欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2024, Vol. 50 ›› Issue (3): 556-575.doi: 10.3724/SP.J.1006.2024.34094

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

大豆巢式关联作图(NAM)群体构建及花色和种皮色遗传分析

宋健1,6(), 熊亚俊1,6, 陈伊洁1,6, 徐瑞新2, 刘康林1, 郭庆元1, 洪慧龙2, 高华伟2, 谷勇哲2, 张丽娟2, 郭勇2, 阎哲2, 刘章雄2, 关荣霞2, 李英慧2, 王晓波3, 郭兵福4, 孙如建5, 闫龙7, 王好让8, 姬月梅9, 常汝镇2, 王俊1,6,*(), 邱丽娟2,*()   

  1. 1长江大学, 湖北荆州 434025
    2中国农业科学院作物科学研究所 / 农作物基因资源与遗传改良国家重大科学工程 / 农业农村部北京大豆生物学重点实验室, 北京 100081
    3安徽农业大学农学院, 安徽合肥 230036
    4江西省农业科学院作物研究所, 江西南昌 330200
    5呼伦贝尔市农业科学研究所, 内蒙古呼伦贝尔 162650
    6农业农村部长江中游作物绿色高效生产重点实验室(部省共建) / 长江大学农学院, 湖北荆州 434025
    7河北省农林科学院粮油作物研究所, 河北石家庄 050035
    8江苏徐怀地区徐州农业科学研究所, 江苏徐州 210031
    9宁夏农林科学院作物研究所, 宁夏银川 750021
  • 收稿日期:2023-06-07 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: *邱丽娟, E-mail: qiulijuan@caas.cn; 王俊, E-mail: wangjagri@yangtzeu.edu.cn
  • 作者简介:宋健, E-mail: songjian@yangtzeu.edu.cn

    **同等贡献

  • 基金资助:
    中国农业科学院农业科技创新计划项目(ASTIP);云南省重点科技项目(202202AE090014)

Genetic analysis of seed coat and flower color based on a soybean nested association mapping population

SONG Jian1,6(), XIONG Ya-Jun1,6, CHEN Yi-Jie1,6, XU Rui-Xin2, LIU Kang-Lin1, GUO Qing-Yuan1, HONG Hui-Long2, GAO Hua-Wei2, GU Yong-Zhe2, ZHANG Li-Juan2, GUO Yong2, YAN Zhe2, LIU Zhang-Xiong2, GUAN Rong-Xia2, LI Ying-Hui2, WANG Xiao-Bo3, GUO Bing-Fu4, SUN Ru-Jian5, YAN Long7, WANG Hao-Rang8, JI Yue-Mei9, CHANG Ru-Zhen2, WANG Jun1,6,*(), QIU Li-Juan2,*()   

  1. 1Yangtze University, Jingzhou 434025, Hubei, China
    2National Key Facility for Gene Resources and Genetic Improvement / Beijing Key Laboratory of Soybean Biology, Ministry of Agriculture and Rural Affairs / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3College of Agriculture, Anhui Agricultural University, Hefei 230036, Anhui, China
    4Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
    5Hulun Buir Institution of Agricultural Sciences, Hulun Buir 162650, Nei Mongol, China
    6MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province) / College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    7Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, Hebei, China
    8Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou 210031, Jiangsu, China
    9Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 750021, Ningxia, China
  • Received:2023-06-07 Accepted:2023-09-13 Published:2024-03-12 Published online:2023-10-07
  • Contact: *E-mail: qiulijuan@caas.cn; E-mail: wangjagri@yangtzeu.edu.cn
  • About author:

    **Contributed equally to this work

  • Supported by:
    Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(ASTIP);Key Science and Technology Project of Yunnan(202202AE090014)

RichHTML

65

PDF

437

摘要：

巢式关联作图(Nested Association Mapping, NAM)群体在作物学遗传与育种研究中具有广泛的应用。本研究在前期大豆种质资源评价基础上, 利用35份不同地区来源的代表性种质与中豆41 (公共母本)杂交, 构建了一套大豆NAM群体。PCA和聚类分析发现, 不同亲本组合的RIL群体基本聚在一起, 显示出清晰的遗传结构。利用该NAM群体亲本间花色和种皮色具有显著差异的RIL群体进行全基因组关联分析, 定位到1个主要位点qFC13-1与花色显著关联, 该位点与W1位点重合; 定位到12个位点与种皮色显著相关, 其中9个位点为3种以上方法共定位, 3个位点为2种方法共定位, 包括4个已知位点和8个新位点。研究结果表明, 构建的NAM群体适于进行大豆相关性状遗传分析, 为大豆复杂性状的遗传解析和育种实践提供了良好的基础材料。

关键词: 大豆, NAM群体, 花色, 种皮色, 遗传分析

Abstract:

Nested Association Mapping (NAM) population is widely applied in genetic study and breeding practice in many crops. A NAM panel was constructed by crossing of 35 parental lines with the common maternal lines (Zhongdou 41) based on previous evaluation of soybean germplasm. Principle component analysis and clustering analysis showed that clear genetic structure was observed between subpanel of RIL populations. Genetic analysis was performed on flower color and seed coat color in NAM subpanel with significant difference between paternal and maternal parents, and we found that qFC13-1 was significantly associated with flower color, which coincided with the W1 locus. Twelve loci identified were significantly correlated with seed coat color, among which nine loci were co-located by more than three methods, and the other three loci were co-located by two methods, including four reported loci and eight novel loci. In conclusion, NAM population was suitable for genetic analysis of soybean, which provided material basis for genetic interpretation and breeding practice for complex traits in soybean.

Key words: soybean, NAM population, flower color, seed coat color, genetic analysis

表1

NAM群体亲本信息"

