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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (10): 2727-2737.doi: 10.3724/SP.J.1006.2023.24210

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide association analysis of growth period traits in soybean of Sichuan and Chongqing

YANG Hao1(), XIANG Shi-Hua2(), LIU Li1, NING Ke-Jun1, YANG Xue1, SHU Ying-Jie1, HE Qing-Yuan1()   

  1. 1Anhui Science and Technology University, Fengyang 233100, Anhui, China
    2Zigong Institute of Agricultural Science, Zigong 643000, Sichuan, China
  • Received:2022-09-14 Accepted:2023-04-17 Online:2023-10-12 Published:2023-04-26
  • Contact: E-mail: heqingyuan1@163.com
  • About author:**Contributed equally to this work
  • Supported by:
    Key Research and Development Projects of Anhui(202104a06020029);National Natural Science Foundation of China(31871711);National Natural Science Foundation of China(32101704);Sichuan Science and Technology Program(2022SZYZF08);Key Research and Development projects of Sichuan(2021YFYZ0018);Science and Technology Program of Sichuan Province(SCCXTD-2020-20);Anhui Provincial College Program for Natural Science(KJ2020A0066);Key Projects of Anhui Science and Technology(2021zrzd13)

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Abstract:

Growth period is the evolution of soybean varieties adaptded to the ecological environment. Which has important effects on the yield and agronomic traits. To lay the foundation for soybean breeding in southern China, especially in Sichuan andChongqing region.the relevant genetic loci of soybean growth period were analyzed and and candidate genes were screened out 227 soybean cultivars or resources from Sichuan and Chongqing regions were identified based on 135 SSR and 107,081 effective single nucleotide polymorphism (SNP) markers. Four growth period traits (vegetative growth, reproductive growth, whole growth and the ratio of vegetative growth / reproductive growth period) were investigated in three environments (Fengyang Anhui in 2016, Zigong Sichuan in 2016,and Fengyang Anhui in 2018).The results showed that the phenotypic variation of four traits followed normal distribution, and the genetic variation was significantly affected by variety, environment and environment interaction. A total of 51 loci and 70 loci significantly associated with growth stage traits were detected by SSR markers and SNP respectively. In particular, there were stable expression related sites in BLK_29175719-29275719 and BLK_30878620-30978620 on chromosome 13, BLK_48763386-48863386 on chromosome 14 and BLK_10093551-10293551 on chromosome 16. And 11 potential candidate genes related to plant growth and development were predicted in these four regions and four genes (namely Glyma.13g177800, Glyma.13g178300, Glyma.13g178500, and Glyma.14g223300) were directly related to soybean growth period traits.

