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作物学报

作物学报 ›› 2024, Vol. 50 ›› Issue (3): 623-632.doi: 10.3724/SP.J.1006.2024.34091

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

大豆叶型性状全基因组关联分析与候选基因鉴定

王琼1(), 朱宇翔1,2, 周密密1, 张威1, 张红梅1, 陈新1, 陈华涛1,*(), 崔晓艳1,*()   

  1. 1江苏省农业科学院经济作物研究所 / 江苏省高效园艺作物遗传改良重点实验室, 江苏南京 210014
    2扬州大学园艺园林学院, 江苏扬州 225009
  • 收稿日期:2023-05-25 接受日期:2023-09-13 出版日期:2024-03-12 网络出版日期:2023-10-07
  • 通讯作者: *陈华涛, E-mail: cht@jaas.ac.cn; 崔晓艳, E-mail: cxy@jaas.ac.cn
  • 作者简介:E-mail: wqwzw@163.com
  • 基金资助:
    江苏省基础研究计划(自然科学基金)项目(BK20220740);江苏省种业振兴揭榜挂帅项目(JBGS[2021]057);江苏省重点研发计划项目(BE2022328);江苏省重点研发计划项目(CX(22)5002)

Genome-wide association analysis and candidate genes predication of leaf characteristics traits in soybean (Glycine max L.)

WANG Qiong1(), ZHU Yu-Xiang1,2, ZHOU Mi-Mi1, ZHANG Wei1, ZHANG Hong-Mei1, CEHN Xin1, CEHN Hua-Tao1,*(), CUI Xiao-Yan1,*()   

  1. 1Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, Jiangsu, China
    2College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2023-05-25 Accepted:2023-09-13 Published:2024-03-12 Published online:2023-10-07
  • Contact: *E-mail: cht@jaas.ac.cn; E-mail: cxy@jaas.ac.cn
  • Supported by:
    Natural Science Foundation of Jiangsu Province(BK20220740);Jiangsu Seed Industry Revitalizing Project(JBGS[2021]057);Key Research and Development Program of Jiangsu Province(BE2022328);Jiangsu Agricultural Science and Technology Innovation Fund(CX(22)5002)

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摘要：

大豆叶片的形状和垂直分布影响群体冠层结构和光合效率并最终影响大豆的产量。植物叶片大小、形态因着生位置不同而产生差异的现象称为异形叶, 虽然异形叶现象在被子植物中广泛存在, 但目前关于大豆叶片发育过程中异形叶的调控的研究还很有限。本研究通过对283份大豆种质资源的叶长、叶宽、叶形指数和异形叶指数等叶型相关的性状在江苏南京进行连续2年的考察, 利用全基因组关联分析检测到181个叶型性状相关位点, 其中能够在2个环境或多个性状中重复检测到的位点18个。利用检测到的与叶型相关的SNP位点, 结合基因的表达谱数据、拟南芥中同源基因的功能, 鉴定与大豆叶片发育和异形叶形成相关的候选基因。其中在20号染色体的相关位点Chr20: 36152820上游发现已知的大豆叶形调控基因Ln (Glyma.20G116200)。此外, 在19号染色体的相关位点Chr19:45155943附近鉴定到2个候选基因Glyma.19G192700、Glyma.19G194100, 分别被注释为Growth-regulating factor 4 (GRF4)和LITTLE ZIPPER 3 (ZPR3)基因的同源基因, 为阐明大豆异形叶等叶型性状遗传的分子机制奠定了基础。

关键词: 大豆, 叶型, 异形叶, 全基因组关联分析, SNP标记

Abstract:

Leaf shape and vertical distribution of soybean affect canopy structure, photosynthetic efficiency, and yield. The existence of different leaf shapes and sizes on the same plant, which is known as heterophylly, has been observed in many flowering plant species. Yet, the genetic characteristics and genetic basis of heterophylly in soybean remain unknown. In this study, leaf characteristics such as leaf length, leaf width, leaf shape index, and heterophylly index were investigated in 283 soybean germplasm resources for two consecutive years in Nanjing, Jiangsu Province. A total of 181 related loci were detected by genome-wide association study (GWAS), among which 18 loci could be repeatedly detected in two environments or among multiple traits. Using the loci associated with leaf characteristics, we integrated the GWAS approach with the expression profiling data and gene-based association and functional annotation of orthologs in Arabidopsis to identify candidate genes involved in leaf development in soybean. The known soybean leaf shape regulatory gene Ln (Glyma.20G116200) was found upstream of locus Chr20:36152820. In addition, two candidate genes (Glyma.19G192700 and Glyma.19G194100) were identified near the related locus Chr19:45155943 on chromosome 19, homologous genes of growth-regulating factor 4 (GRF4), and LITTLE ZIPPER 3 (ZPR3), respectively. These results lay a solid foundation for expanding our understanding of the genetic mechanism of heterophylly in soybean.

Key words: soybean, leaf characteristics, heterophylly, GWAS, SNP markers

图1

试验设计示意图"

表1

大豆群体叶型相关性状的统计分析"

环境
Environment		 性状
Trait		 最小值
Min.		 最大值
Max.		 平均值±标准差
Mean±SD		 变异系数
CV (%)
2021南京
2021 Nanjing		 上部叶长 Upper leaf length 7.00 18.00 11.25±1.94 0.17
上部叶宽 Upper leaf width 2.50 9.70 5.66±1.41 0.25
上部叶形 Upper leaf shape 1.36 3.24 2.05±0.42 0.20
下部叶长 Lower leaf length 4.00 12.10 7.44±1.42 0.19
下部叶宽 Lower leaf width 2.80 8.03 4.94±1.00 0.20
下部叶形 Lower leaf shape 1.12 2.14 1.50±0.22 0.15
异形叶指数 Heterophylly leaf index 0.90 2.11 1.36±0.25 0.18
2022南京
2022 Nanjing		 上部叶长 Upper leaf length 6.67 17.23 11.28±1.86 0.16
上部叶宽 Upper leaf width 3.53 11.17 6.13±1.39 0.23
上部叶形 Upper leaf shape 1.38 2.90 1.90±0.32 0.17
下部叶长 Lower leaf length 4.83 15.13 9.24±1.58 0.17
下部叶宽 Lower leaf width 2.90 9.60 5.72±1.29 0.23
下部叶形 Lower leaf shape 1.20 2.91 1.67±0.35 0.21
异形叶指数 Heterophylly leaf index 0.68 1.76 1.16±0.19 0.16

图2

大豆关联群体叶型相关性状的分布"

表2

叶型相关性状的相关系数"

性状
Trait		 相关系数
Correlation coefficient		 P值
P-value
上部叶长 Upper leaf length 0.41 6.10E-09
上部叶宽 Upper leaf width 0.61 1.02E-19
上部叶形 Upper leaf shape 0.64 6.19E-22
下部叶长 Lower leaf length 0.26 4.24E-04
下部叶宽 Lower leaf width 0.36 9.75E-07
下部叶形 Lower leaf shape 0.59 4.49E-18
异形叶指数 Heterophylly leaf index 0.53 1.73E-13

图3

大豆关联群体叶型性状间的相关系数 *、**、***分别表示在0.05、0.01、0.001概率水平显著相关。"

表3

叶型相关性状的关联信号"

信号
Signal		 标记
Marker		 染色体
Chr.		 位置
Position		 P值
P-value		 性状
Trait
5_10.7 Chr05:10705738 5 10705738 7.47E-07 2021下部叶长 Lower leaf length in 2021
5_10.7 Chr05:10705738 5 10705738 1.93E-06 2021下部叶宽 Lower leaf width in 2021
10_50.7 Chr10:50760191 10 50760191 2.01E-06 2021上部叶形 Upper leaf shape in 2021
10_50.7 Chr10:50760191 10 50760191 1.10E-06 2021异形叶指数 Heterophylly index in 2021
13_39.7 Chr13:39721130 13 39721130 1.53E-06 2022上部叶宽 Upper leaf width in 2022
13_39.7 Chr13:39772387 13 39772387 8.95E-06 2021上部叶形 Upper leaf shape in 2021
16_32.2 Chr16:32235624 16 32235624 3.05E-06 2021上部叶长 Upper leaf length in 2021
16_32.2 Chr16:32236735 16 32236735 1.41E-06 2021下部叶长 Lower leaf length in 2021
17_40.9 Chr17:40908625 17 40908625 9.14E-06 2022 上部叶长 Upper leaf length in 2022
17_40.9 Chr17:40908625 17 40908625 2.91E-06 2022下部叶长 Lower leaf length in 2022
19_23.9 Chr19:23901295 19 23901295 2.43E-06 2021上部叶宽 Upper leaf width in 2021
19_23.9 Chr19:23901508 19 23901508 6.92E-06 2022上部叶宽 Upper leaf width in 2022
19_45.1 Chr19:45151266 19 45151266 6.05E-06 2022上部叶形 Upper leaf shape in 2022
19_45.1 Chr19:45155931 19 45155931 9.51E-06 2022上部叶宽 Upper leaf width in 2022
19_45.1 Chr19:45155943 19 45155943 2.45E-07 2021上部叶形 Upper leaf shape in 2021
19_45.1 Chr19:45155943 19 45155943 2.84E-08 2021异形叶指数 Heterophylly index in 2021
20_19.2 Chr20:19295767 20 19295767 8.08E-06 2022上部叶形 Upper leaf shape in 2022
20_19.2 Chr20:19295767 20 19295767 3.39E-06 2022下部叶形 Lower leaf shape in 2022

附图1

叶型相关性状关联分析曼哈顿图"

图4

候选基因Glyma.19G192700在大豆各组织中的表达模式"

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