群体编号
Population number		 亲本名称
Parental name		 系统编号
Systematic code		 亲本类型
Parent type		 来源地
Geographic origination		 种质类型
Germ type		 生态类型
Ecological type		 种皮色
SSC		 花色
FC		 百粒重
100-SW (g)		 蛋白
PC (%)		 脂肪
OC (%)		 蛋白脂肪和
POC (%)		 群体大小 鉴定株系
Population size Genotyped Individuals
N001 羊眼豆
Yangyandou		 ZDD17457 父本 云南 地方品种 南方夏 暗绿 白 14.1 43.6 16.1 59.6 524 72
Male parent Yunnan Landrace SSu Dark green White
N002 夏黑豆 ZDD02400 父本 山西 地方品种 黄淮夏 黑 紫 10 43.5 19.2 62.7 171 72
Xiaheidou Male parent Shanxi Landrace HHSu Black Purple
N003 柘城小红豆 Zhechengxiaohongdou ZDD03533 父本 河南 地方品种 黄淮夏 褐 紫 9.8 43.9 17.5 61.4 387 72
Male parent Henan Landrace HHSu Brown Purple
N004 邳县四粒糙 Pixiansilicao ZDD03741 父本 江苏 地方品种 黄淮春 黄 紫 14.2 46 17.8 63.8 333 72
Male parent Jiangsu Landrace HHSp Yellow Purple
N005 东农36号 ZDD06851 父本 黑龙江 选育品种 北方春 黄 紫 18.3 42 20.1 62.2 135 72
Dongnong 36 Male parent Heilongjiang Cultivar NSp Yellow Purple
N006 莆豆451 ZDD14125 父本 福建 选育品种 南方夏 黄 白 16.6 41.9 18.8 60.7 216 72
Pudou 451 Male parent Fujian Cultivar SSu Yellow White
N007 下台子磨石豆 ZDD18524 父本 河北 地方品种 黄淮夏 褐 紫 9.7 44.9 16.5 61.5 206 72
Xiataizimoshidou Male parent Hebei Landrace HHSu Brown Purple
N008 东山69 ZDD18870 父本 福建 选育品种 黄淮夏 黄 紫 13.3 42.1 21.4 63.5 336 72
Dongshan 69 Male parent Fujian Cultivar HHSu Yellow Purple
N009 商951099 ZDD23269 父本 河南 选育品种Cultivar 黄淮夏 黄 紫 15.5 42.1 20.9 63.1 44 44
Shang 951099 Male parent Henan HHSu Yellow Purple
N010 郑92116 ZDD23277 父本 河南 选育品种 黄淮夏 黄 紫 19.2 45.2 18.7 63.9 132 72
Zheng 92116 Male parent Henan Cultivar HHSu Yellow Purple
N011 中豆24 ZDD11581 父本 湖北 选育品种 南方夏 黄 白 14.3 48.2 16.4 64.6 170 72
Zhongdou 24 Male parent Hubei Cultivar SSu Yellow White
N012 吉育202 ZDD30837 父本 吉林 选育品种 北方春 黄 白 17.2 38 21.9 59.9 87 64
Jiyu 202 Male parent Jilin Cultivar NSp Yellow White
N013 牛毛黄 ZDD03603 父本 陕西 地方品种 黄淮夏 黄 紫 15.4 42.6 20.6 63.2 201 72
Niumaohuang Male parent Shaanxi Landrace HHSu Yellow Purple
N014 信阳羊眼豆 ZDD03570 父本 河南 地方品种 黄淮夏 虎斑 白 13.5 43.4 19.4 62.9 97 72
Xinyangyangyandou Male parent Henan Landrace HHSu Bicolor White
N015 淮阴春豆 ZDD03776 父本 江苏 选育品种Cultivar 黄淮春 黄 紫 17 46.6 16.1 62.7 356 72
Huaiyinchundou Male parent Jiangsu HHSp Yellow Purple
N016 皂角豆 ZDD15624 父本 贵州 地方品种 南方夏 褐 白 18.6 42.1 21.2 63.3 198 72
Zaojiaodou Male parent Guizhou Landrace SSu Brown White
N017 科丰1号 ZDD18394 父本 北京 选育品种 黄淮夏 黑 白 9.3 45.3 17.3 62.6 91 72
Kefeng 1 Male parent Beijing Cultivar HHSu Black White
N018 冀豆7 ZDD18632 父本 河北 选育品种 黄淮夏 黄 紫 19.5 43.2 19.3 62.5 91 72
Jidou 7 Male parent Hebei Cultivar HHSu Yellow Purple
N019 高作选1号 ZDD19381 父本 山东 选育品种 黄淮夏 黄 紫 11.7 42.9 20.2 63.1 100 72
Gaozuoxuan 1 Male parent Shandong Cultivar HHSu Yellow Purple
N020 豫豆18 ZDD19409 父本 河南 选育品种 黄淮夏 黄 紫 16.5 38.1 23.5 61.6 257 72
Yudou 18 Male parent Henan Cultivar HHSu Yellow Purple
N021 铁丰31 ZDD23829 父本 辽宁 选育品种 北方春 黄 紫 18 42.8 21 63.8 476 72
Tiefeng 31 Male parent Liaoning Cultivar NSp Yellow Purple
N022 中黄13 ZDD23876 父本 北京 选育品种 黄淮夏 黄 紫 24.1 43.2 20.4 63.6 72 72
Zhonghuang 13 Male parent Beijing Cultivar HHSu Yellow Purple
N023 垦丰16 ZDD24344 父本 黑龙江 选育品种 北方春 黄 白 18 41 20.8 61.9 59 59
Kenfeng 16 Male parent Heilongjiang Cultivar NSp Yellow White
N024 中黄30 ZDD24632 父本 北京 选育品种 黄淮夏 黄 紫 18.1 44.9 19.9 64.8 131 72
Zhonghuang 30 Male parent Beijing Cultivar HHSu Yellow Purple
N025 荷豆18 ZDD24748 父本 山东 选育品种 黄淮夏 黄 紫 19.6 43.6 20.3 63.9 129 72
Hedou 18 Male parent Shandong Cultivar HHSu Yellow Purple
N026 徐豆16 ZDD24783 父本 江苏 选育品种 黄淮夏 黄 紫 21.8 43.4 19.1 62.5 135 72
Xudou 16 Male parent Jiangsu Cultivar HHSu Yellow Purple
N027 皖豆28 ZDD24832 父本 安徽 选育品种 黄淮夏 黄 紫 22.1 46.1 20.9 67 106 72
Wandou 28 Male parent Anhui Cultivar HHSu Yellow Purple
N028 天隆一号 ZDD24847 父本 湖北 选育品种 南方春 黄 白 18.1 44.2 19.2 63.4 483 72
Tianlongyihao Male parent Hubei Cultivar SSp Yellow White
N029 川豆9号 ZDD24861 父本 四川 选育品种 南方夏 黄 白 20 47.6 18.9 66.5 44 44
Chuandou 9 Male parent Sichuan Cultivar SSu Yellow White
N030 湘春豆26 ZDD25213 父本 湖南 选育品种 南方春 黄 白 19 41.7 18.9 60.7 131 72
Xiangchundou 26 Male parent Hunan Cultivar SSp Yellow White
N031 华春2号 ZDD25258 父本 广东 选育品种 南方春 黄 白 18.9 42.5 19.8 62.4 576 72
Huachun 2 Male parent Guangdong Cultivar SSp Yellow White
N032 晋品82号 ZDD23181 父本 山西 选育品种 黄淮夏 黑 紫 17.8 45.6 19 64.5 77 71
Jinpin 82 Male parent Shanxi Cultivar HHSu Black Purple
N033 冀豆12 ZDD23040 父本 河北 选育品种 黄淮夏 黄 紫 24 43.7 20.7 64.4 343 72
Jidou 12 Male parent Hebei Cultivar HHSu Yellow Purple
N034 五星1号 ZDD23915 父本 河北 选育品种 黄淮夏 黄 紫 19.8 30.9 25.2 56 64 64
Wuxing 1 Male parent Hebei Cultivar HHSu Yellow Purple
N035 海门等西风甲 ZDD11320 父本 江苏 地方品种 南方夏 绿 紫 30.2 39.1 21.1 60.2 58 58
Haimendengxifengjia Male parent Jiangsu Landrace SSu Green Purple
NA 中豆41 ZDD31206 母本 湖北 选育品种 南方夏 黄 白 23.2 42.7 18.2 60.9
Zhongdou 41 Female parent Hubei Cultivar SS Yellow White

