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玉米叶夹角性状的全基因组关联分析与关键位点优异等位变异挖掘

秦文萱1,**,鲍建喜1,**,王彦博1,马雅杰1,龙艳1,李金萍2,董振营1,2,*,万向元1,2,*   

  1. 1 北京科技大学生物与农业研究中心 / 化学与生物工程学院 / 顺德研究生院 / 北京中智生物农业国际研究院, 北京 100083; 2 北京首佳利华科技有限公司 / 主要作物生物育种北京市工程实验室 / 生物育种北京市国际科技合作基地, 北京 100192
  • 收稿日期:2022-02-27 修回日期:2022-05-05 接受日期:2022-05-05 网络出版日期:2022-05-24
  • 基金资助:
    本研究由国家重点研发计划项目“农业生物种质资源挖掘与创新利用”重点专项(2021YFD1200700)资助。

Genome-wide association study of leaf angle traits and mining of elite alleles from the major loci in maize

QIN Wen-Xuan1,**,BAO Jian-Xi1,**,WANG Yan-Bo1,MA Ya-Jie1,LONG Yan1,LI Jin-Ping2,DONG Zhen-Ying1,2,*,WAN Xiang-Yuan1,2,*   

  1. 1 Zhongzhi International Institute of Agricultural Biosciences, Shunde Graduate School, School of Chemistry and Biological Engineering, Research Center of Biology and Agriculture, University of Science and Technology Beijing (USTB), Beijing 100083, China; 2 Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
  • Received:2022-02-27 Revised:2022-05-05 Accepted:2022-05-05 Published online:2022-05-24
  • Supported by:
    This study was supported by the National Key Research and Development Program of China (2021YFD1200700).

摘要:

玉米叶夹角是冠层结构的重要组成之一,可直接影响光和CO2在冠层的分布及群体的光能利用效率,从而影响玉米产量。为解析玉米叶夹角的遗传基础,挖掘与玉米叶夹角性状相关的SNP位点和候选基因,本研究利用854份玉米自交系作为关联群体,在5个环境下对玉米穗位上1叶(ULA1)、上2叶(ULA2)和上3叶(ULA3)的叶夹角性状进行测定和统计分析,并分别利用均匀分布于玉米基因组10条染色体的2795个单核苷酸多态性(single nucleotide polymorphism, SNP)标记进行全基因组关联分析(genome-wide association study, GWAS)。基于FarmCPU算法,共检测到81个与叶夹角性状显著关联的SNP,其中与ULA1性状显著关联的SNP为26个,解释的表型变异率在0.03%~9.68%;与ULA2性状显著关联的SNP为27个,解释的表型变异率在0.06%~9.30%;与ULA3性状显著关联的SNP为28个,解释的表型变异率在0.01%~8.23%。进一步鉴定出17个可被重复检测到的高可信显著关联SNP,其中3个SNP关联区间为本研究首次报道,14个SNP标记位于前人已定位QTL置信区间或/和已知叶夹角显著SNP标记1 Mb之内,9个SNP标记可与不同节位叶夹角性状同时显著关联。鉴定出7个PVE > 5%的主效SNP,通过等位变异效应分析进一步挖掘出9份聚合7个主效位点优异等位变异、叶夹角性状显著降低的优异种质资源。在17个高可信显著SNP候选区间共鉴定出131个候选基因,其中1号染色体PZE-101039301 标记下游70 kb存在调控叶夹角的已知基因DRL1,其他候选基因均尚未验证其调控玉米叶夹角的功能。本研究采用GWAS策略所挖掘玉米叶夹角遗传位点和候选基因有助于揭示叶夹角的遗传机制,并为今后克隆玉米叶夹角调控基因提供理论指导,所鉴定优异等位变异和种质资源有助于利用分子标记辅助选择改良叶夹角性状和提高玉米产量。

关键词: 玉米, 叶夹角, 全基因组关联分析, 候选基因, 优异等位变异

Abstract: Leaf angle (LA) is one of the important components of the canopy structure in maize, which can directly affect the distribution of light and CO2 in the canopy and the light capture efficiency of the population, thus affecting the yield of maize. In order to analysis the genetic basis of maize LA traits, an association panel including 854 maize inbred lines was used to analyze the first (ULA1), second (ULA2), and third (ULA3) upper leaf angle of ears in five environments, and then 2795 single nucleotide polymorphic (SNP) markers distributed on 10 chromosomes of maize genome were used for genome-wide association analysis (GWAS) of LA traits based on FarmCPU (fixed and random model circulating probability unification) model. 81 significant SNP associations were identified, among which 26, 27, and 28 significant SNPs associated with ULA1, ULA2, and ULA3, and phenotypic variation explained (PVE) for each SNP was 0.03%9.68%, 0.06%9.30%, and 0.01%8.23%, respectively. We further identified 17 heigh-confidence SNPs repeatedly detected for specific trait, among which three loci were firstly reported in this study, 14 loci located within the intervals that had been previously mapped, and nine SNPs were associated with more than one LA trait. Seven SNPs with PVE > 5% were classified as major SNPs, and thus nine germplasms combining the seven elite alleles with small LAs were isolated. Through searching the candidate regions of the 17 high-confidence SNPs, a total of 131 candidate genes were predicated, and a key gene DRL1 known to regulate LA of maize that located 70 kb downstream of PZE-101039301 on chromosome 1 was also identified as one of candidate genes. In summary, the genetic loci and candidate genes identified by this study will be useful for revealing the genetic mechanism of maize LA traits, and provide clues for cloning LA correlated genes. The identified elite alleles and germplasm resources can be used to increase maize yield by molecular marker-assisted selection of LA traits.

Key words: maize, leaf angle, genome-wide association study, candidate gene, elite allele

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