  • Hongling Yang,
  • Qing Xu,
  • Yizheng Li,
  • Huiyi Gou,
  • Qianyi Sun,
  • Rui Wang,
  • Xiaohui Sun,
  • Yan Zhao

摘要

Key message

GWAS of 17 spike traits in 246 wheat varieties identifies three novel QTLs, 70 candidate genes, and seven validated KASP markers for spike architecture.

Abstract

Spike morphology is a critical determinant of wheat yield, influencing grain formation and photoassimilate partitioning. To dissect its genetic basis, we conducted a genome-wide association study (GWAS) on 17 spike-related traits. A natural population comprising 246 wheat varieties was evaluated in five field environments over two growing seasons. Genotyping was performed using a 60 K SNP array, yielding 36,591 high-quality markers (36,554 SNPs and 37 InDels) for analysis. GWAS identified 1,246 significant markers, including 139 with pleiotropic effects (associated with ≥ 2 traits) and 26 that were stable across multiple environments (traits detected in ≥ 3 environments). These stable markers delineated 16 quantitative trait loci (QTLs) for eight key traits, such as spike length, grain dimensions, and spikelet density. Among these, we discovered three novel QTLs: one for spike length and two for total spikelet number per spike. Gene annotation within the QTL intervals yielded 98 candidate genes. Subsequent expression analysis refined this set to 70 high-confidence candidates, five of which are known wheat genes with potential novel roles in spike development. To facilitate breeding, we developed seven Kompetitive Allele-Specific PCR (KASP) markers and subsequently validated them in an independent cohort: five for spike length and two for spikelet density. This study provides novel genetic insights and practical molecular tools, facilitating marker-assisted selection for improved wheat spike architecture and yield.