表2

大豆NAM群体构建进程"

时间
Time		 地点
Location		 世代
Generation
2015年5-11月
May-November 2015		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 杂交, 收获F1
Cross, harvest F1
2016年5-11月
May-November 2016		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 种植F1, 收获F2
Plant F1, harvest F2
2017年5-11月
May-November 2017		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 种植F2, 收获F3
Plant F2, harvest F3
2017年11月-2018年3月
November 2017-March 2018		 海南三亚Sanya, Hainan (18.25°N, 109.51°E) 种植F3, 收获F4
Plant F3, harvest F4
2018年5-11月
May-November 2018		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 种植F4, 收获F5
Plant F4, harvest F5
2018年11月-2019年3月
November 2018-March 2019		 海南三亚Sanya, Hainan (18.25°N, 109.51°E) 种植F5, 收获F6
Plant F5, harvest F6
2019年5-11月
May-November 2019		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 种植F6, 收获F7
Plant F6, harvest F7
2019年11月-2020年3月
November 2019-March 2020		 海南三亚Sanya, Hainan (18.25°N, 109.51°E) 种植F7, 收获F8
Plant F7, harvest F8
2020年5-11月
May-November 2020		 湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 种植F8, 收获F9
Plant F8, harvest F9
2020年11月-2021年3月
November 2020-March 2021		 海南三亚Sanya, Hainan (18.25°N, 109.51°E) 种植F9, 收获F10
Plant F9, harvest F10
2021年5-11月
May-November 2021		 河南商丘Shangqiu, Henan (34.41°N, 115.98°E) 种植F10, 收获F11
Plant F10, harvest F11
2022年5-11月
May-November 2022		 安徽宿州Suzhou, Anhui (33.69°N, 117.10°E) 种植F11, 收获F12
Plant F11, harvest F12

图1

大豆NAM群体亲本地理来源、分类与群体大小 (A) NAM群体亲本生态类型。HHSp: 黄淮春; HHSu: 黄淮夏; NSp: 北方春; SSp: 南方春; SSu: 南方夏。(B)~(E) NAM群体亲本种质类型(B)、花色(C)、种皮色(D)、百粒重及品质性状(E); (F) NAM群体中不同RIL群体大小, N001~N035群体详细信息见表1。"

图2

NAM群体遗传结构分析 (A) 大豆NAM群体亲本最大似然树, 基于127,184 SNP标记, 模型选择: TVM+F+R3, Bootstrap值为1000; (B) 大豆NAM群体最大似然树, 群体父本标注在RIL株系相对集中的区域; (C) 主成分PC1与PC2散点图; (D) 主成分PC1、PC2、PC3 3D散点图。"

表3

种皮色9个属性表型数据统计分析"

性状
Trait		 最小值Min. 最大值Max. 均值Mean 变异范围Range 变异系数CV 方差
Variance		 标准差SD 偏度Skewness 峰度Kurtosis
红Red 56.74 224.83 157.11 168.09 0.22 1240.28 35.22 -1.25 0.40
绿Green 66.14 225.36 152.64 159.21 0.23 1192.48 34.53 -0.69 -0.99
蓝Blue 71.41 206.22 128.15 134.80 0.18 524.63 22.90 -0.14 -0.72
光度Luminosity 60.34 203.82 134.87 143.48 0.19 678.15 26.04 -0.73 -0.42
L值L-value 26.85 88.92 62.32 62.06 0.21 164.89 12.84 -0.81 -0.67
a值a-value -17.16 16.28 -5.51 33.44 -1.23 45.76 6.76 1.36 1.12
b值b-value -9.08 39.43 16.58 48.51 0.59 96.16 9.81 -0.84 0.23
色调Hue 26.88 242.16 116.67 215.28 0.35 1659.97 40.74 1.19 1.81
饱和度Chroma 2.47 42.64 19.71 40.17 0.40 60.80 7.80 -0.12 -0.36

表4

种皮色9种不同属性值相关性分析"

性状 红 绿 蓝 光度 L值 a值 b值 色调 饱和度
Trait Red Green Blue Luminosity L-value a-value b-value Hue Chroma
红Red 1
绿Green 0.912*** 1
蓝Blue 0.752** 0.879*** 1
光度 Luminosity 0.960*** 0.964 *** 0.905*** 1
L值 L-value 0.951*** 0.994*** 0.866*** 0.982*** 1
a值 a-value -0.255 -0.615* -0.521* -0.404 -0.528* 1
b值 b-value 0.835*** 0.742** 0.353 0.695** 0.773** -0.300 1
色调 Hue -0.595* -0.256 -0.060 -0.399 -0.348 -0.462 -0.600* 1
饱和度 Chroma 0.727** 0.683** 0.280 0.600** 0.700** -0.369 0.950*** -0.412 1

表5

花色和种皮色全基因组关联位点"