Key words: soybean, growth period, SNP, genome-wide association analysis

Table S1

227 Sichuan and Chongqing soybean varieties and sources"

类型 Type 品种名称来源地 Name and region
育成品种
Breeding species		 贡秋豆4号(自贡)，贡秋豆5号(自贡)，贡秋豆8号(自贡)，贡秋豆9号(自贡)，贡秋豆10号(自贡)，贡选1号(自贡)，南豆5号(南充), 南豆8号(南充)，南豆11(南充)，南豆12(南充)，南豆20(南充)，南豆25(南充)，贡豆5号(自贡)，贡豆6号(自贡)，贡豆7号(自贡)，贡豆10(自贡)，贡豆11(自贡)，贡豆12(自贡)，贡豆13(自贡)，贡豆14(自贡)，贡豆15(南充)
Gongqiudou 4 (Zigong), Gongqiudou 5 (Zigong), Gongqiudou 8 (Zigong), Gongqiudou 9 (Zigong), Gongqiudou 10 (Zigong), Gongxuan 1 (Zigong), Nandou 5 (Nanchong), Nandou 8 (Nanchong), Nanchong 11 (Nanchong), Nandou 12 (Nanchong), Nandou 20 (Nanchong), Nandou 25 (Nanchong), Gongdou 5 (Zigong), Gongdou 6 (Zigong), Gopngdou 7 (Zigong), Gongdou 7 (Zigong), Gongdou 10 (Zigong), Gongdou 11 (Zigong), Gongdou 12 (Zigong), Zigong 13 (Zigong), Zigong 14 (Zigong), Zigong 15 (Zigong)
地方品种
Local species		 荣县棕毛豆(荣县)，西昌大豆(西昌)，荞窝黄豆(普格)，平武高脚黄(平武)，梁平早(梁平)，六月黄②(崇州)，平坝皂角五月黄(什邡)，黄豆(中江)，二黄豆(郫县)，小黄豆(郫县)，二早黄(大邑)，豆芽豆(宜宾)，小白毛(泸定)，果元大白豆(会理)，绿皮豆(巫山)，绿蓝早(合江)，黑豆(峨边)，黑豆(渠县)，棕豆(温江)，紫皮豆(南川)，花脸豆①(隆昌)，绿皮豆(西昌)，红皮豆(平武)，马庄褐豆(金川)，黄豆(威远)，猴巴掌豆(开县)，城南早豆-2(梁平)，大白黄豆(普格)，大黄豆-1(丰都)，大黄豆-2(中江)，二番早(酉阳)，大早黄(青神)，七月黄(达县)，黄皮豆(九龙)，七十早(金川)，大白豆(茂汶)，三河大白豆(昭觉)，大奶白色(昭觉)，波波豆(甘洛)，裸曲(甘洛)，马抓豆-1(雷波)，古中豆(雷波)，新进白豆(美姑)，抱鸡黄-2(金阳)，大香豆(自贡)，棕色豆(沐川)，洛史-1(雷波)，罗石大都(雅安)，皂角豆(西昌)，扁子酱色豆(攀枝花)，杂色黄豆-2(九龙)，堵格松子豆(金城)，花大豆(富顺)，花腰子(峨眉)，8107-6-3(成都)，六月爆(宝兴)，早豆(重庆巴南)，抱脚黄(冕宁)，青皮豆(重庆万州)，高产黄豆(酉阳)，五月黄(达县)，春黄豆-3(大竹)，黄豆(合川)，绿蓝子大黄豆(潼南)，青香豆(叙永)，绿蓝豆(叙永)，黄豆(合川)，六月黄(苍溪)水白豆(德阳)，大圆豆(潼南)，红毛大豆(中江)，城关八月黄(绵竹)，十月黄(盐亭)，马鞭梢(北川)，八月黄(绵竹)，早黄豆(梁平)，灰儿豆-1(庐山)，青皮豆(重庆万州)，早黄豆-2(泸州)，矮杆材料(自贡)，绿蓝豆(叙永)，绿皮豆-2(荥经)，绿蓝子-2(青川)，绿豆子(平武)，绿黄豆(梓潼)，鸡肉豆-2(雅安)，绿香豆(汉源)，穿心豆(天全)，六月黄(崇州)，黄壳子(邛崃)，六月爆(宝兴)，草坝黄壳豆(雅安)，仲思海白水豆(汉源)，双溪11-41(汉源)，前进黄壳子(汉源)，宣东大黄豆(汉源)，大豆子(安岳)，金黄豆(江津)，大黄豆(丰都)，落水白-1(忠县)，白水豆(垫江)，遍山白(黔江)，黄豆(中江)，金黄豆(隆昌)，圆黄豆(潼南)，大白毛豆(潼南)，二季豆(芦山)，早豆(喜德)，百荚六月黄(仁寿)，转转豆(沐川)，苌子豆(通江)，鸡母豆(通江)，阴山豆(通江)，黄豆(丹巴)，冬豆(攀枝花)，五爪豆(富顺)，芭蕉坟(珙县)，桩桩豆(筠连)，冬黄豆(丰都)，黄壳豆(洪雅)，大早黄(武隆)，大白豆(布拖)，大白豆-1(普格)，大白黄(盐源)，洛悉(喜德)，大黄壳(越西)，六月黄(南充)，黄壳豆(洪雅)，大白黄毛(西昌)，永郎小白豆(德昌)，白豆-2(德昌)，大黄壳(越西)，红毛豆(金堂)，贡豆89-2(自贡)，小白水豆(叙永)，白毛六月黄(乐至)，龙会早(安岳)，早黄豆(芦山)，青相豆(叙永)，圆黄豆-2(广元)，田坎豆-1(阆中)，田坎豆-1(仪陇)，黄豆(中江)，团结透绿黄豆(眉山)，绿皮豆(彭山)，绿皮豆(巫山)，绿蓝子(雅安)，早鸡母肉豆(名山)，绿皮豆-2(荥经)，金黑粒(安岳)，黑黄豆(遂宁)，黑豆(渠县)，红皮黄豆(重庆万州)，早豆(乐山)，一刀叶(名山)，高脚青(名山)，白毛子(石棉)，六月早(石棉)，永兴黄豆(天全)，白花豆(天全)，细毛子(宝兴)，白毛子(都江堰)，大颗豆(宝兴)，白皮豆(丹巴)，黄豆-1(九龙)，绿蓝子(西昌)，黑冬豆(雅安)，半年豆-2(绵竹)，黑豆子(峨边)，黑药王(筠连)，扬尘豆-2(荥经)，高粱豆(巫山)，棕子豆(宝兴)，马油包-2(汉源)，猪腰子(绵竹)，猪肝豆(荣县)，水豆子(眉山)，六十早(丹棱)，黄壳子①(青神)，六月爆①(乐山)，十月黄(盐亭)，淡黄毛豆(合江)，92-526(成都)，六月黄(苍溪)，六月爆-1(酉阳)，黄豆(彭山)，绿蓝早(合江)，小毛豆(峨眉)，小粒春豆(武胜)，六月黄(黔江)，大八月黄(绵竹)，小金黄(遂宁)，绿蓝子(雅安)，黄壳豆(洪雅)，卫城高脚黄(盐源)，平川黄豆-3(盐源)，小白毛豆(攀枝花)，新街八月黄(绵竹)，红毛豆-2(眉山)，六月黄-1(黔江)，大粒冬豆(南充)，六月黄(崇州)，大黑眉毛(北川)，大豆(广安)，黑脐黄豆-2(自贡)，南充9707-23-2(南充)
Rongxianzongmaodou (Rongxian), Xichangdadou (Xichang), Qiaowodadou (Puge), Pingwugaojiaohuang (Pingwu), Liangpingzao (Liangping). Liuyuehuang (Chongzhou), Pingbazaojiaowuyuehuang (Shifang), Huangdou (Zhongjiang), Erhuangdou (Pixian), Xiaohuangdou (Pixian), Erzaohuang (Dayi), Diuyadou (Yibin), Xiaobaimao (Luding), Guoyuandabaidou (Huili), Lvpidou (Wushan), Lvlanzao (Hejiang),Heidou (Quxian), Zongdou (Wenjiang), Heidou (Quxian), Zongdou (Wenjiang), Zipidou (Nanchuan), Hualiandou① (Longchang), Lvpidou (Xichang), Hongpidou (Pingwu), Mazhuanghedou (Jinchuan), Huangdou (Weiyuan), Houbazhangdou (Kaixian), Chengnanzaodou-2 (Liangping), Dabaihuangdou (Puge), Dahuangdou-1 (Fengdu), Gahuangdou-2 (Zhongjiang), Erfanzao (Youyang), Dazaohuang (Qingshen), Qiyuehuang (Daxian), Huangpidou (Jiulong), Qishizao (Jinchuan), Dabaidou (Maowen), Sanhedabaidou (Zhaojue), Bobodou (Ganluo), Luoqu (Ganluo), Mazhuadou-1 (Leibo), Guzhongdou (Leibo), Xinjinbaidou (Meigu), Baojihuang-2 (Jinyang), Daxiangdou (Zigong), Zongsedou (Muchuan), Luoshi-1 (Leibo), Luoshidadu (Yaan), Zaojiaodou (Xichang), Bianzijiangsedou (Panzhihua), zasehuangdou-2 (Jiulong), Dugesongzidou (Jincheng), Huadadou (Fushun), Huayaozi (Ermei), 8107-6-3 (Chengdu), Liuyuebao (Baoxing), Zaodou (Chongqingbana), Baojiaohuang (Mianning), Qingpidou (Chongqingwanzhou), Gaochanhuangdou (Youyang), Wuyuehuang (Daxian), Chunhuangdou-3 (Dazhu), Huangdou (Hechuan), Lvlanzidahuangdou (Tongnan), Qingxiangdou (Xuyong), Lvlandou (Xuyong), Huangdou (Hechuan), Liuyuehuang (Cangxi), Shuibaidou (Deyang), Dayuandou (Tongnan), Hongmaodadou (Zhongjiang), Chengguanbayuehuang (Mianzhu), Shiyuehuang (Yanting), Mabianshao (Beichuan), Bayuehuang (Mianzhu), Zaohuangdou (Liangping), Huierdou-1(Lushan), Qingpidou (Chongqingwanzhou), Zaohuangdou-2 (Luzhou), Aigancailiao (Zigong), Lvlandou (Xuyong), Lvpidou-2 (Yingjing), Lvlanzi-2 (Qingchuan), Lvdouzi (Pingwu), Lvhuangdou (Hanyuan), Chuanxindou (Tianquan), Liuyuehuang (Chongzhou), Huangkezi (Qiongjia), Liuyuebao ((Baoxing), Caobahuangkedou (Yaan), Zhongsihaibaishuidou (Hanyuan), Shuangxi11-41 (Hanyuan), Qianjinhuangkezi (Hanyuan), Yidongdahuagdou (Hanyuan), Dadouzi (Anyue), Jinhuangdou (Jiangjin), Dahuangdou (Fengdu), Luoshuibai-1 (Zhongxain), Baishuidou (Dianjiang), Bianshanbai (Qianjiang), Huangdou (Zhongjiang), Jinhuangdou (Longchang), Yuanhuangdou (Tongnan), Dabaimaodou (Tongnan), Erjidou (Lushan), Zaodou (Dexi), Baijialiuyuehuang (Renshou), Zhuanzhuandou (Muchuan), Changzidou (Tongjiang), Jimudou (Tongjiang), Yinshandou (Tongjiang), Huangdou (Danba), Dongdou (Panzhihua), Wuzhuadou (Fushun), Bajiaofen (Gongxain), Zhuangzhuangdou (Junlian), Donghuangdou (Fengdu), Huangkedou (Hongya), Dazaohuang (Wulong), Dabaidou (Butuo), Dabaidou-1 (Puge)， Dabaihuang (Yanyuan), Luoxi (Xide), Dahuangke (Yuexi), Hongmaodou (Jintang), Gongdou 89-2 (Zigong), Xiaoshuibaidou (Xuyong), Baimaoliuyuehuang (Lezhi), Longhuizao (Anyue), Zaohuangdou (Lushan), Qingxiangdou (Xuyong), Huangyuandou-2 (Guangyuan), Tiankandou-1 (Langzhong), Tiankandou (Yilong), Huangdou (Zhongjiang), Tuanjietoulvhuangdou (Meishan), Lvpidou (Pengshan), Lvpidou (Wushan), Lvlanzi (Yaan), Zaojimuroudou (Mingshan), Lvpidou-2 (Yingjing), Jinheili (Anyue), Heihuangdou (Suining), Heidou (Quxian), Hongpihuangdou (Chongqingwanzhou), Zaodou (Leshan), Yidaoye (Mingshan), Gaojiaoqing (Mingshan), Baimaozi (Shimian), Liuyuezao (Shimian), Yongxinghuangdou (Tianquan), Baihuadou (Tianquan), Ximaozi (Baoxing), Baimaozi (Dujiangyan), Dakedou (Baoxing), Baipidou (Danba), Huangdou-1 (Jiulong), Lvlanzi (Xichang), Heidongdou (Yaan), Banniandou-2 (Mianzhu), Heidouzi (Erbian), Heiyaowang (Junlian), Yangchendou-2 (Yingjing), Gaoliangdou (Wushan), Zongzidou(Baoxing), Mayoubao-2 (Hanyuan), Zhuyaozi (Mianzhu), Zhugandou (Rongxian), Shuidouzi (Meishan), Liushizao (Danling), Huangkezi① (Qingshen), Liuyuebao① (Leshan), Shiyuehuang (Yanting), Danhuangmaodou (Hejiang), 92-526 (Chengdu), Liuyuehuang (Cangxi), Liuyuebao-1 (Youyang), Huangdou (Pengshan), Lvlanzao (Hejiag), Xioamaodou (Ermei), Xiaolichundou (Wusheng), Liuyuehuang (Qianjiang), Dabayuehuang (Mianzhu), Xiaojinhuang (Suining), Lvlanzi (Yaan), Huangkedou (Hongya), Weichenggaojiaohuang (Yanyuan), Pingchuanhuangdou-3 (Yanyuan), Xiaobaimaodou (Panzhihua), Xinjiebayuehuang (Mianzhu), Hongmaodou-2 (Meishan), Liuyuehuang-1 (Qianjiang), Dalidongdou (Nanchong), Liuyuehuang (Chongzhou), Daheimeimao (Beichuan), Dadou (Guangan), Heiqihuangdou-2 (Zigong), Nanchong 9707-23-2 (Nanchong)

