Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica

   

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 Online:2025-06-13 Published: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).

PDF

15

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

[1] Colin C M, Stephen S J. Breeding perennial grain crops based on wheat. Crop Sci, 2017, 57: 1172–1188.

[2] Tahira T, Muhammad F, Riaz A, Ali Z, Abdul W, Muhammad S. Terminal drought and seed priming improves drought tolerance in wheat. Physiol Mol Biol Plants, 2018, 24: 845–856.

[3] Stuart C, Julie E. Gray. Influence of environmental factors on stomatal development. New Phytol, 2008, 178:9–23

[4] 王声锋, 段爱旺, 张展羽,徐建新. 基于随机降水的冬小麦灌溉制度制定. 农业工程学报, 2010, 26(12): 47–52.

Wang S F, Duan A W, Zhang Z Y, Xu J X. Winter wheat irrigation schedule on stochastic precipitation. Trans CSAE, 2010, 26(12): 47–52(in Chinese with English abstract).

[5] 刘梦龙, 魏健, 任姿蓉, 张亚黎, 王愔. 气孔研究进展: 从保卫细胞到光合作用. 生命科学, 2024, 36: 1289–1304.

Liu M L, Wei J, Ren Z R, Zhang Y L, Wang Y. Research progress of stomata: from guard cells to photosynthesis. Chin Bull Life Sci, 2024, 36: 1289–1304(in Chinese with English abstract).

[6] 方静, 史功赋, 魏淑丽, 程玉臣, 张向前, 王建国, 安玉, 赵小庆, 路战远. 干旱胁迫对春小麦旗叶生理特征及其根系抗旱基因表达特征的影响. 干旱地区农业研究, 2022, 40(3): 46–55.

Fang J, Shi G F, Wei S L, Cheng Y C, Zhang X Q, Wang J G, An Y, Zhao X Q, Lu Z Y. Effects of drought stress on physiological characteristics of flag leaves and expression characteristics of drought-resistant genes in roots of spring wheat. Agric Res Arid Areas, 2022, 40(3): 46–55 (in Chinese with English abstract).

[7] 陈倩倩, 范阳阳, 郝影宾, 刘西平. 不同土壤水分含量对玉米气孔发育过程和蒸腾耗水量的影响. 干旱地区农业研究, 2011, 29(3):75–79.

Chen Q Q, Fan Y Y, Hao Y B, Liu X P. Effects of different soil water content on stomata development and water consumption of maize. Agric Res Arid. Areas, 2011, 29(3):75–79(in Chinese with English abstract).

[8] 燕雯, 金秀良, 李龙, 徐子涵, 苏悦, 张跃强, 景蕊莲, 毛新国, 孙黛珍. 基于无人机多源影像数据的灌浆期人工合成小麦抗旱性评价. 中国农业科学, 2024, 57: 1674–1686.

Yan W, Jin X L, Li L, Xu Z H, Su Y, Zhang Y Q, Jing R L, Mao X G, Sun D Z. Drought resistance evaluation of synthetic wheat at grain filling using UAV-Based Multi-Source imagery data. Sci Agric Sin, 2024, 57: 1674–1686 (in Chinese with English abstract).

[9] 王士强, 胡银岗, 佘奎军, 周琳璘, 孟凡磊. 小麦抗旱相关农艺性状和生理生化性状的灰色关联度分析. 中国农业科学, 2007, 40:2452–2459.

Wang S Q, Hu Y G, She K J, Zhou L L, Meng F L. Gray relational grade analysis of agronomical and Physi-biochemical traits related to drought tolerance in wheat. Sci Agric Sin, 2007, 40: 2452–2459 (in Chinese with English abstract).

[10] Shahinia F, Le Roy J, Laborde B, Sznajder B, Kalambettu P, Mahjourimajd S, Tilbroook J, Fleury D. Genetic association of stomatal traits and yield in wheat grown in low rainfall environments. BMC plant Biol, 2016, 16: 150–163.

[11] Ahmed H G M, Iqbal M N, Iqbal M A, Zeng Y W, Ullah A, Iqbal M, Raza H, Yar M M, Sarwar N, Imran M, et al.Genome-wide association mapping for stomata and yield indices in bread wheat under water limited conditions. Agronomy, 2021, 11: 1646.