性状
Trait		 位点
Locus		 染色体
Chr.		 起始
Start		 终止
End		 最显著SNP位点Most significant SNP 最显著SNP P值
P-value of tagSNP		 重复关联性状
Correlated trait		 关联方法
Method		 经典位点Classic loci
种皮色
Seed coat color		 qSCC1-1 1 16769772 16960836 Chr01_16862797 4.09E-09 a, Hue Emmax, RTM, Tassel
qSCC1-2 1 53062691 53307617 Chr01_53162691 1.81E-07 Chroma, a, b, Green, Blue Emmax, RTM, 3VmrMLM G
qSCC5-1 5 36175387 36290717 Chr05_36193584 4.85E-13 a, b, L, Red, Green, Chroma, Luminosity, Hue Emmax, RTM, Tassel
qSCC6-1 6 18409621 19314852 Chr06_19275710 2.72E-13 a, b, L, Red, Green, Chroma, Luminosity, Hue Emmax, RTM, Tassel, 3VmrMLM T/F3’H
qSCC6-2 6 40810608 42012070 Chr06_41686979 3.69E-08 b, Red, Hue, Green, Chroma Emmax, RTM, 3VmrMLM
qSCC8-1 8 7088758 9481774 Chr08_8400595 1.49E-54 a, b, L, Red, Green, Blue, Chroma, Luminosity, Hue Emmax, RTM, Tassel, 3VmrMLM I/CHS
qSCC9-1 9 45305565 45822016 Chr09_48482371 8.96E-11 a, b, L, Red, Green, Blue, Chroma, Luminosity, Hue Emmax, RTM, Tassel, 3VmrMLM R/MYB
qSCC12-1 12 4401461 4591803 Chr12_4496838 6.48E-08 a, b, L, Red, Green, Blue, Luminosity Emmax, RTM, Tassel
qSCC10-1 10 43550478 44132066 Chr10_44033177 1.72E-16 a, b, Red, Green, Hue, Chroma Tassel, RTM, 3VmrMLM
qSCC11-1 11 3209682 6768477 Chr11_3309682 4.47E-30 Chroma, Red, Luminosity RTM, 3VmrMLM
qSCC11-2 11 32477382 33390337 Chr11_32487220 0.0001984 a, L, Red, Green RTM, 3VmrMLM
qSCC13-1 13 34811493 36307740 Chr13_34911493 8.93E-18 Red, Green, Blue, L, a, b, Luminosity RTM, 3VmrMLM
花色
Flower color		 qFC13-1 13 17215500 17425536 Chr13_17315536 5.53E-211 Emmax, RTM, Tassel, 3VmrMLM W1/F3’5’H

图3

基于EMMAX的花色和种皮色全基因组关联分析Manhattan图和QQ图 a、b、L、Red、Green、Blue、Luminosity、Chroma、Hue为种皮色9个颜色属性, FC表示花色。"

图4

基于3VmrMLM的花色和种皮色全基因组关联分析 a、b、L、Red、Green、Blue、Luminosity、Chroma、Hue为种皮色9个颜色属性, FC表示花色。"

表6

关联定位区间候选基因"

位点
Locus		 区间
Range
(kb)		 基因数目
Number genes		 候选基因
Candidate gene ID		 基因名
Gene name		 基因位置
Gene position		 功能注释
Gene annotation
qSCC1-1 191.1 5 Glyma.01G075200 36147019..36148009 60S核糖体蛋白
60S ribosomal protein
qSCC5-1 115.3 20 Glyma.05G171700 36197575..36199801
Glyma.05G172400 36241411..36245575 染色体凝聚调节因子(RCC1)家族蛋白
Regulator of chromosome condensation (RCC1) family protein
Glyma.05G173300 36277504..36281700 糖基水解酶家族5
Glycosyl hydrolase family 5
Glyma.05G153200 CHS 34687008..34693243 查尔酮合成酶
Naringenin-chalcone synthase
qSCC6-2 1201.5 44 Glyma.06G242200 40186035..40189770 WRKY家族转录因子家族蛋白
WRKY family transcription factor family protein
Glyma.06G247200 41703993..41711389 转导素/WD40重复样超家族蛋白
Transducin/WD40 repeat-like superfamily protein
qSCC12-1 190.3 20 Glyma.12G060700 4406789..4408502 锌指(C3HC4型)家族蛋白
Zinc finger (C3HC4-type RING finger) family protein
Glyma.12G061600 4499104..4499532 二磷酸核酮糖羧化酶
Ribulose-bisphosphate carboxylases
qSCC10-1 581.6 49 Glyma.10G204800 LAR2 43605676..43608465 无色花青素还原酶/无色花青素还原酶
Leucoanthocyanidin reductase/Leucocyanidin reductase
qSCC11-1 2791.8 446 Glyma.11G027700 ANS 1992155..1993544 无色花青素双加氧酶有关
Leucoanthocyanidin dioxygenase related
Glyma.11G077200 CHI 5785880..5787797 查尔酮-黄酮异构酶家族蛋白
Chalcone-flavanone isomerase family protein
Glyma.11G054600 4115043..4119025 碱性螺旋-环-螺旋(bHLH) DNA结合超家族蛋白
Basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Glyma.11G060200 4545030..4548660 细胞色素P450
Cytochrome P450
qSCC11-2 913 100 Glyma.11G212900 GST 30575282..30577501 谷胱甘肽S-转移酶F11相关
Glutathione S-Transferase F11-related
Glyma.11G231300 32690044..32692317 碱性螺旋-环-螺旋(bHLH) DNA结合超家族蛋白
Basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Glyma.11G236300 33112560..33118486 bZIP转录因子家族蛋白bZIP
Transcription factor family protein
qSCC13-1 1396.2 201 Glyma.13G256900 36204841..36216179 K-box和MADS-box转录因子家族蛋白
K-box region and MADS-box transcription factor family protein
qSCC1-2 244.9 27 Glyma.01G198500 53226420..53229986 CAAX蛋白酶自身免疫(Abi)
CAAX protease self-immunity (Abi)
qSCC6-1 905.2 16 Glyma.06G202300 F3’H 18731104..18738025 类黄酮3’单氧酶
Flavonoid 3’-monooxygenase
qSCC8-1 2393 297 Glyma.08G109400 CHS 8391363..8394840 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G109200 CHS 8384741..8386542 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G109500 CHS 8397943..8399751 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G109300 CHS 8387508..8391327 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G110300 CHS 8475792..8477410 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G110500 CHS 8504478..8506020 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G110700 CHS 8513951..8515719 查尔酮合成酶
Naringenin-chalcone synthase
Glyma.08G110900 CHS 8517798..8519303 查尔酮合成酶
Naringenin-chalcone synthase
qSCC9-1 516.5 67 Glyma.09G235100 MYB 45758761..45760773 转录因子MYB113类
Transcription MYB113-related
qFC13-1 210.04 10 Glyma.13G072100 F3’5’H 17312471..17317198 类黄酮3’,5’-羟化酶
Flavonoid 3’,5’-hydroxylase

图5

种皮色、花色及色素合成相关候选基因表达模式[69]"

