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作物学报 ›› 2022, Vol. 48 ›› Issue (6): 1333-1345.doi: 10.3724/SP.J.1006.2022.14102

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于783份大豆种质资源的叶柄夹角全基因组关联分析

陈玲玲1,2(), 李战1, 刘亭萱1, 谷勇哲2, 宋健1,*(), 王俊1,*(), 邱丽娟1,2,*()   

  1. 1长江大学, 湖北荆州 434025
    2农作物基因资源与遗传改良国家重大科学工程 / 农业农村部种质资源利用重点实验室 / 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2021-06-10 接受日期:2021-10-19 出版日期:2022-06-12 网络出版日期:2021-11-15
  • 通讯作者: 宋健,王俊,邱丽娟
  • 作者简介:E-mail: 905540072@qq.com
  • 基金资助:
    大豆种质资源保存(19211205);荆州市科技计划项目(2020CB21-28)

Genome wide association analysis of petiole angle based on 783 soybean resources (Glycine max L.)

CHEN Ling-Ling1,2(), LI Zhan1, LIU Ting-Xuan1, GU Yong-Zhe2, SONG Jian1,*(), WANG Jun1,*(), QIU Li-Juan1,2,*()   

  1. 1Yangtze University, Jingzhou 434025, Hubei, China
    2National Key Facility for Gene Resources and Genetic Improvement / Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-06-10 Accepted:2021-10-19 Published:2022-06-12 Published online:2021-11-15
  • Contact: SONG Jian,WANG Jun,QIU Li-Juan
  • Supported by:
    Preservation of Soybean Germplasm Resources(19211205);Jingzhou Science and Technology Plan Project(2020CB21-28)

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摘要：

叶柄夹角是影响植株高效受光态势的重要因素, 通过调节叶柄夹角实现大豆株型改良, 对大豆产量提高非常重要。大豆叶柄夹角为数量性状, 目前大多数研究处于QTL定位阶段, 已报道的控制叶柄夹角GmILPA1基因也是从突变体中克隆得到, 因此亟须发掘更多调控基因及优异等位变异, 以促进大豆叶柄夹角调控机制的解析及育种利用。本研究于2019年和2020年分别在海南、北京种植783份和690份大豆种质资源并调查叶柄夹角表型, 通过分布于大豆全基因组的单核苷酸多态性(SNP)标记对叶柄夹角进行关联分析。结果表明, 不同节位叶柄夹角呈现正态分布, 属于典型的数量遗传特征。全基因组关联分析共统计到325个与叶柄夹角显著相关的SNP位点, 在顶部节位关联到51个SNP位点, 中部节位关联到230个SNP位点, 底部节位关联到10个SNPs位点, 3个节位的平均值关联到34个SNP位点。显著位点LD block进一步分析得到3个候选基因, 第1个是生长素类调节蛋白相关的基因Glyma.05G059700, 在茎尖分生组织中特异性表达, 第2个是生长素反应因子(AFR)类蛋白相关基因Glyma.06G076900, 在叶片和茎尖分生组织中高表达; 第3个是COP9信号体复合物相关的基因Glyma.06G076000, 在叶片、茎尖分生组织以及茎中均高表达。

关键词: 大豆, 叶柄夹角, 全基因组关联分析

Abstract:

Petiole angle is one of the important factors that affects the high-efficiency light posture of plants. It is very important to improve soybean plant architecture by adjusting the leaf angle petioles. Soybean petiole angle is a quantitative trait, which is limited to QTLs mapping for most studies up to date. The reported gene GmILPA1controlling leaf petiole angle gene was cloned from mutants. Identification of more regulatory genes and elite alleles is urgent both for the clarification of genetic mechanism for petiole angle and its breeding utilization. In this study, 783 and 690 soybean germplasms were phenotypic for petiole angle in Hainan and Beijing in 2019 and 2020, respectively, and genome-wide associated study (GWAS) were performed using genome-wide distributed SNPs. Results showed that the petiole angle at different nodes (top, middle, and bottom nodes) were in normal distribution, suggesting that the trait of typical quantitative was inheritance. A total of 325 SNPs associated with petiole angle were identified by two-point GWAS analysis in two years, including 51, 230, 10, and 34 SNPs for petiole angles of the top, middle, bottom, and mean value of different nodes, respectively. Three candidate genes (Glyma.05G059700: auxin regulatory protein, Glyma.06G076900: AFR, and Glyma.06G076000: COP9) were obtained by LD block analysis. Transcriptional analysis revealed that all these three candidate genes had high expression level in shoot apical meristem (SAM), however, high expression level were also identified in leaf for Glyma.06G076900, leaf and stem for Glyma.06G076000.