[12] Yates S A, Bruun A, Hodel M, Grieder C, Hund A, Walter A, Studer B. Genetic determination of stomatal patterning in winter wheat (Triticum aestivum L.). bioRxiv, 2018: 490029.

[13] Li S M, Yu S Z, Zhang Y F, Zhu D H, Li F F, Chen B, Mei F M, Du L Y, Ding L, Chen L, et al. Genome-wide association study revealed Ta HXK3-2A as a candidate gene controlling stomatal index in wheat seedlings. Plant Cell Environ, 2022, 45: 2306–2323

[14] 丁浦洋, 周界光, 赵聪豪, 唐华苹, 牟杨, 唐力为, 邓梅, 魏育明, 兰秀锦, 马建. 小麦小穗数调控基因WAPO1的单倍型, 遗传效应, 地理分布及育种利用分析. 作物学报, 2022, 48: 2196–2209.

Ding P Y, Zhou J G, Zhao C H, Tang H P, Mou Y, Tang L W, Deng M, Wei Y M, Lan X J, Ma J, Dissection of haplotypes, geographical distribution and breeding utilization of WAPO1 associated with spike development in wheat. Acta Agron Sin, 2022, 48: 2196–2209 (in Chinese with English abstract).

[15] 魏迪, 常平, 刘佳熠, 杨阳, 张璇, 陈亮, 胡银岗. 小麦EPF/EPFL基因家族的全基因组鉴定及TaEPF1-2B与气孔性状的关系分析. 麦类作物学报, 2021, 41:1317–1329.

Wei D, Chang P, Liu J Y, Yang Y, Zhang X, Chen L, Hu Y G. Genome-Wide identification of EPF/EPFL gene family in wheat (Triticum aestivum) and analysis of TaEPF1-2B associated with stomatal traits.J Triticeae Crops, 2021, 41:1317–1329(in Chinese with English abstract).

[16] Nassuth N, Rahman M.A, Nguyen T, Ebadi A. Lee C. Leaves of more cold hardy grapes have a higher density of small, sunken stomata. Vitis, 2021, 60: 63–67.

[17] 韩贝, 王旭文, 李保奇,余渝, 田琴, 杨细燕. 陆地棉种质资源抗旱性状的关联分析. 作物学报, 2021, 47:438–450.

Han B, Wang X W, Li B Q, Yu Y, Tian Q, Yang X Y. Association analysis of drought tolerance traits of upland cotton accessions(Gossypium hirsutum L.). Acta Agron Sin, 2021, 47:438–450(in Chinese with English abstract).

[18] Zhang J, Nilda R.B, Ma K, Zhou Y J, Geng R M, Yu L Q. Genetic diversity and relationship of weedy rice in Taizhou city, Jiangsu province, China. Rice Sci, 2008, 15:295–302.

[19] 黄婧, 张敏. 基于SNP分子标记的乌饭树种质遗传多样性研究. 植物遗传资源学报, 2025, 26: 530–538.

Huang J, Zhang M. Genetic diversity analysis of Vaccinium bracteatum germplasm based on SNP markers.J Plant Genet Resour, 2025, 26: 530–538(in Chinese with English abstract).

[20] 栾海业,孟炜,张英虎,李钰, 朱琳洁, 王裕, 刘雨倩, 徐肖, 刘方方, 沈会权. 大麦耐盐相关性状的全基因组关联分析. 麦类作物学报, 2024, 44:729–734.

Luan H Y, Meng W, Zhang Y H, Li Y, Zhu L J, Wang Y, Liu Y Q, Xu X, Liu F F, Shen H Q. Genome-Wide association analysis of traits related to salt tolerance in barley. J Triticeae Crops, 2024, 44:729–734(in Chinese with English abstract).

[21] Yu J M, Pressoir G, Briggs W H, Vroh Bi I, Yamasaki M, Doebley J F, Mcmullen M D, Gaut B S, Nielsen D M, Holland J B, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 2006, 38: 203–208.