[1] Gireesh C, Sundaram R M, Anantha S M, Pandey M K, Madhav M S, Rathod S, Yathish K R, Senguttuvel P, Kalyani B M, Ranjith E, Subbarao L V, Mondal T K, Swamy M, Rakshit S. Nested association mapping (NAM) populations: present status and future prospects in the genomics era. Crit Rev Plant Sci, 2021, 40: 49-67.
doi: 10.1080/07352689.2021.1880019
[2] Nordborg M, Tavaré S. Linkage disequilibrium: what history has to tell us. Trends Genet, 2002, 18: 83-90.
pmid: 11818140
[3] Visscher P M, Wray N R, Zhang Q, Sklar P, McCarthy M I, Brown M A, Yang J. 10 Years of GWAS discovery: biology, function, and translation. Am J Hum Genet, 2017, 101: 5-22.
doi: S0002-9297(17)30240-9 pmid: 28686856
[4] Yu J, Holland J B, McMullen M D, Buckler E S. Genetic design and statistical power of nested association mapping in maize. Genetics, 2008, 178: 539-551.
doi: 10.1534/genetics.107.074245 pmid: 18202393
[5] Lu Y, Zhang S, Shah T, Xie C, Hao Z, Li X, Farkhari M, Ribaut J M, Cao M, Rong T, Xu Y. Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci USA, 2010, 107: 19585-19590.
doi: 10.1073/pnas.1006105107 pmid: 20974948
[6] McMullen M D, Kresovich S, Villeda S H, Bradbury P, Li H, Sun Q, Flint-Garica S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell S E, Peterson B, Pressoir G, Romero S, Rosas M O, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz J C, Goodman M, Ware D, Holland J B, Buckler E S. Genetic properties of the maize nested association mapping population. Science, 2009, 325: 737-740.
doi: 10.1126/science.1174320 pmid: 19661427
[7] Kump K L, Bradbury P J, Wisser R J, Buckler E S, Belcher A R, Oropeza-Rosas M A, Zwonitzer J C, Kresovich S, Mcmullen M D, Ware D, Balint-Kurti P J, Holland J B. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet, 2011, 43: 163-168.
doi: 10.1038/ng.747 pmid: 21217757
[8] Poland J A, Bradbury P J, Buckler E S, Nelson R J. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA, 2011, 108: 6893-6898.
doi: 10.1073/pnas.1010894108 pmid: 21482771
[9] Tian F, Bradbury P J, Brown P J, Hung H, Sun Q, Flint-Garcia S, Rocheford T R, McMullen M, Holland J B, Buckler E S. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet, 2011, 43: 159-162.
doi: 10.1038/ng.746 pmid: 21217756
[10] Cook J P, McMullen M D, Holland J B, Tian F, Bradbury P, Ross-Ibarra J, Buckler E S, Flint-Garcia S A. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol, 2012, 158: 824-834.
doi: 10.1104/pp.111.185033 pmid: 22135431
[11] Peiffer J A, Flint-Garcia S A, Leon N D, McMullen M, Kaeppler S M, Buckler E S. The genetic architecture of maize stalk strength. PLoS One, 2013, 8: e67066.
doi: 10.1371/journal.pone.0067066
[12] Zhang N, Gibon Y, Wallace J G, Lepak N, Li P, Dedow L, Chen C, So Y S, Kremling K, Bradbury P J, Brutnell T, Stitt M, Buckler E S. Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population. Plant Physiol, 2015, 168: 575-583.
doi: 10.1104/pp.15.00025 pmid: 25918116
[13] Li C, Sun B, Li Y, Cheng L, Xun W, Zhang D, Shi Y, Song Y, Buckler E S, Zhang Z, Wang T, Li Y. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations. BMC Genomics, 2016, 17: 894.
doi: 10.1186/s12864-016-3170-8
[14] Schnaithmann F, Kopahnke D, Pillen K. A first step toward the development of a barley NAM population and its utilization to detect QTLs conferring leaf rust seedling resistance. Theor Appl Genet, 2014, 127: 1513-1525.
doi: 10.1007/s00122-014-2315-x pmid: 24797143
[15] Bajgain P, Rouse M N, Tsilo T J, Macharia G K, Bhavani S, Jin Y, Anderson J A. Nested association mapping of stem rust resistance in wheat using genotyping by sequencing. PLoS One, 2016, 11: e0155760.
doi: 10.1371/journal.pone.0155760
[16] Hoyos-Villegas V, Song Q, Wright E M, Beebe S E, Kelly J D. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Sci, 2016, 56: 2546-2563.
doi: 10.2135/cropsci2016.01.0063
[17] Li J, Bus A, Spamer V, Stich B. Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations. BMC Plant Biol, 2016, 16: 26.
doi: 10.1186/s12870-016-0707-6
[18] Pandey M K, Roorkiwal M, Singh V K, Ramalingam A, Kudapa H, Thudi M, Chitikineni A, Rathore A, Varshney R K. Emerging genomic tools for legume breeding: current status and future prospects. Front Plant Sci, 2016, 7: 455.
doi: 10.3389/fpls.2016.00455 pmid: 27199998
[19] Bouchet S, Olatoye M O, Marla S R, Perumal R, Tesso T, Yu J, Tuinstra M, Morris G P. Increased power to dissect adaptive traits in global sorghum diversity using a nested association mapping population. Genetics, 2017, 206: 573-585.
doi: 10.1534/genetics.116.198499 pmid: 28592497
[20] Fragoso C A, Moreno M, Wang Z, Heffelfinger C, Arbelaez L J, Aguirre J A, Franco N, Romero L E, Labadie K, Zhao H, Dellaporta S L, Lorieux M. Genetic architecture of a rice nested association mapping population. Genes Genom Genet, 2017, 7: 1913-1926.
[21] Maranna S, Kumawat G, Nataraj V, Gireesh C, Gupta S, Satpute G K, Ratnaparkhe M B, Yadav D P. NAM population: a novel genetic resource for soybean improvement: development and characterization for yield and attributing traits. Plant Genet Resour, 2019, 17: 545-553.
