全基因组关联分析(GWAS)鉴定水稻氮素利用效率候选基因
收稿日期: 2023-10-26
修回日期: 2023-12-08
网络出版日期: 2024-09-10
基金资助
国家重点研发计划资助项目(2022YFE0139400);国家自然科学基金青年科学基金资助项目(32101718);深圳市科技计划资助项目(GJHZ20190821163601707);埃及科学、技术和创新基金管理局项目[the Science, Technology, and Innovation Funding Authority (STDF), Egypt under the grant: Chinese-Egyptian Research Fund(CERF,5th call)Project ID at the Egyptian side: 46512]
Identification of Candidate Genes for Rice Nitrogen Use Efficiency by Genome-wide Association Analysis
Received date: 2023-10-26
Revised date: 2023-12-08
Online published: 2024-09-10
【目的】挖掘水稻氮高效的种质和基因资源，揭示其分子机制和遗传效应，是当前水稻氮素利用效率（NUE）研究的重要内容和目标。【方法】为了鉴定与水稻NUE相关的变异位点和候选基因，我们收集了190份亚洲稻为关联群体，通过质量过滤和群体频率过滤筛选出3,934,195个高质量的单核苷酸多态性（SNPs）位点，在大田条件下设置低氮（N1，90 kg/hm2）和常规氮（N2，180 kg/hm2）水平，成熟期调查水稻剑叶叶宽在低氮和常规氮处理下的表型数据，结合FarmCPU和MLM模型进行全基因组关联分析（GWAS）。【结果】通过植株在不同氮水平下的叶宽表型数据，计算该群体在低氮和常规氮水平下的剑叶宽表型比值Q（N1／N2），Q值呈现正态分布的特征。对Q值进行全基因组关联分析，在12条染色体上共鉴定了100个显著位点，确定了39个候选QTLs，包括已克隆NUE相关基因OsNR1.2和OsNAC42。进一步鉴定了候选基因OsNR1.2和OsNAC42的优异单倍型和潜在的优势单倍型组合，为水稻NUE的改良提供了有价值的资源和信息。【结论】利用GWAS和单倍型分析，揭示了水稻剑叶叶宽在不同氮处理下的遗传基础，鉴定了与NUE相关的候选QTLs和基因，包括OsNR1.2和OsNAC42。通过组合单倍型分析，鉴定了两个基因的优势单倍型组合，为水稻NUE的改良提供了有价值的资源和信息。
吕阳, 刘聪聪, 杨龙波, 曹兴岚, 王月影, 童毅, Mohamed Hazman, 钱前, 商连光, 郭龙彪 . 全基因组关联分析(GWAS)鉴定水稻氮素利用效率候选基因[J]. 中国水稻科学, 2024 , 38(5) : 516 -524 . DOI: 10.16819/j.1001-7216.2024.231010
【Objective】 The exploration of germplasm and gene resources in rice for high nitrogen efficiency, along with the elucidation of their molecular mechanisms and genetic effects, represents a significant focus and goal within current research efforts on rice nitrogen use efficiency (NUE).【Method】 To identify the variant loci and candidate genes associated with rice NUE, we collected 190 Asian rice accessions as an association population. After thorough filtering and screening, we obtained 3,934,195 high-quality single nucleotide polymorphisms (SNPs). Under field conditions, two nitrogen treatment levels were established: low nitrogen (N1, 90 kg/hm²) and normal nitrogen (N2, 180 kg/hm²). We investigated the phenotypic data of rice leaf width in response to both low and normal nitrogen treatments at the maturity stage. Genome-wide association analysis (GWAS) was conducted by integrating the FarmCPU and MLM models. 【Result】By calculating the phenotypic ratio Q (N1/N2) of leaf width under low and normal nitrogen levels, we found that the Q value exhibited a normal distribution. A total of 100 significant loci were identified on 12 chromosomes through GWAS for the Q value, leading to the determination of 39 candidate QTLs. This included the cloned NUE-related genes OsNR1.2 and OsNAC42. Additionally, we identified superior haplotypes and potential advantageous haplotype combinations of the candidate genes OsNR1.2 and OsNAC42, which provide valuable resources and information for enhancing rice NUE. 【Conclusion】This study elucidated the genetic basis of rice leaf width under varying nitrogen treatments using GWAS and haplotype analysis. We identified candidate QTLs and genes associated with NUE, including OsNR1.2 and OsNAC42. Through haplotype analysis, we recognized advantageous haplotype combinations of these two genes, offering valuable resources and insights for the improvement of rice NUE.
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