[22] Cattivelli L, Rizza F, Badeck F W, Mazzucotelli E, Mastrangelo A M, Francia E, Mare C, Tondelli A, Stanca A M. Drought tolerance improvement in crop plants: An integrated view from breeding to genomics. Field Crops Res. 2008, 105:1–14.

[23] 赵广才. 中国小麦种植区划研究(一).麦类作物学报, 2010, 30: 886–895.

Zhao G C. Study on Chinese wheat planting regionalization (I). J Triticeae Crops, 2010, 30: 886–895 (in Chinese with English abstract).

[24] 陈晨, 张永成. 马铃薯不同品种间气孔密度及叶绿素含量的差异性研究. 中国农学通报, 2013, 29(27):83–87.

Chen C, Zhang Y C. Research on the differences in stomatal density and chlorophyll content among different potato varieties. Chin Agric Sci Bull, 2013, 29(27):83–87(in Chinese with English abstract).

[25] 李方杰, 常志杰, 史大坤,卫晓轶, 魏锋, 洪德峰, 马俊峰. 郑秋道. 不同基因型玉米间作对气孔特征和产量的影响. 河南农业科学, 2024, 53(8):21–29.

Li F J, Chang Z J, Shi D K, Wei X Y, Wei F, Hong D F, Ma J F, Zheng Q D. Effects of intercropping of different genotypes of maize on stomatal characteristics and yield. J Henan Agric Sci, 2024, 53(8):21–29(in Chinese with English abstract).

[26] Baute J, Polyn S, De Block.J, Blomme J, Van Lijsebettens M, Inzé D. F-box protein FBX92 affects leaf size in Arabidopsis thaliana.Plant Cell Physiol, 2017, 58: 962–975.

[27] 刘德政.调控小麦叶片气孔性状关键基因及其优异位点的挖掘.西北农林科技大学硕士学位论文,陕西杨凌, 2023.

Liu D Z. Discovery of Key Genes Regulating Wheat Leaf Stomatal Traits and Their Superior Sites. Northwest A&F University Master’s thesis, Yanglin, Shaanxi, China, 2023 (in Chinese with English abstract).

[28] 王睿, 任毅, 程宇坤, 王伟, 张志辉, 耿洪伟. 小麦旗叶形态相关性状全基因组关联分析. 作物学报, 2023, 49: 2886–2901.

Wang R, Ren Y, Cheng Y K, Wang W, Zhang Z H, Geng H W. Genome-wide association analysis of morphological traits of flag leaf in wheat. Acta Agron Sin, 2023, 49: 2886–2901(in Chinese with English abstract).

[29] 陈玲玲,刘亭萱,谷勇哲,宋健,王俊,邱丽娟.大豆叶柄夹角相关基因GmILPA1单倍型分析.植物遗传资源学报,2021,22:1698–1707.

Chen L L, Liu T X, Gu Y Z, Song J, Wang J, Qiu L J. Haplotype analysis of petiole angle-related gene GmILPA1 in soybean. JPlant Genet Resour,2021,22:1698–1707(in Chinese with English abstract).

[30] 刘德政,卢山,高珅奥,王脉, 乔朋放, 董清峰, 任昊, 陈亮, 胡银岗.大田和旱棚环境下小麦旗叶气孔性状变异及其与光合参数的关系.麦类作物学报,2024,44:360–369.

Liu D Z, Lu S, Gao S A, Wang M, Qiao P F, Dong Q F, Ren H, Chen L, Hu Y G. Variations of flag leaf and stomatal traits of wheat in field and drought shed environment. J Triticeae Crops, 2024,44:360–369(in Chinese with English abstract).

[31] Zhang Y, Xu W, Li Z, Deng X W, WuW H, XueY B. F-box protein DOR functions as a novel inhibitory factor for abscisic acid-induced stomatal closure under drought stress in Arabidopsis.Plant Physiol, 2008, 148, 751–763.

[32] Kim S, Yamaoka Y, Ono H, Kim H, Shin D, Meashima M, Martinoia E, Cahoon E B, Nishida I, Lee Y. At ABCA9 transporter supplies fatty acids for lipid synthesis to the endoplasmic reticulum. Proc NatlAca. Sci USA., 2013,110:773–778.