Fig. 1

Distribution of Vp, Rp, Wp, and Rp/Vp in three environments Vp: the vegetative period; Rp: the reproductive period; Wgp: whole growth period; Rp/Vp: the reproductive period/vegetative period. 16FY: in 2016 in Fengyang; 18FY: in 2018 in Fengyang; 16ZG: in 2016 in Zigong."

Table 1

Phenotypic analysis of soybean fertility traits in three environments"

性状
Trait		 环境
Environment		 均值±标准差
Means ± SD		 范围
Range		 变异系数
GCV (%)		 广义遗传率
h2 (%)		 偏度
Skewness		 峰度
Kurtosis
营养生长期Vp 16FY 48.57±11.71 33-83 24.11 97.49 1.048 0.008
18FY 47.26±8.59 14-78 17.21 89.67 1.554 2.256
16ZG 40.36±8.27 24-68 20.50 88.60 1.127 1.149
生殖生长期Rp 16FY 65.54±12.40 22-100 16.47 77.64 0.523 0.305
18FY 57.99±14.02 15-88 24.08 56.85 0.241 0.111
16ZG 60.91±8.19 38-97 13.44 84.38 0.500 0.309
全生育期Wgp 16FY 113.87±17.55 65-159 15.41 92.72 0.325 1.527
18FY 105.25±16.21 74-131 15.40 71.90 0.133 0.631
16ZG 101.91±12.98 82-133 12.82 94.82 0.614 0.783
生育期结构Rp/Vp 16FY 1.40±0.32 0.395-2.857 22.72 85.65 0.324 1.504
18FY 1.28±0.49 0.246-2.05 27.17 40.20 0.060 0.163
16ZG 1.56±0.32 0.779-3.071 20.70 92.68 0.792 2.308

Table 2

Analysis of variance for fertility traits in soybean"

