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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (6): 1558-1568.doi: 10.3724/SP.J.1006.2025.44166

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

Genome-wide association analysis and candidate genes prediction of flowering time and maturity date traits in soybean (Glycine max L.)

WANG Qiong1(), ZOU Dan-Xia1, CHEN Xing-Yun1, ZHANG Wei1, ZHANG Hong-Mei1, LIU Xiao-Qing1, JIA Qian-Ru1, WEI Li-Bin2, CUI Xiao-Yan1, CHEN Xin1, WANG Xue-Jun2,*(), CHEN Hua-Tao1,*()   

  1. 1Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong 226541, Jiangsu, China
  • Received:2024-09-29 Accepted:2025-03-26 Online:2025-06-12 Published:2025-04-07
  • Contact: *E-mail: cht@jaas.ac.cn;E-mail: wangxj4002@sina.com
  • Supported by:
    This study was supported by the Natural Science Foundation of Jiangsu Province(BK20220740);the Key Research and Development Program ofJiangsu Province(BE2022328);the Jiangsu Seed Industry Revitalization “Unveiling and Commanding” Project(JBGS [2021] 057)

Abstract:

Soybean is a typical short-day crop that is highly sensitive to photoperiod, with its cultivation and yield constrained by field photoperiodic conditions. In this study, we analyzed the flowering time and pod maturity date in 264 diverse soybean accessions. We examined the relationships between flowering-related traits and key agronomic traits, including protein content (PC), oil content (OC), 100-seed weight (HSW), and plant height (PH). A genome-wide association study (GWAS) identified 235 loci associated with flowering time and pod maturity date. Additionally, we predicted 14 candidate genes involved in the regulation of these traits, including 10 genes related to flowering time and 5 genes associated with pod maturity date. Notably, one gene exhibited pleiotropic effects on both traits. These findings provide valuable genomic insights into the regulatory pathways of flowering in soybean and offer a foundation for genetic improvement aimed at enhancing soybean adaptation across broader latitudinal regions.

Key words: soybean, flowering time, maturity date, GWAS, SNP markers

Fig. 1

Frequency distribution and phenotypic correlation analysis of flowering-related traits in soybean (a): distribution of pod flowering time in all accessions; (b): distribution of pod maturity date in all accessions; (c): correlation coefficients among flowering-related traits; (d): correlation coefficients among flowering-related traits, oil content (OC), protein content (PC), 100-seed weight (HSW), and plant height (PH). *, **, and *** indicate significant correlation at the 0.05, 0.01, and 0.001 probability levels, respectively. NJ21: Nanjing in 2019; NJ21: Nanjing in 2021; NJ22: Nanjing in 2022."

Fig. S1

Genome-wide association mapping of flowering time and maturity date in soybean (a)-(d): Manhattan plots of flowering time in BLUP, NJ19, NJ21 and NJ22, respectively; (e)-(h): Manhattan plots of pod maturity date in BLUP, NJ19, NJ21 and NJ22, respectively. The arrowheads indicate the positions of the known flowering genes. Chromosomes are depicted in different colors. The horizontal solid line corresponds to a ?log10(P) ≥ 5 threshold and SNPs above this line are plotted as orange dots, the dashed line corresponds to a significant threshold and SNPs above this line are plotted as red dots."

Fig. S2

QQ plots for GWAS of flowering time and maturity date traits (a)-(d): QQ plots of flowering time in BLUP, NJ19, NJ21 and NJ22, respectively; (e)-(h): QQ plots of pod maturity date in BLUP, NJ19, NJ21 and NJ22, respectively"

Table S1

Associated loci identified in this study and the overlapped information between known genes"