[33] Park J J, Jin P, Yoon J, Yang J I, Jeong H J, Ranathunge K, Schreiber L, Franke R, Lee I J, An G. Mutation in wilted dwarf and le-thal 1 (WDL1) causes abnormal cuticle formation and rapid water loss in rice. Plant Mol Biol, 2010, 74: 91–103.

[34] 陈默, 陈璐, 李双江, 谢海弘, 宋勇. 干旱胁迫对不同木薯苗期生理特性及气孔形态的影响. 四川农业大学学报, 2024, 42:1049–1056.

Chen M, Chen L, Li S J, Xie H H, Song Y. Effects of drought stress on physiological characteristics and stomatal morphology of different cassava seedlings. JSichuan AgricUniv, 2024, 42:1049–1056(in Chinese with English abstract).

[35] 韩慧, 张秀海, 郭建波,张来喜, 杨风萍, 董然. DELLA蛋白在植物中的功能. 分子植物育种,网络首发[2024-12-16],https://link.cnki.net/urlid/46.1068.S.20241216.1105.002.

Han H, Zhang X M, Guo J B, Zhang L X, Yang F P, Dong R. The function of DELLA protein in plants. Mol Plant Breed., Published online [2024-12-16](in Chinese with English abstract).

[36] 春宇, 李向颖, 元元, 萨日娜. 盐碱胁迫对藜麦生理生化及代谢水平的影响综述. 农业科学研究, 2024, 45(4): 67–77.

Chun Y, Li X Y, Yuan Y, Sa R N. A review on the impact of saline-alkali stress on the physiological, biochemical, and metabolic levels of quinoa. JAgric Res, 2024, 45(4): 67–77 (in Chinese with English abstract).