性状
Trait		 品系与环境
Strain and environment		 III 类平方和
Class III sum of squares		 自由度
DF		 均方
Mean square		 F值
F-value		 显著性
P
Vp 品系Strain 124,209.174 226 549.598 78.114 <0.0001*
环境Environment 25,653.768 2 12,826.884 1823.081 <0.0001*
品系×环境Strain×Environment 29,707.315 452 65.724 9.341 <0.0001*
Rp 品系Strain 96,176.752 226 425.561 7.768 <0.0001*
环境Environment 15,469.475 2 7,734.738 141.183 <0.0001*
品系×环境Strain×Environment 58,051.692 452 128.433 2.344 <0.0001*
Wgp 品系Strain 315,597.057 226 1,396.447 24.878 <0.0001*
环境Environment 55,976.999 2 27,988.500 498.615 <0.0001*
品系×环境Strain×Environment 48,980.417 452 108.364 1.931 <0.0001*
Rp/Vp 品系Strain 87.235 226 0.386 6.673 <0.0001*
环境Environment 22.463 2 11.231 194.156 <0.0001*
品系×环境Strain×Environment 95.245 452 0.211 3.643 <0.0001*

Table 3

SSR markers in more than two environments with fertility-related QTLs"

性状
Trait		 SSR标记
SSR marker		 染色体
Chr.		 基因位置
Gene
position		 物理位置
Physical
position		 R2 (%) P值
P-value		 环境
Environment
营养生长期Vp Satt129 1 93.502 54,257,719 3.3, 2.7 0.013 16FY, 18FY
Satt359 11 93.137 36,868,269 3.6, 4.7 0.010 16FY, 16ZG
Satt553 15 67.910 6.5, 3.2 0.011 16FY, 16ZG
生殖生长期Rp Sat_137 5 3.630 995,889 3.3, 2.3 0.043 16ZG, 18FY
全生育期Wgp Satt129 1 93.502 54,257,719 5.1, 3.0, 3.5 0.010 16FY,16ZG, 18FY
Satt553 15 67.910 4.1, 3.9, 2.9 0.011 16FY,16ZG,18FY
Satt594 18 52.440 22,611,420 3.2, 3.5, 3.6 0.008 16FY,16ZG,18FY
Sat_406 8 24.078 3,987,618 1.8, 1.8 0.049 16ZG, 18FY
Satt332 11 79.791 22,137,813 2.4, 3.1 0.049 16ZG,18FY
Satt359 11 93.137 36,868,269 3 1, 2.8 0.021 16ZG,18FY
生育期结构Rp/Vp Sct_189 20 109.270 45,550,622 2.5, 2.4 0.020 16FY,18FY

Table S2

SNPs with statistically significant loci"

性状
Trait		 标记
Marker		 染色体
Chr.		 位置
Position		 F P 贡献率
R2		 BP1 BP2 KB
18FYRSVG Gm02_45896774 2 45896774 10.28907 5.59E-05 0.09775 45888424 45954698 66.275
18FYRSVG Gm03_3426134 3 3426134 10.19263 5.94E-05 0.09516 /
18FYVG Gm05_32195936 5 32195936 11.29353 2.23E-05 0.10921 32127581 32308154 180.574
16FYVG Gm05_4193179 5 4193179 16.89039 5.60E-05 0.07628 4166497 4249773 83.277
16FYVG Gm05_4199580 5 4199580 16.17331 7.96E-05 0.07304
16FYVG Gm05_4209068 5 4209068 16.15321 8.05E-05 0.07309
16FYVG Gm05_4233543 5 4233543 16.8401 5.75E-05 0.0762
18FYWGP Gm08_7511038 8 7511038 18.92766 2.08E-05 0.08589 7504657 7511038 6.382
18FYRSVG Gm10_37323694 10 37323694 19.43665 1.65E-05 0.09073 37323694 37325590 1.897
18FYRSVG Gm10_37325590 10 37325590 19.43665 1.65E-05 0.09073
18FYRSVG Gm11_1666367 11 1666367 16.7513 6.11E-05 0.07848 1653110 1704559 51.45
18FYVG Gm12_34341783 12 34341783 9.99367 7.16E-05 0.09298 34285556 34411821 126.266
18FYVG Gm12_34361675 12 34361675 10.42346 4.81E-05 0.09689
18FYVG Gm12_34732042 12 34732042 23.06918 2.96E-06 0.10721 34732042 34762880 30.839
18FYVG Gm12_34869856 12 34869856 15.21584 6.69E-07 0.14144 /
18FYVG Gm12_34957065 12 34957065 20.38032 1.05E-05 0.09473 34957065 34980724 23.66
18FYVG Gm12_34960150 12 34960150 20.38032 1.05E-05 0.09473
18FYVG Gm12_35007106 12 35007106 16.34172 7.39E-05 0.07595 34983273 35032491 49.219
18FYVG Gm12_35035967 12 35035967 15.9315 9.04E-05 0.07405 35035967 35091257 55.291
18FYVG Gm12_35053190 12 35053190 15.9315 9.04E-05 0.07405
16ZGWGP Gm12_5516516 12 5516516 10.62238 3.97E-05 0.09548 5310845 5522341 211.497
18FYRSVG Gm13_10795948 13 10795948 11.69744 1.58E-05 0.12021 10789413 10822298 32.886
18FYRSVG Gm13_1107204 13 1107204 9.9166 7.65E-05 0.09436 996802 1145999 149.198
18FYVG Gm13_13884143 13 13884143 17.18668 4.94E-05 0.08272 /
18FYVG Gm13_13948127 13 13948127 19.27951 1.79E-05 0.09088 13941138 13973360 32.223
18FYVG Gm13_13962173 13 13962173 15.95283 9.23E-05 0.07796
18FYRSVG Gm13_23755545 13 23755545 11.63772 1.62E-05 0.10884 23755545 23774804 19.26
16FYRSVG Gm13_29225719 13 29225719 10.28283 5.41E-05 0.09285 29159606 29225719 66.114
16FYVG Gm13_29225719 13 29225719 12.11646 1.02E-05 0.10944
16ZGWGP Gm13_29225719 13 29225719 10.28199 5.41E-05 0.09241
16ZGWGP Gm13_30487826 13 30487826 11.57276 1.67E-05 0.10401 /
16FYVG Gm13_30923025 13 30923025 9.91937 7.56E-05 0.09021 30923025 30928620 5.596
16FYVG Gm13_30928620 13 30928620 19.04184 1.98E-05 0.08702
16ZGWGP Gm13_30928620 13 30928620 19.03735 1.98E-05 0.08572
18FYRSVG Gm13_32314474 13 32314474 27.52447 3.74E-07 0.12848 /
16ZGVG Gm14_48813386 14 48813386 16.64167 6.46E-05 0.0781 48784275 48821059 36.785
16ZGWGP Gm14_48813386 14 48813386 18.78875 2.27E-05 0.08693
18FYVG Gm16_10008824 16 10008824 15.90682 9.24E-05 0.07499 9862326 10707927 845.602
16ZGVG Gm16_10193551 16 10193551 17.22349 4.82E-05 0.07976
18FYVG Gm16_10193551 16 10193551 21.2747 6.93E-06 0.09909
18FYVG Gm16_10335623 16 10335623 15.90493 9.37E-05 0.07702
18FYVG Gm16_10397918 16 10397918 20.09628 1.20E-05 0.09341
18FYVG Gm16_10402991 16 10402991 20.09628 1.20E-05 0.09341
18FYVG Gm16_10409411 16 10409411 20.08693 1.21E-05 0.09343
18FYVG Gm16_10461269 16 10461269 20.10598 1.20E-05 0.09351
18FYVG Gm16_10472334 16 10472334 20.09628 1.20E-05 0.09341
18FYVG Gm16_10478117 16 10478117 20.09628 1.20E-05 0.09341
18FYVG Gm16_10481997 16 10481997 20.13791 1.18E-05 0.09365
18FYVG Gm16_10491818 16 10491818 20.14516 1.18E-05 0.09383
18FYVG Gm16_10529507 16 10529507 20.09628 1.20E-05 0.09341
18FYVG Gm16_10533546 16 10533546 17.10253 5.10E-05 0.07949
18FYVG Gm16_10549686 16 10549686 17.08172 5.19E-05 0.08024
18FYVG Gm16_10554296 16 10554296 17.10253 5.10E-05 0.07949
18FYVG Gm16_10562700 16 10562700 17.10253 5.10E-05 0.07949
18FYVG Gm16_10591319 16 10591319 17.10253 5.10E-05 0.07949
18FYVG Gm16_10596619 16 10596619 17.10253 5.10E-05 0.07949
18FYVG Gm16_10605095 16 10605095 17.15704 4.98E-05 0.07982
18FYVG Gm16_10610103 16 10610103 17.10253 5.10E-05 0.07949
18FYVG Gm16_10616274 16 10616274 17.10253 5.10E-05 0.07949
18FYVG Gm16_10619619 16 10619619 17.05878 5.21E-05 0.07975
18FYVG Gm16_10648367 16 10648367 17.10253 5.10E-05 0.07949
18FYVG Gm16_21827582 16 21827582 17.70072 3.82E-05 0.08229 21422691 21961387 538.697
18FYVG Gm16_21832714 16 21832714 17.70072 3.82E-05 0.08229
18FYVG Gm16_21905912 16 21905912 17.68549 3.84E-05 0.0822
18FYVG Gm16_21934615 16 21934615 17.68549 3.84E-05 0.0822
18FYVG Gm16_21944024 16 21944024 17.68549 3.84E-05 0.0822
16ZGWGP Gm16_2415358 16 2415358 16.73941 6.03E-05 0.07522 2395322 2468461 73.14
16ZGRSVG Gm17_37915466 17 37915466 15.91994 9.11E-05 0.07494 37889813 37944755 54.943
16ZGVG Gm20_15095950 20 15095950 17.00806 5.39E-05 0.08172 14942718 15112358 169.641
18FYRSVG Gm20_35870580 20 35870580 10.87992 3.28E-05 0.10523 /

Fig. 2

Manhattan and QQ-Plot maps for genome-wide association analysis of soybean fertility-related traits The red line represents P=1×10-4. 16ZG: in 2016 in Zigong; 18FY: in 2018 in Fengyang; 16FY: in 2016 in Fengyang; VG: the vegetative period; RS: the reproductive period; WGP: whole growth period; RSVG: the reproductive period/vegetative period."

Table 4

QTNs using SNPs in more than two environments associated with fertility traits"

标记
Marker		 环境
Environment		 染色体
Chr.		 物理位置
Physical position		 P值
P-value		 贡献率
R2(%)
Gm13_29225719 16ZGWgp 13 29,225,719 5.41E-05 9.241
16FYVp 13 29,225,719 1.02E-05 10.944
16FYRp/Vp 13 29,225,719 5.41E-05 9.285
Gm13_30928620 16ZGWgp 13 30,928,620 1.98E-05 8.572
16FYVp 13 30,928,620 1.98E-05 8.702
Gm14_48813386 16ZGVp 14 48,813,386 6.46E-05 7.810
16ZGWgp 14 48,813,386 2.27E-05 8.693
Gm16_10193551 16ZGVp 16 10,193,551 4.82E-05 7.976
18FYVp 16 10,193,551 6.93E-06 9.909

Table S3

Two types of markers with close physical location"

染色体
Chr.		 SNP 物理位置
Physical position		 关联性状
Associated traits		 SSR 物理位置
Physical position		 关联性状
Associated traits		 距离
Distance (kb)
5 Gm5_32195936 32195936 18FYVp Satt648 34158320-34158355 18FYWgp 1963
14 Gm14_48813386 48813386 16ZGVp Satt534 45763101-45763190 18FYVp 3000
16 Gm16_21944024 21944024 18FYVp Satt620 28837769-28837813 16FYVp
16FYWgp		 6894

Table S4

Candidate genes associated with soybean fertility and functional annotation"

单倍型区块
Haplotype blocks		 位点
Location		 候选基因
Candidate genes		 功能注释
Function annotation
BLK_29175719_29275719 Gm13_29225719 Glyma.13g177400 含有SBP-box，编码SBP-域，与DNA结合，参与调节开花
Contains the SBP-box, which encodes the SBP-domain, It binds DNA, may directly regulate AP1, and is involved in regulation of flowering
Glyma.13g177600 锌指结构域
Dof domain, zinc finger
Glyma.13g177800 核糖体蛋白S6家族蛋白
Ribosomal protein S6 family protein
Glyma.13g177900 核糖体蛋白S5家族蛋白
Ribosomal protein S5 family protein
Glyma.13g178100 含MIF4G域的蛋白/含MA3域的蛋白
MIF4G domain-containing protein / MA3 domain-containing protein
Glyma.13g178200 端粒酶激活蛋白Est1
Telomerase activating protein Est1
Glyma.13g178300 钙介导的信号传递
Calcium-mediated signaling
Glyma.13g178500 含VQ运动蛋白质
VQ motif-containing protein
Glyma.13g178600 核糖体蛋白L7Ae/L30e/S12e/Gadd45家族蛋白
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
Glyma.13g179000 对激活的(GTP结合的)p21cdc42Hs有特异性的酪氨酸激酶
Tyrosine kinase specific for activated (GTP-bound) p21cdc42Hs
BLK_30878620_30978620 Gm13_30928620 Glyma.13g195300 二腺苷和二磷酸肌醇聚磷酸酯水解酶
Diadenosine and diphosphoinositol polyphosphate phosphohydrolase
Glyma.13g195200 负向调节赤霉酸激活的信号通路
Negative regulation of abscisic acid-activated signaling pathway
Glyma.13g195600 富含亮氨酸的重复蛋白
Leucine-rich repeat-containing protein
Glyma.13g195700 肽酶S24/S26A/S26B/S26C家族蛋白
Peptidase S24/S26A/S26B/S26C family protein
Glyma.13g195800 转录因子GT-2和相关蛋白，含有三螺旋DNA结合/SANT结构域
Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain
Glyma.13g195900 ARM重复超家族蛋白
ARM repeat superfamily protein
Glyma.13g196200 真核细胞天冬氨酸蛋白酶家族蛋白
Eukaryotic aspartyl protease family protein
BLK-48763386_48863386 Gm14_48813386
Glyma.14g222500		 编码一种类似硫氧还蛋白的蛋白质。定位于叶绿体，并在热胁迫下重新分配到叶绿体包膜。它参与非宿主抗性和耐温性。
Encodes a thioredoxin-like protein. Localizes to chloroplasts and redistributes to the chloroplast envelope in response to heat stress. It is involved in non-host resistance and temperature tolerance.
Glyma.14g222600 α-淀粉酶
Alpha-amylase
Glyma.14g222700 脯氨酰寡肽酶家族
Protease family s9a oligopeptidase
Glyma.14g223000 多铜氧化酶I型家族相关蛋白
Multi-copper oxidase type Ifamily protein-related
Glyma.14g222800 脯氨酰寡肽酶家族蛋白
Prolyl oligopeptidase family protein
Glyma.14g223100 类似生物素的超家族蛋白
Ubiquitin-like superfamily protein
Glyma.14g223200 酰基-CoA合成酶
Acyl-CoA synthetase
Glyma.14g223300 四肽重复(TPR)类超家族蛋白
Tetratricopeptide repeat (TPR)-like superfamily protein
Glyma.14g223400 含BTB/POZ结构域的蛋白
BTB/POZ domain-containing protein
BLK_10093551_10293551 Gm16_10193551 Glyma.16g085700 含亮氨酸丰富的重复蛋白
Leucine-rich repeat-containing protein
Glyma.16g085500 线粒体转录终止因子家族蛋白
Mitochondrial transcription termination factor family protein

