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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (3): 556-575.doi: 10.3724/SP.J.1006.2024.34094


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 Online:2024-03-12 Published: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)


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

Table 1

Basic information of NAM parents"

Population number
Parental name
Systematic code
Parent type
Geographic origination
Germ type
Ecological type
100-SW (g)
PC (%)
OC (%)
POC (%)
群体大小 鉴定株系
Population size Genotyped Individuals
N001 羊眼豆
ZDD17457 父本 云南 地方品种 南方夏 暗绿 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 23.2 42.7 18.2 60.9
Zhongdou 41 Female parent Hubei Cultivar SS Yellow White

Table 2

Construction process of soybean NAM population"

May-November 2015
湖北荆州Jingzhou, Hubei (30.37°N, 112.06°E) 杂交, 收获F1
Cross, harvest F1
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
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
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
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
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
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
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
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
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
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
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

Fig. 1

Geographic origination, classification of NAM parents and population size (A): ecology type distribution of NAM parents, HHSp: Huanghuai Spring; HHSu: Huanghuai Summer; NSp: Northern Spring; SSp: Southern Spring; SSu: Southern Summer. (B)-(E): germplasm type (B), flower color (C), seed coat color (D), and 100-seed weight and quality traits (E) of NAM parents; (F): population size of each RIL of NAM, detailed information of N001-N035 is shown in Table 1."

Fig. 2

Genetic structure of NAM population (A): the maximum likelihood tree of NAM parents based on 127,184 SNPs, model selected: TVM+F+R3, bootstrap value is 1000; (B): the maximum likelihood tree of NAM population, NAM paternal parent name was labelled on the region where RILs derived from certain parent clustered; (C): the scatter plot of PC1 and PC2 by principal component analysis; (D): 3D scatter plot of PC1, PC2, and PC3 by principal component analysis."

Table 3

Statistical analysis of 9 different attributes of seed coat color"

最小值Min. 最大值Max. 均值Mean 变异范围Range 变异系数CV 方差
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

Table 4

Correlation analysis of 9 different attributes of seed coat colors"

性状 绿 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

Table 5

Significant loci associated to flower color and seed coat color by GWAS"

最显著SNP位点Most significant SNP 最显著SNP P
P-value of tagSNP
Correlated trait
经典位点Classic loci
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
Flower color
qFC13-1 13 17215500 17425536 Chr13_17315536 5.53E-211 Emmax, RTM, Tassel, 3VmrMLM W1/F3’5’H

Fig. 3

Manhattan-plots and QQ-plots for genome-wide association analysis of flower color and seed coat color by EMMAX a, b, L, Red, Green, Blue, Luminosity, Chroma, and Hue are the 9 color attributes of the seed coat, and FC represents flower color."

Fig. 4

Manhattan-plots and QQ-plots for genome-wide association analysis of flower color and seed coat color by 3VmrMLM a, b, L, Red, Green, Blue, Luminosity, Chroma, and Hue are the 9 color attributes of the seed coat, and FC represents flower color."

Table 6

Candidate genes within association region"

Number genes
Candidate gene ID
Gene name
Gene position
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 F35H 17312471..17317198 类黄酮3’,5’-羟化酶
Flavonoid 3’,5’-hydroxylase

Fig. 5

Relative expression pattern of candidate genes related to seed coat color, flower color, and pigment synthesis[69]"

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