doi: 10.1017/S1479262119000352
[22] Gangurde S S, Wang H, Yaduru S, Pandey M K, Fountain J C, Chu Y, Isleib T, Holbrook C C, Xavier A, Culbreath A K, Ozias-Akins P, Varshney R K, Guo B Z. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Plant Biotechnol J, 2020, 18: 1457-1471.
doi: 10.1111/pbi.13311 pmid: 31808273
[23] Song Q L, Yan L, Quigley C V, Jordan B, Fickus E, Schroeder S, Song B H, Charles An Y Q, Hyten D L, Nelson R L, Rainey K M, Beavis W, Specht J, Diers B, Cregan P. Genetic characterization of the soybean nested association mapping population. Plant Genome, 2017, 10: 3835.
[24] Xavier A, Jarquin D, Howard R, Ramasubramanian V, Specht J E, Graef G L, Beavis W D, Diers B W, Song Q, Cregan P, Nelson R, Mian R, Shannon J G, Mchale L K, Wang D, Schapaugh W, Lorenz A J, Xu S, Muir W M, Rainey K M. Genome-wide analysis of grain yield stability and environmental interactions in a multiparental soybean population. Genes Genom Genet, 2018, 8: 519-529.
[25] Diers B W, Specht J, Rainey K M, Cregan P, Song Q, Ramasubramanian V, Graef G L, Nelson R, Schapaugh W, Wang D, Shannon J G, Mchale L K, Kantartzi S K, Xavier A, Mian R, Stupar R M, Michno J M, Charles An Y Q, Goettel W, Ward R, Fox C, Lipka A E, Hyten D L, Cary T, Beavis W. Genetic architecture of soybean yield and agronomic traits. Genes Genom Genet, 2018, 8: 3367-3375.
[26] Scott K, Balk C, Veney D, Mchale L K, Dorrance A E. Quantitative disease resistance loci towards and three species of in six soybean nested association mapping populations. Crop Sci, 2019, 59: 605-623.
doi: 10.2135/cropsci2018.09.0573
[27] Lopez M A, Xavier A, Rainey K M. Phenotypic variation and genetic architecture for photosynthesis and water use efficiency in soybean (Glycine max L. Merr.). Front Plant Sci, 2019, 10: 680.
doi: 10.3389/fpls.2019.00680
[28] Beche E, Gillman J D, Song Q J, Nelson R, Beissinger T, Decker J, Shannon G, Scaboo A M. Genomic prediction using training population design in interspecific soybean populations. Mol Breed, 2021, 41: 15.
doi: 10.1007/s11032-021-01203-6
[29] 李曙光, 曹永策, 贺建波, 王吴彬, 邢光南, 杨加银, 赵团结, 盖钧镒. 大豆巢式关联作图群体蛋白质含量的遗传解析. 中国农业科学, 2020, 53: 1743-1755.
doi: 10.3864/j.issn.0578-1752.2020.09.005
Li S G, Cao Y C, He J B, Wang W B, Xing G N, Yang J Y, Zhao T J, Gai J Y. Genetic dissection of protein content in a nested association mapping population of soybean. Sci Agric Sin, 2020, 53: 1743-1755 (in Chinese with English abstract).
doi: 10.3864/j.issn.0578-1752.2020.09.005
[30] He J, Meng S, Zhao T, Xing G, Yang S, Li Y, Guan R, Lu J, Wang Y, Xia Q, Yang B, Gai J. An innovative procedure of genome- wide association analysis fits studies on germplasm population and plant breeding. Theor Appl Genet, 2017, 130: 2327-2343.
doi: 10.1007/s00122-017-2962-9
[31] 刘晓冬, 王英男, 齐广勋, 赵勇, 仲晓芳, 董英山, 王玉民. 大豆花色研究进展. 东北农业科学, 2017, 42(6): 53-57.
Liu X D, Wang Y N, Qi G X, Zhao Y, Zhong X F, Dong Y S, Wang Y M. A review of researches on flower color of soybean. J Northeast Agric Sci, 2017, 42(6): 53-57 (in Chinese with English abstract).
[32] 邱红梅, 陈亮, 侯云龙, 王新风, 陈健, 马晓萍, 崔正果, 张玲, 胡金海, 王跃强, 邱丽娟. 大豆种子颜色遗传调控机制研究进展. 作物学报, 2021, 47: 2299-2313.
doi: 10.3724/SP.J.1006.2021.14022
Qiu H M, Chen L, Hou Y L, Wang X F, Chen J, Ma X P, Cui Z G, Zhang L, Hu J H, Wang Y Q, Qiu L J. Reserch progress on genetic regulatory mechanism of seed color in soybean (Glycine max). Acta Agron Sin, 2021, 47: 2299-2313 (in Chinese with English abstract).
[33] Song J, Liu Z, Hong H, Ma Y, Tian L, Li X, Li Y H, Guan R, Guo Y, Qiu L J. Identification and validation of loci governing seed coat color by combining association mapping and bulk segregation analysis in soybean. PLoS One, 2016, 11: e0159064.
doi: 10.1371/journal.pone.0159064
[34] Yuan B, Yuan C, Wang Y, Liu X, Qi G, Wang Y, Dong L, Zhao H, Li Y, Dong Y. Identification of genetic loci conferring seed coat color based on a high-density map in soybean. Front Plant Sci, 2022, 13: 968618.
doi: 10.3389/fpls.2022.968618
[35] Park G T, Sundaramoorthy J, Lee J D, Kim J H, Seo H S, Song J T, Martina S. Elucidation of molecular identity of the W3 locus and its implication in determination of flower colors in soybean. PLoS One, 2015, 10: e0142643.
doi: 10.1371/journal.pone.0142643
[36] Zabala G, Vodkin L O. A rearrangement resulting in small tandem repeats in the F3’5’H gene of white flower genotypes is associated with the soybean W1 locus. Crop Sci, 2007, 47: S113-S124.
[37] Takahashi R, Dubouzet J G, Matsumura H, Yasuda K, Iwashina T. A new allele of flower color gene W1 encoding flavonoid 3’5’-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja. BMC Plant Biol, 2010, 10: 155.
doi: 10.1186/1471-2229-10-155 pmid: 20663233
[38] Sundaramoorthy J, Park G T, Chang J H, Lee J D, Kim J H, Seo H S, Chung G, Hoe K J, Soo S H, Gyuhwa C, Song J T. Identification and molecular analysis of four new alleles at the W1 locus associated with flower color in soybean. PLoS One, 2016, 11: e0159865.
doi: 10.1371/journal.pone.0159865
[39] Yan F, Di S, Rodas F R, Rodriguez Torrico T, Murai Y, Iwashina T, Anai T, Takahashi R. Allelic variation of soybean flower color gene W4 encoding dihydroflavonol 4-reductase 2. BMC Plant Biol, 2014, 14: 58.
doi: 10.1186/1471-2229-14-58
[40] Xu M, Brar H K, Grosic S, Palmer R G, Bhattacharyya M K. Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean [Glycine max (L.) Merr.]. Genetics, 2010, 184: 53-63.
doi: 10.1534/genetics.109.107904
[41] Xu M, Palmer R G. Genetic analysis and molecular mapping of a pale flower allele at the W4 locus in soybean. Genome, 2005, 48: 334-340.
doi: 10.1139/g04-105
[42] Zabala G, Vodkin L O. The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell, 2005, 17: 2619-2632.
doi: 10.1105/tpc.105.033506
[43] Iwashina T, Githiri S M, Benitez E R, Takemura T, Kitajima J, Takahashi R. Analysis of flavonoids in flower petals of soybean near-isogenic lines for flower and pubescence color genes. J Hered, 2007, 98: 250-257.
doi: 10.1093/jhered/esm012 pmid: 17420179
[44] Sundaramoorthy J, Park G T, Lee J D, Kim J H, Seo H S, Song J T. A P3A-type ATPase and an R2R3-MYB transcription factor are involved in vacuolar acidification and flower coloration in soybean. Front Plant Sci, 2020, 11: 580085.
doi: 10.3389/fpls.2020.580085
[45] Senda M, Masuta C, Ohnishi S, Goto K, Kasai A, Sano T, Hong J S, MarFarlane S. Patterning of virus-infected Glycine max seed coat is associated with suppression of endogenous silencing of chalcone synthase genes. Plant Cell, 2004, 16: 807-818.
doi: 10.1105/tpc.019885
[46] Cho Y B, Jones S I, Vodkin L O. Mutations in argonaute5 illuminate epistatic interactions of the K1 and I loci leading to saddle seed color patterns in Glycine max. Plant Cell 2017, 29: 708-725.
doi: 10.1105/tpc.17.00162
[47] Zabala G, Vodkin L. Cloning of the pleiotropic T locus in soybean and two recessive alleles that differentially affect structure and expression of the encoded flavonoid 3' hydroxylase. Genetics, 2003, 163: 295-309.
doi: 10.1093/genetics/163.1.295
[48] Gillman J D, Tetlow A, Lee J D, Shannon J G, Bilyeu K. Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in brown hilum and brown seed coats. BMC Plant Biol, 2011, 11: 155.
doi: 10.1186/1471-2229-11-155 pmid: 22070454
[49] Zabala G, Vodkin L O, Cui Z. Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLos One, 2014, 9: e111959.
[50] Gao R, Han T, Xun H, Zeng X, Li P, Li Y, Wang Y, Shao Y, Cheng X, Feng X, Zhao J, Wang L, Gao X. MYB transcription factor GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean. J Exp Bot, 2021, 72: 4401-4418.
doi: 10.1093/jxb/erab152
[51] Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet, 2018, 50: 1435-1441.
doi: 10.1038/s41588-018-0229-2 pmid: 30250128
[52] Xie M, Chung C Y, Li M W, Wong F L, Wang X, Liu A, Wang Z, Leung K Y, Wong T H, Tong S W, Xiao Z, Fan K, Ng M S, Qi X, Yang L, Deng T, He L, Chen L, Fu A, Ding Q, He J, Chung G, Isobe S, Tanabata T, Valliyodan B, Nguyen H T, Cannon S B, Foyer C H, Chan T F, Lam H M. A reference-grade wild soybean genome. Nat Commun, 2019, 10: 1216.
doi: 10.1038/s41467-019-09142-9 pmid: 30872580
[53] Tokumitsu Y, Kozu T, Yamatani H, Ito T, Nakano H, Hase A, Sasada H, Takada Y, Kaga A, Ishimoto M, Kusaba M, Nakashima T, Abe J, Yamada T. Functional divergence of G and its homologous genes for green pigmentation in soybean seeds. Front Plant Sci, 2021, 12: 796981.
doi: 10.3389/fpls.2021.796981
[54] Liu C, Chen X, Wang W, Hu X, Han W, He Q, Yang H, Xiang S, Gai J. Identifying wild versus cultivated gene-alleles conferring seed coat color and days to flowering in soybean. Int J Mol Sci, 2021, 22: 1559.
doi: 10.3390/ijms22041559
[55] Lu N, Rao X, Li Y, Jun J H, Dixon R A. Dissecting the transcriptional regulation of proanthocyanin and anthocyanin biosynthesis in soybean (Glycine max). Plant Biotechnol J, 2021, 19: 1429-1442.
doi: 10.1111/pbi.v19.7
[56] 宋喜娥, 李英慧, 常汝镇, 郭平毅, 邱丽娟. 中国栽培大豆(Glycine max (L.) Merr.) 微核心种质的群体结构与遗传多样性. 中国农业科学, 2010, 43: 2209-2219.
Song X E, Li Y H, Chang R Z, Guo P Y, Qiu L J. Population structure and genetic diversity of mini core collection of cultivated soybean (Glycine max (L.)Merr.) in China. Sci Agric Sin, 2010, 43: 2209-2219 (in Chinese with English abstract).
[57] Li Y H, Qin C, Wang L, Jiao C, Hong H, Tian Y, Li Y, Xing G, Wang J, Gu Y, Gao X, Li D, Li H, Liu Z, Jing X, Feng B, Zhao T, Guan R, Guo Y, Liu J, Yan Z, Zhang L, Ge T, Li X, Wang X, Qiu H, Zhang W, Luan X, Han Y, Han D, Chang R, Guo Y, Reif J C, Jackson S A, Liu B, Tian S, Qiu L J. Genome-wide signatures of the geographic expansion and breeding of soybean. Sci China Life Sci, 2023, 66: 350-365.
doi: 10.1007/s11427-022-2158-7
[58] Darrigues A, Hall J, van der Knaap E, Francis D M, Gray S. Tomato analyzer-color test: a new tool for efficient digital phenotyping. J Am SocHortic, 2008, 133: 579-586.
[59] Rodríguez G R, Moyseenko J B, Robbins M D, Huarachi Morejón N, Francis D M, Esther V D K. Tomato analyzer: a useful software application to collect accurate and detailed morphological and colorimetric data from two-dimensional objects. J Vis Exp, 2010, 16: 1856.