[1] LYU Guo-Feng, FAN Jin-Ping, WU Su-Lan, ZHANG Xiao, ZHAO Ren-Hui, LI Man, WANG Ling, GAO De-Rong, BIE Tong-De, LIU Jian. Genetic analysis of key target traits in the early-maturing wheat cultivar Yangmai 37 [J]. Acta Agronomica Sinica, 2025, 51(6): 1538-1547.
[2] WU Mei-Juan, ZHANG Yin-Hui, LI Yuan-Hao, LIU Hai-Xia, HUANG Yi-Lin, LI Tian, LIU Hong-Xia, ZHANG Xue-Yong, HAO Chen-Yang, GUO Jie, HOU Jian. Functional dissection of sucrose synthase gene TaSUS2 regulating grain starch synthesis and quality in wheat [J]. Acta Agronomica Sinica, 2025, 51(6): 1514-1525.
[3] YANG Si-Jie, DU Qi-Di, CHAI Shou-Xi, XIONG Hong-Chun, XIE Yong-Dun, ZHAO Lin-Shu, GU Jia-Yu, GUO Hui-Jun, LIU Lu-Xiang. Genetic mapping of mutant genes on flag leaf length and width in wheat [J]. Acta Agronomica Sinica, 2025, 51(6): 1548-1557.
[4] ZHAO Gang, ZHANG Jian-Jun, DANG Yi, FAN Ting-Lu, WANG Lei, ZHOU Gang, WANG Shu-Ying, LI Xing-Mao, NI Sheng-Li, MI Wen-Bo, ZHOU Xu-Jiao, CHENG Wan-Li, LI Shang-Zhong. Effects of straw mulching on soil water temperature effect and winter wheat yield in different rainfall years in Dryland Loess Plateau [J]. Acta Agronomica Sinica, 2025, 51(6): 1643-1653.
[5] MENG Xiang-Yu, DIAO Deng-Chao, LIU Ya-Rui, LI Yun-Li, SUN Yu-Chen, WU Wei, ZHAO Wen, WANG Yu, WU Jian-Hui, LI Chun-Lian, ZENG Qing-Dong, HAN De-Jun, ZHENG Wei-Jun. Genetic analysis of high yield and yield stability characteristics of new wheat variety Xinong 877 [J]. Acta Agronomica Sinica, 2025, 51(5): 1261-1276.
[6] LI Wen-Jia, LIAO Yong-Jun, HUANG Lu, LU Qing, LI Shao-Xiong, CHEN Xiao-Ping, JIN Jing-Wei, WANG Run-Feng. Genome-wide associate analysis of flowering traits and identification of candidate genes in peanut [J]. Acta Agronomica Sinica, 2025, 51(5): 1400-1408.
[7] ZHANG Jin-Ze, ZHOU Qing-Guo, XIAO Li-Jing, JIN Hai-Run, OU-YANG Qing-Jing, LONG Xu, YAN Zhong-Bin, TIAN En-Tang. QTL mapping and candidate gene analysis of glucosinolate content in various tissues of Brassica juncea [J]. Acta Agronomica Sinica, 2025, 51(5): 1166-1177.
[8] WANG Ya-Wen, QI Zheng-Yang, YOU Jia-Qi, NIE Xin-Hui, CAO Juan, YANG Xi-Yan, TU Li-Li, ZHANG Xian-Long, WANG Mao-Jun. Preparation of cotton 60K functional locus gene chip and its application to genetic research [J]. Acta Agronomica Sinica, 2025, 51(5): 1178-1188.
[9] WANG Qing, WANG Yi-Xiu, LI Yue-Nan, LYU Yong-Hui, ZHANG Hai-Bo, LIU Na, CHENG Hong-Yan. Differences in transcriptomic responses to cadmium stress in high/low-Cd- accumulation wheat [J]. Acta Agronomica Sinica, 2025, 51(5): 1230-1247.
[10] WANG Jia-Jie, WANG Zheng-Nan, BATOOL Maria, WANG Wang-Nian, WEN Jing, REN Chang-Zhong, HE Feng, WU You-You, XU Zheng-Hua, WANG Jing, KUAI Jie, WANG Bo, ZHOU Guang-Sheng, FU Ting-Dong. Comparison of physiological characteristics of salt and alkali tolerance between rapeseed and wheat [J]. Acta Agronomica Sinica, 2025, 51(5): 1215-1229.
[11] WANG Dong, WANG Sen, SHANG Li, FENG Hao-Wei, ZHANG Yong-Qiao, CUI Jia-Ming, LI Shuang, ZHANG Jia-Cong, CHE Huan. Effect of supplementary irrigation on winter wheat yield and water use efficiency in semi humid areas of the Loess Plateau [J]. Acta Agronomica Sinica, 2025, 51(5): 1312-1325.
[12] LI Pei-Hua, LI Jie, MENG Xiang-Yu, SUN Yu-Chen, FENG Yong-Jia, LI Yun-Li, DIAO Deng-Chao, ZHAO Wen, WU Wei, HAN De-Jun, ZHANG Song-Wu, ZHENG Wei-Jun. Evaluation of stress tolerance and physiological response of cold-type wheat under heat stress [J]. Acta Agronomica Sinica, 2025, 51(4): 1118-1130.
[13] LI Qiao, YE Yang-Chun, CHANG Xu-Hong, WANG De-Mei, WANG Yan-Jie, YANG Yu-Shuang, MA Rui-Qi, ZHAO Guang-Cai, CAI Rui-Guo, ZHANG Min, LIU Xi-Wei. Effects of high temperature and drought stresses on photosynthetic characteristics and yield of winter wheat after anthesis [J]. Acta Agronomica Sinica, 2025, 51(4): 1077-1090.
[14] WANG Jiao, BAI Hai-Xia, HAN Yu-Yan, LIANG Hui, FENG Ya-Nan, ZHANG Dong-Sheng, LI Ping, ZONG Yu-Zheng, SHI Xin-Rui, HAO Xing-Yu. Effects of elevated CO2 concentration, increased temperature and their interaction on the carbon and nitrogen metabolism in Liangxing 99 winter wheat leaves [J]. Acta Agronomica Sinica, 2025, 51(4): 1061-1076.
[15] LIN Wei-Jin, GUO Ze-Jia, LIU Hao, LI Hai-Fen, WANG Run-Feng, HUANG Lu, YU Qian-Xia, CHEN Xiao-Ping, HONG Yan-Bin, LI Shao-Xiong, LU Qing. QTL mapping and candidate gene analysis of peanut pod yield-related traits [J]. Acta Agronomica Sinica, 2025, 51(4): 969-981.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd