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小麦叶片气孔相关性状全基因组关联分析

李璐琪1,2,程宇坤1,2,白斌3,雷斌4,耿洪伟1,2,*   

  1. 1新疆农业大学农学院/新疆农业大学优质专用麦类作物工程技术研究中心, 新疆乌鲁木齐 830052; 2丝绸之路经济带作物生物育种联合实验室, 新疆乌鲁木齐830052; 3甘肃省农业科学院小麦研究所, 甘肃兰州730070; 4新疆农业科学院, 新疆乌鲁木齐830091
  • 收稿日期:2025-03-11 修回日期:2025-06-01 接受日期:2025-06-01 出版日期:2025-06-13 网络出版日期:2025-06-13
  • 基金资助:
    本研究由新疆维吾尔自治区科学技术厅自然科学基金杰出青年科学基金项目(2022D01E46), 新疆维吾尔自治区重点研发计划(2023B02006)和新疆维吾尔自治区青年科技拔尖人才专项(2022TSYCCX0079)资助。

Genome-wide association analysis of stomatal-related traits in wheat leaves

LI Lu-Qi1,2, CHENG Yu-Kun1,2, BAI Bin3, LEI Bin4, GENG Hong-Wei1,2,*   

  1. 1 College of Agronomy / Special High Quality Triticeae Crops Engineering and Technology Research Center, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China; 2 Joint International Research Laboratory of Crop Biological Breeding along the Silk Road Economic Belt, Urumqi 830052, Xinjiang, China;3Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, Gansu, China; 4 Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, China
  • Received:2025-03-11 Revised:2025-06-01 Accepted:2025-06-01 Published:2025-06-13 Published online:2025-06-13
  • Supported by:
    This study was supported by the Xinjiang Uygur Autonomous Region Department of Science and Technology, the National Natural Science Fund for Distinguished Young Scholars(2022D01E46), Xinjiang Uygur Autonomous Region Key Research and Development Program (2023B02006), and Xinjiang Uygur Autonomous Region Youth Science and Technology Talent Program (2022TSYCCX0079).

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摘要：

小麦气孔是调节光合作用和蒸腾作用的微观孔隙，对产量有着关键作用，了解小麦气孔性状的遗传机制，挖掘关于小麦气孔相关性状的候选基因对于提高小麦产量具有重要意义。本研究以276份冬小麦品种(系)为研究对象，在正常灌溉和干旱胁迫2个处理下，对小麦抽穗期和灌浆期的气孔密度、气孔平均面积、气孔所占比等叶片气孔相关性状进行测定，并结合90K小麦芯片，对上述3个性状进行全基因组关联分析。研究结果显示，在不同水分处理条件下，小麦气孔相关性状在2个时期均表现出较大的表型变异，变异系数介于0.06至0.28之间。全基因组关联结果显示，共检测到88个位于除4D的其他20条染色体上与气孔相关性状显著关联的位点(P < 0.001)，其中与气孔平均面积显著相关的稳定遗传位点有4个，分布于1B, 3A, 6A染色体上，可解释遗传变异为2.78%~6.55%，均在正常灌溉下的灌浆期检测到。在抽穗期和灌浆期同时检测到2个与气孔密度显著关联的位点，其中在正常灌溉下6A染色体上检测到的位点Ex_c69429_328，可解释表型变异为2.31%~3.06%；在干旱胁迫下4A染色体上检测到的位点BS00064423_51，可解释表型变异的4.40%~6.09%。在1A、1B、3A、4A、5A、6A、6D染色体上检测到8个“一因多效”遗传位点，可解释表型变异的1.25%~7.31%。对贡献率大于5.00%且在2个环境或2个性状以上检测到位点进行单倍型分析，发现与气孔平均面积和气孔所占比显著相关的wsnp_Ex_rep_c69627_68580121(R2=6.47%)位点存在Hap1、Hap2两个单倍型，在276份品种(系)中含有Hap1(频率为81.20%)单倍型品种(系)的气孔平均面积显著小于含有Hap2(18.80%)单倍型品种(系)的气孔平均面积(P<0.05)，不同单倍型在不同麦区的占比不同，其中单倍型Hap1在西南冬麦区出现的频率最高，单倍型Hap2则在北部冬麦区出现的频率最高。对2个环境检测到的及“一因多效”的位点进行候选基因的挖掘，共筛选出9个与小麦气孔性状相关的候选基因，这些基因在气孔发育、光合作用和抗逆性等方面具有潜在功能，可作为进一步研究气孔相关性状的重要基因。

关键词: 小麦, 气孔, 全基因组关联分析, 单倍型, 候选基因

Abstract:

Wheat stomata are microscopic pores that regulate photosynthesis and transpiration, playing a critical role in determining yield. Understanding the genetic mechanisms underlying stomatal traits and identifying candidate genes associated with these characteristics are essential for improving wheat productivity. In this study, 276 winter wheat varieties (lines) were evaluated under two irrigation treatments—normal irrigation and drought stress. Stomatal traits, including stomatal density, average stomatal area, and stomatal pore proportion, were measured at both the heading and filling stages. A genome-wide association study (GWAS) was conducted using a 90K wheat SNP chip to analyze these traits. The results revealed significant phenotypic variation in stomatal traits across the two irrigation regimes and developmental stages, with coefficients of variation ranging from 0.06 to 0.28. GWAS identified 88 loci significantly associated with stomatal traits across 20 chromosomes, excluding chromosome 4D (P < 0.001). Among these, four stable genetic loci related to average stomatal area were identified on chromosomes 1B, 3A, and 6A, explaining 2.78% to 6.55% of the phenotypic variance. These loci were all detected during the filling stage under normal irrigation. Two loci associated with stomatal density were identified at both the heading and filling stages: Ex_c69429_328 on chromosome 6A under normal irrigation explained 2.31% to 3.06% of the variation, while BS00064423_51 on chromosome 4A under drought stress accounted for 4.40% to 6.09%. Additionally, eight loci with pleiotropic effects were identified on chromosomes 1A, 1B, 3A, 4A, 5A, 6A, and 6D, explaining 1.25% to 7.31% of the phenotypic variation. Haplotype analysis was performed on loci with a contribution rate greater than 5.00% that were detected in at least two environments or associated with two or more traits. Notably, the wsnp-Ex_rep_c69627_68580121 locus (R2=6.47%), significantly associated with both average stomatal area and stomatal pore proportion, exhibited two haplotypes—Hap1 and Hap2. Among the 276 wheat lines, those carrying Hap1 (frequency: 81.20%) had a significantly smaller average stomatal area than those with Hap2 (frequency: 18.80%) (P< 0.05). Haplotype distribution varied across wheat-growing regions, with Hap1 most prevalent in the southwest winter wheat region, while Hap2 was more common in northern regions. A total of nine candidate genes associated with stomatal traits were identified based on loci detected in multiple environments and those with pleiotropic effects. These genes are likely involved in stomatal development, photosynthesis, and stress responses, offering promising targets for further research and genetic improvement of wheat stomatal traits.

Key words: wheat, stomata, genome-wide association analysis, haplotype, candidate genes

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