[60] Sadohara R, Long Y, Izquierdo P, Urrea C A, Morris D, Cichy K. Seed coat color genetics and genotype × environment effects in yellow beans via machine-learning and genome-wide association. Plant Genome, 2021, 15: e20173.
doi: 10.1002/tpg2.v15.1
[61] Sun R, Sun B, Tian Y, Su S, Zhang Y, Zhang W, Wang J, Yu P, Guo B, Li H, Li Y, Gao H, Gu Y, Yu L, Ma Y, Su E, Li Q, Hu X, Zhang Q, Guo R, Chai S, Feng L, Wang J, Hong H, Xu J, Yao X, Wen J, Liu J, Li Y, Qiu L J. Dissection of the practical soybean breeding pipeline by developing ZDX1, a high-throughput functional array. Theor Appl Genet, 2022, 135: 1413-1427.
doi: 10.1007/s00122-022-04043-w pmid: 35187586
[62] Price M N, Dehal P S, Arkin A P. FastTree 2-approximately maximum-likelihood trees for arge alignments. PLoS One, 2010, 5: e9490.
doi: 10.1371/journal.pone.0009490
[63] Minh B Q, Schmidt H A, Chernomor O, Schrempf D, Woodhams M, Haeseler A V, Lanfear R. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol, 2020, 37: 1530-1534.
doi: 10.1093/molbev/msaa015 pmid: 32011700
[64] Yang J, Lee S H, Goddard M E, Visscher P M. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet, 2011, 88: 76-82.
doi: 10.1016/j.ajhg.2010.11.011 pmid: 21167468
[65] Browning B L, Tian X, Zhou Y, Browning S R. Fast two-stage phasing of large-scale sequence data. Am J Hum Genet, 2021, 108: 1880-1890.
doi: 10.1016/j.ajhg.2021.08.005 pmid: 34478634
[66] Li M, Zhang Y W, Zhang Z C, Xiang Y, Liu M H, Zhou Y H, Zuo J F, Zhang H Q, Chen Y, Zhang Y M. A compressed variance component mixed model for detecting QTNs and QTN-by- environment and QTN-by-QTN interactions in genome-wide association studies. Mol Plant, 2022, 15: 630-650.
doi: 10.1016/j.molp.2022.02.012
[67] Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 2633-2635.
doi: 10.1093/bioinformatics/btm308 pmid: 17586829
[68] Kang H M, Zaitlen N A, Wade C M, Kirby A, Heckerman D, Daly M J, Eskin E. Efficient control of population structure in model organism association mapping. Genetics, 2008, 178: 1709-1723.
doi: 10.1534/genetics.107.080101 pmid: 18385116
[69] Yu Y, Zhang H, Long Y, Shu Y, Zhai J. Plant public RNA-seq database: a comprehensive online database for expression analysis of -45 000 plant public RNA-Seq libraries. Plant Biotechnol J, 2022, 20: 806-808.
[70] Toda K, Yang D, Yamanaka N, Watanabe S, Harada K, Takahashi R. A single-base deletion in soybean flavonoid 3’-hydroxylase gene is associated with gray pubescence color. Plant Mol Biol, 2002, 50: 187-196.
doi: 10.1023/A:1016087221334
[71] Yang K, Jeong N, Moon J K, Lee Y H, Lee S H, Kim H M, Hwang C H, Back K, Palmer R G, Jeong S C. Genetic analysis of genes controlling natural variation of seed coat and flower colors in soybean. J Hered, 2010, 101: 757.
doi: 10.1093/jhered/esq078 pmid: 20584753
[72] Lim Y J, Kwon S J, Qu S, Kim D G, Eom S H. Antioxidant contributors in seed, seed coat, and cotyledon of γ-ray-induced soybean mutant lines with different seed coat colors. Antioxidants, 2021, 10: 353.
doi: 10.3390/antiox10030353
[73] Kim J H, Park J S, Lee C Y, Jeong M G, Xu J L, Choi Y, Jung H W, Choi H K. Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 glycine accessions. PLoS One, 2020, 15: e0243085.
doi: 10.1371/journal.pone.0243085
[74] Cho Y B, Jones S I, Vodkin L O. Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus. Plant Direct, 2019, 3: e00162.
doi: 10.1002/pld3.2019.3.issue-8
[1] 金昱何, 王雪菲, 徐张一娃, 缪怡宁, 蒋云杰, 伊莹, 缪德麟, 朱静仪, 钟一帆, 陈铭亨, 方芳, 刘鹏. 外源激素对低温胁迫下大豆叶片叶绿素荧光参数及抗氧化酶系统的影响[J]. 作物学报, 2026, 52(6): 1817-1829.
[2] 唐宽强, 李公允, 宋美毅, 赵雪, 常春玲. 大豆株高性状全基因组关联分析及预测模型构建[J]. 作物学报, 2026, 52(6): 1743-1756.
[3] 姚术, 郭凯悦, 翟慧慧, 姚佳慧, 邓文琪, 闫玲, 黄驰, 高阳, 俞嫣然, 赵振邦, 李英慧, 王晓波, 李佳佳. 大豆苗期耐低铁综合评价及优异种质筛选[J]. 作物学报, 2026, 52(5): 1373-1387.
[4] 张晴, 杨昱, 郭茜, 岳霈尧, 殷丛丛, 牛景萍, 赵晋忠, 杜维俊, 岳爱琴. 大豆GmARA6a的克隆及响应盐胁迫的功能分析[J]. 作物学报, 2026, 52(2): 480-493.
[5] 王克晶, 李向华. 我国珍稀的大豆属多年生烟豆和短绒野大豆物种遗传资源濒危性评估分析[J]. 作物学报, 2025, 51(8): 2009-2019.
[6] 孟然, 李赵嘉, 冯薇, 陈悦, 刘路平, 杨春燕, 鲁雪林, 王秀萍. 大豆不同生育时期耐盐性综合评价及耐盐种质筛选[J]. 作物学报, 2025, 51(8): 1991-2008.
[7] 贺红利, 张雨涵, 杨静, 程云清, 赵杨, 李星诺, 司洪亮, 张兴政, 杨向东. 大豆e1-as基因突变体的创制及生理分析[J]. 作物学报, 2025, 51(8): 2228-2239.
[8] 胡蒙, 沙丹, 张晟瑞, 谷勇哲, 张世碧, 李静, 孙君明, 邱丽娟, 李斌. 大豆分枝数QTL定位及候选基因筛选[J]. 作物学报, 2025, 51(7): 1747-1756.
[9] 杨思杰, 杜启迪, 柴守玺, 熊宏春, 谢永盾, 赵林姝, 古佳玉, 郭会君, 刘录祥. 小麦小旗叶突变性状基因定位与遗传分析[J]. 作物学报, 2025, 51(6): 1548-1557.
[10] 王琼, 邹丹霞, 陈兴运, 张威, 张红梅, 刘晓庆, 贾倩茹, 魏利斌, 崔晓艳, 陈新, 王学军, 陈华涛. 大豆开花时间和成熟期性状全基因组关联分析与候选基因预测[J]. 作物学报, 2025, 51(6): 1558-1568.
[11] 殷丛丛, 李睿琦, 岳霈尧, 李晨, 牛景萍, 赵晋忠, 杜维俊, 岳爱琴. 基于闭合哑铃介导等温扩增可视化检测大豆花叶病毒SC15方法的建立及应用[J]. 作物学报, 2025, 51(5): 1248-1260.
[12] 夏琦, 郭滢, 王坤美, 王思忆, 巨建业, 彭雅雯, 刘忠松, 夏石头. 甘蓝型油菜种子和种皮中水杨酸含量与原花色素积累的关系研究[J]. 作物学报, 2025, 51(5): 1189-1197.
[13] 许睿, 何妙华, 王昊, 李卫, 任杰, 夏志强. 基于空间转录组技术解析大豆种胚对X射线辐射的响应机制[J]. 作物学报, 2025, 51(12): 3121-3132.
[14] 林洋, 史晓蕾, 陈强, 刘兵强, 杨庆, 于慧娟, 闫龙, 武小霞, 杨春燕. 大豆蛋白质脂肪及脂肪酸组分相关QTL定位[J]. 作物学报, 2025, 51(11): 2899-2910.
[15] 王浩辰, 王克晶, 韩娟, 李向华. 东南沿海短绒野大豆两种代表性生境自然种群的空间遗传结构特征:种群内取样策略研究[J]. 作物学报, 2025, 51(11): 2875-2885.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2