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小麦苗期耐低磷相关基因位点的挖掘与候选基因分析

曹志洋1,**，高丽锋2,**，姜东言1，王曙光1，杨进文1，贾继增2，李宁1,*，孙黛珍1,*   

  1. 1 山西农业大学农学院, 山西太谷 030801; 2 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2025-03-27 修回日期:2025-07-09 接受日期:2025-07-09 网络出版日期:2025-07-22
  • 通讯作者: 孙黛珍, E-mail: sdz64@126.com; 李宁, E-mail: 13159862006@163.com
  • 基金资助:
    本研究由国家重点研发计划项目(2022YFD1200201, 2024YFD1201100)和山西农业大学农学院育种工程专项计划项目(YZ2021-0)资助。

Identification of genetic loci related to low phosphorus tolerance at the seedling stage in wheat and analysis of candidate genes

CAO Zhi-Yang1,**,GAO Li-Feng2,**,JIANG Dong-Yan1,WANG Shu-Guang1,YANG Jin-Wen1,JIA Ji-Zeng2,LI Ning1,*,SUN Dai-Zhen1,*   

  1. 1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2025-03-27 Revised:2025-07-09 Accepted:2025-07-09 Published online:2025-07-22
  • Supported by:
    This study was supported by the National Key R&D Program of China (2022YFD1200201, 2024YFD1201100) and the Breeding Engineering Program of College of Agriculture, Shanxi Agricultural University (YZ2021-0).

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摘要：

磷是作物生长发育所必需的大量元素之一，土壤中只有少部分磷可被植物有效利用，而长期施用磷肥又可能造成环境污染。因此筛选强耐低磷品种、挖掘耐低磷相关QTL与候选基因具有重要意义。本研究采用389份小麦品种组成的自然群体，在正常磷(对照)和低磷条件下进行3年(2022—2024)的苗期水培试验，测定苗高、主根长、根条数、茎叶干重、根干重、总根长、根面积、根直径和根尖数9个性状，并计算每个性状的耐低磷系数和BLUP值，然后根据耐低磷系数计算综合评价D值。基于3个环境下的BLUP值进行相关性分析，发现低磷和对照条件下，除根直径外，大多数性状之间呈显著正相关。利用综合评价D值进行聚类分析显示，“丰德存麦1号”在4个环境(2022、2023、2024、BLUP)下均被鉴定为强耐低磷型品种。结合660K SNP芯片，对4个环境下9个性状的耐低磷系数和D值进行全基因组关联分析，共检测到1197个显著关联的SNP标记，形成了464个QTL。其中在2个环境下重复检测到20个QTL，在3个和4个环境下重复检测到7个QTL，标记位点解释的贡献率R2范围为4.09%~10.58%。然后，利用前人报道的转录组数据结合基因功能注释，在这7个QTL区间内筛选到3个耐低磷相关候选基因，其中TraesCS4D02G022900和TraesCS4D02G023300编码F-box家族蛋白，拟南芥的同源基因At5g21040编码一种同时含有WD40和F-box结构域的蛋白，是磷饥饿响应的负调控因子；TraesCS6D02G154700编码的类受体蛋白激酶与植物的生长、发育、抗逆以及抗病有关。进一步分析这3个候选基因低磷胁迫下叶片和根系的表达模式，发现均具有差异表达，与前人的转录组结果一致。这些发现为选育耐低磷小麦品种，解析低磷胁迫相关基因的功能和调控机制提供了基础。

关键词: 小麦, 低磷胁迫, 全基因组关联分析, SNP, 候选基因

Abstract:

Phosphorus (P) is an essential macronutrient for crop growth and development. However, only a small fraction of the phosphorus present in soil is effectively utilized by plants, and long-term application of P fertilizers can lead to environmental pollution. Therefore, it is of great significance to screen for varieties with strong tolerance to low-P conditions and to identify associated QTLs and candidate genes. In this study, a natural population consisting of 389 wheat varieties was used as experimental material. A three-year hydroponic experiment (2022, 2023, and 2024) was conducted under both normal-P (control) and low-P conditions at the wheat seedling stage. Nine traits were measured, including seedling height, main root length, root number, shoot dry weight, root dry weight, total root length, root surface area, root diameter, and number of root tips. For each trait, the low-P tolerance coefficient and BLUP values were calculated, and comprehensive evaluation D-values were derived based on these coefficients. Correlation analysis of BLUP values across the three environments revealed significant positive correlations among most traits, except for root diameter, under both low-P and control conditions. Cluster analysis of the comprehensive D-values identified ‘Fengdecunmai 1’ as a strongly low-P-tolerant variety across all four environments (2022, 2023, 2024, and BLUP). A genome-wide association study (GWAS) was carried out using low-P tolerance coefficients and D-values for the nine traits across the four environments, based on the 660K SNP chip. A total of 1,197 significant SNP markers were detected, forming 464 QTLs. Among these, 20 QTLs were repeatedly detected in two environments, and 7 QTLs were detected in three or four environments, with the phenotypic variance explained (R2) ranging from 4.09% to 10.58%. Based on previously published transcriptomic data and gene functional annotation, three candidate genes associated with low-P tolerance were identified within the regions of the seven QTLs. TraesCS4D02G022900 and TraesCS4D02G023300 encode F-box family proteins. Their Arabidopsis ortholog, At5g21040, encodes a protein containing both WD40 and F-box domains and functions as a negative regulator of the P starvation response. TraesCS6D02G154700 encodes a receptor-like protein kinase involved in plant growth, development, and responses to stress and disease. Further analysis of the expression patterns of these three candidate genes in both leaves and roots under low-P stress revealed differential expression consistent with previous transcriptomic results. These findings provide a solid foundation for the development of low-P-tolerant wheat cultivars and for elucidating the functions and regulatory mechanisms of genes associated with low-P stress.

Key words: wheat, low phosphorus stress, GWAS, SNP, candidate genes

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