Table S5

Tissue-specific expression analysis of candidate genes"

基因
Genes		 根
Root		 嫩叶
Young_leaf		 花
Flower		 1cm荚
One cm pod		 10d种子
Seed 10DAF		 14d种子
Seed 14DAF		 21d种子
Seed 21DAF		 25d种子
Seed 25DAF		 28d种子
Seed 28DAF		 35d种子
Seed 35DAF
Glyma.13g177400 4 97 10 26 6 7 1 0 0 0
Glyma.13g177800 134 135 115 178 83 113 71 126 102 175
Glyma.13g178300 0 0 77 0 0 0 0 0 0 0
Glyma.13g178500 113 151 58 163 34 83 43 166 125 104
Glyma.13g179000 93 18 23 9 10 8 2 5 3 16
Glyma.13g195200 190 30 30 34 15 22 13 27 16 22
Glyma.13g195600 6 4 8 2 1 1 0 3 1 4
Glyma.13g195800 372 59 219 174 52 57 33 57 54 70
Glyma.13g195900 68 38 45 27 11 29 15 46 28 47
Glyma.14g223300 247 114 946 304 152 145 81 194 62 136
Glyma.14g223400 19 43 30 18 16 15 13 14 7 38
Glyma.16g085700 49 4 32 7 3 2 1 2 4 1

Table 5

Candidate genes associated with soybean fertility and functional annotation"

单倍型区块
Haplotype blocks		 候选基因
Candidate genes		 功能注释
Annotation		 同源基因功能预测
Function prediction
BLK_29175719_
29275719		 Glyma.13g177400 类Squamosa 启动子结合蛋白3
Squamosa promoter binding protein-like 3		 参与花期和营养变化的调控
Involved in the regulation of flowering and nutritional changes
Glyma.13g177600 锌指结构域
Dof domain, zinc finger		 光敏色素和隐花色素信号调节因子
Light-sensitive pigments and cryptoglobin signaling regulators
Glyma.13g177800 核糖体蛋白S6家族蛋白
Ribosomal protein S6 family protein		 参与花期调控并调节植物对赤霉素的反应
Involved in flowering regulation and regulates plant response to gibberellin
Glyma.13g178500 含VQ运动蛋白质
VQ motif-containing protein		 调节植物不同的发育过程, 包括对生物和非生物胁迫的反应、种子发育和光形态发生
Regulation of different developmental processes in plants, including responses to biotic and abiotic stresses, seed development and photomorphogenesis
BLK_30878620_
30978620		 Glyma.13g195200 负向调节脱落酸激活的信号通路
Negative regulation of abscisic acid-activated signaling pathway		 参与脱落酸信号传导调控的大豆的生长发育
Growth and development of soybean involved in the regulation of abscisic acid signaling
Glyma.13g195600 富含亮氨酸的重复蛋白
Leucine-rich repeat-containing protein		 调节植物发育、参与植物抗逆反应
Regulates plant development, participates in plant stress response
Glyma.13g195800 转录因子GT-2和相关蛋白, 含有三螺旋DNA结合/SANT结构域
Transcription factor GT-2 and related
proteins, contains trihelix DNA-binding/SANT domain		 调节植物发育和应对不同非生物压力的功能
Functions regulating plant development and coping with different abiotic stresses
Glyma.13g195900 ARM重复超家族蛋白
ARM repeat superfamily protein		 在非生物胁迫和植物生长发育有关
In abiotic stresses and plant growth and development related
BLK_48763386_
48863386		 Glyma.14g223300 四肽重复(TPR)类超家族蛋白
Tetratricopeptide repeat (TPR)-like
superfamily protein		 与激素信号、应激反应和开花时间的控制有关
Associated with hormonal signaling, stress response and control of flowering time
Glyma.14g223400 含BTB/POZ结构域的蛋白
BTB/POZ domain-containing protein		 调节大豆对嗜酸菌感染的反应
Regulation of soybean response to acidophilus infection
BLK_10093551_
10293551		 Glyma.16g085700 富含亮氨酸的重复蛋白
Leucine-rich repeat-containing protein		 调节植物发育、参与植物抗逆反应
Regulates plant development, participates in plant stress response

Fig. 3

Analysis of phenotypic data corresponding to different SNP type materials"

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