Key words: soybean, leaf petiole angle, GWAS

图1

783份大豆材料地理分布"

表1

690份材料2年2点叶柄夹角基本数据分析"

地点
Location		 节位
Node		 极大值
Max (°)		 极小值
Min (°)		 均值
Average (°)		 标准差
Standard deviation (°)		 变异系数
Coefficient of variation(%)
2019年海南
2019 Hainan		 顶部Top 110.6 17.0 41.0 12.0 29.3
中部Middle 109.9 14.6 39.8 10.7 26.9
底部Bottom 99.8 21.7 57.6 13.0 22.6
平均值Average 104.2 24.4 46.1 9.9 21.5
2020年北京
2020 Beijing		 顶部Top 111.9 22.0 48.4 14.1 29.1
中部Middle 119.5 22.0 49.5 10.3 20.8
底部Bottom 108.9 27.2 55.9 11.2 20.0
平均值Average 99.1 27.5 51.3 8.4 16.4

图2

自然群体叶柄夹角表型分布 A、C、E为2019海南顶部、中部和底部节位叶柄夹角分布频率直方图, 每个样本3个重复; B、D、F为2020北京顶部、中部和底部节位叶柄夹角频率分布直方图, 每个样本3个重复。"

表2

2年2点不同节位叶柄夹角相关性分析"

地点
Location		 节位
Node		 北京Beijing 海南Hainan
顶部Top 中部Middle 底部Bottom 顶部Top 中部Middle 底部Bottom
北京
Beijing		 顶部Top 1
中部Middle 0.203** 1
底部Bottom 0.142** 0.419** 1
海南
Hainan		 顶部Top 0.088* -0.068 -0.119* 1
中部Middle 0.042 -0.014 -0.048 0.601** 1
底部Bottom 0.004 -0.082* -0.068 0.426** 0.584** 1

图3

2年2点表型差异性分析 A: 2年2点相同节位表型差异性显著性分析; B: 不同差异等级材料比例分析; C: 2年表型差异在0°~20°材料地理分布; D: 2年表型差异在21°~40°材料地理分布; E: 2年表型差异大于40°材料地理分布。"

图4

2年2点各个节位叶柄夹角GWAS定位 A~D: 海南顶部、中部、底部节位叶柄夹角和3个节位叶柄夹角平均值关联分析Q-Q plot图和Manhattan图; E~H: 北京顶部、中部、底部节位叶柄夹角和3个节位叶柄夹角平均值关联分析Q-Q plot图和Manhattan图。"

表3

各个节位叶柄夹角均关联显著SNP"

地点
Location		 节位
Node		 染色体
Chr.		 SNP数目
SNP number		 区间位置
Position interval		 极显著SNP位置
Peak SNP position		 等位基因型
Alleles		 -log10 P值极大值
(-log10 Pmax)		 已报道区间
Reported interval
海南Hainan
顶部Top 6 34 20081726-29191958 24044918 A/G 9.08 —
顶部Top 18 2 33523827-33523832 33523832 G/T 6.91 —
中部Middle 4 4 5596149-15210458 15210440 C/A 7.42 —
中部Middle 9 3 17234567-17234585 17234573 T/A 6.23 —
底部Bottom 1 5 3190286-3193332 3190286 A/T 7.21 —
平均值Average 5 3 5476726-5488204 5476976 A/C 11.37 —
北京Beijing
顶部Top 3 2 10230350-10230362 10230350 A/T 7.72 —
顶部Top 3 6 17497236-17497310 17497236 C/T 8.41 —
顶部Top 7 2 21264942-26216740 21264942 G/A 8.08 —
顶部Top 11 3 17811042-17811056 17811042 C/T 7.45 [9]
顶部Top 17 2 37154449-39977197 37154449 C/A 12.11 [9]
中部Middle 6 131 5787577-5947566 5889343 A/G 8.33 —
中部Middle 6 5 20003640-20973899 20071106 A/G 11.92 —
中部Middle 13 49 37043663-37156881 37117542 A/G 8.71 —
中部Middle 14 5 15953346-19558649 15953346 A/G 9.23 [9]
中部Middle 14 6 24281424-25306741 24281424 A/G 9.35 [9]
中部Middle 14 3 27024699-27783925 27076700 C/T 9.35 [9]
中部Middle 14 5 29151458-30357161 29151458 A/G 9.96 [9]
中部Middle 14 19 32044124-41988610 32044124 A/G 9.35 [9]
中部Middle 19 2 37695290-37695805 37695805 G/T 7.13 —
中部Middle 19 3 46080617-46082050 46080617 C/G 10.25 —
底部Bottom 3 3 1997994-1998818 1997994 C/G 7.35 —
底部Bottom 19 2 41151600-41169499 41169499 C/T 7.27 —
平均值Average 6 31 5859032-5958396 5948057 A/G 8.06 —

图5

显著位点分析 A: 极显著SNP位点Gm05_5476976等位基因差异显著性分析, 其中AA和CC表示该位点出现AA和CC纯合的频率, AC表示该位点出现AC杂合的频率; B: 极显著SNP位点Gm05_5476976 LD block分析, 其中红色阈值线上的红点表示在Gm05_5476976 LD block区域内与叶柄夹角性状紧密连锁的位点; C: 极显著SNP位点Gm06_5948057等位基因差异显著性分析, 其中AA和GG表示该位点出现AA和GG的频率, GA表示该位点出现GA杂合的频率; D: 极显著SNP位点Gm06_24044918 LD block分析, 其中红色阈值线上的红点表示在Gm06_24044918 LD block区域内与叶柄夹角性状紧密连锁的位点。"

图6

候选基因表达谱 A: Gm05_5476976 LD block区间内候选基因表达谱; B: Gm06_24044918 LD block区间内候选基因表达谱。"

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