关联信号
Signal
最显著位点
Peak loci
染色体
Chromosome
位置
Position (bp)
P
P
环境
Environment
性状
Trait
基因名称
Gene
基因编号
Gene ID
开始
Start (bp)
结束
End (bp)
1_16.8 Chr.01: 16756203 01 16,756,203 2.82E-06 NJ19 开花时间Flowering time
1_19.8 Chr.01: 19797880 01 19,797,880 9.72E-06 NJ22 开花时间Flowering time
1_50.1 Chr.01: 50113489 01 50,113,489 6.79E-06 NJ22 开花时间 Flowering time
2_0.1 Chr.02: 90922 02 90,922 7.54E-06 NJ22 开花时间 Flowering time
2_0.2 Chr.02: 198739 02 198,739 9.87E-06 NJ21 开花时间 Flowering time
2_11.6 Chr.02: 11628488 02 11,628,488 5.55E-06 NJ19 开花时间 Flowering time AP1d Glyma.02G121600 12,084,714 120,890,43
2_13.6 Chr.02: 13554490 02 13,554,490 6.40E-06 NJ19 开花时间 Flowering time
2_30 Chr.02: 29989462 02 29,989,462 1.67E-06 NJ21 开花时间 Flowering time
2_39.4 Chr.02: 39385406 02 39,385,406 3.66E-06 NJ19 开花时间 Flowering time
3_1.1 Chr.03: 1131854 03 1,131,854 1.63E-06 NJ21 开花时间 Flowering time
3_7 Chr.03: 6956708 03 6,956,708 4.13E-06 NJ21 开花时间 Flowering time
3_11.4 Chr.03: 11386468 03 11,386,468 5.14E-06 NJ21 开花时间 Flowering time
3_17 Chr.03: 16963162 03 16,963,162 6.30E-06 NJ21 开花时间 Flowering time
3_33.2 Chr.03: 33154866 03 33,154,866 8.19E-06 NJ19 开花时间 Flowering time
3_33.6 Chr.03: 33551605 03 33,551,605 2.47E-07 NJ21 开花时间 Flowering time
3_40.6 Chr.03: 40635793 03 40,635,793 5.59E-06 NJ19 开花时间 Flowering time
3_40.6 Chr.03: 40635793 03 40,635,793 8.87E-06 NJ21 开花时间 Flowering time
3_43.3 Chr.03: 43294123 03 43,294,123 7.10E-07 NJ19 开花时间 Flowering time
4_24.1 Chr.04: 24085510 04 24,085,510 9.73E-06 NJ21 开花时间 Flowering time
5_0.1 Chr.05: 66789 05 66,789 5.31E-06 NJ21 开花时间 Flowering time
5_17.8 Chr.05: 17804685 05 17,804,685 8.57E-06 NJ22 开花时间 Flowering time
5_25.8 Chr.05: 25798559 05 25,798,559 7.67E-06 NJ21 开花时间 Flowering time
6_11.7 Chr.06: 11735349 06 11,735,349 2.02E-06 NJ21 开花时间 Flowering time
6_11.8 Chr.06: 11765729 06 11,765,729 6.82E-06 NJ21 开花时间 Flowering time
6_17.1 Chr.06: 17072269 06 17,072,269 1.11E-06 NJ22 开花时间 Flowering time
6_18.9 Chr.06: 18915994 06 18,915,994 5.23E-06 NJ22 开花时间 Flowering time
6_19 Chr.06: 19018252 06 19,018,252 5.71E-06 NJ22 开花时间 Flowering time QNE1 Glyma.06G204300 19,210,586 19,213,448
6_20.7 Chr.06: 20734601 06 20,734,601 4.66E-06 NJ21 开花时间 Flowering time E1 Glyma.06G207800 20,207,077 20,207,940
6_42.7 Chr.06: 42698406 06 42,698,406 2.05E-06 NJ21 开花时间 Flowering time
6_43 Chr.06: 43014590 06 43,014,590 9.48E-06 NJ21 开花时间 Flowering time
6_45.5 Chr.06: 45525901 06 45,525,901 7.14E-06 NJ22 开花时间 Flowering time
6_51.3 Chr.06: 51347716 06 51,347,716 6.05E-06 NJ21 开花时间 Flowering time
7_9.1 Chr.07: 9139724 07 9,139,724 2.93E-06 NJ21 开花时间 Flowering time
7_9.3 Chr.07: 9281382 07 9,281,382 1.16E-06 NJ21 开花时间 Flowering time
7_9.4 Chr.07: 9412365 07 9,412,365 6.75E-06 NJ21 开花时间 Flowering time
9_16.7 Chr.09: 16690457 09 16,690,457 1.45E-06 NJ22 开花时间 Flowering time
9_33.5 Chr.09: 33543971 09 33,543,971 4.58E-06 BLUP 开花时间 Flowering time
10_13.9 Chr.10: 13877946 10 13,877,946 8.76E-06 NJ19 开花时间 Flowering time
10_14.1 Chr.10: 14063324 10 14,063,324 2.22E-06 NJ19 开花时间 Flowering time
10_14.4 Chr.10: 14393613 10 14,393,613 1.59E-06 NJ19 开花时间 Flowering time
10_18.5 Chr.10: 18549131 10 18,549,131 9.70E-06 NJ19 开花时间 Flowering time
10_29.1 Chr.10: 29145960 10 29,145,960 3.23E-06 NJ19 开花时间 Flowering time
10_44.9 Chr.10: 44948729 10 44,948,729 1.75E-06 NJ21 开花时间 Flowering time
10_45 Chr.10: 45045188 10 45,045,188 7.64E-07 NJ21 开花时间 Flowering time GI Glyma.10G221500 45,294,735 45,316,121
11_6 Chr.11: 6010522 11 6,010,522 7.50E-07 NJ22 开花时间 Flowering time
11_24.4 Chr.11: 24387887 11 24,387,887 7.46E-07 NJ21 开花时间 Flowering time
11_26.5 Chr.11: 26451428 11 26,451,428 2.39E-06 NJ21 开花时间 Flowering time
13_41.8 Chr.13: 41789036 13 41,789,036 8.54E-06 BLUP 开花时间 Flowering time
13_41.9 Chr.13: 41873651 13 41,873,651 9.06E-07 BLUP 开花时间 Flowering time
14_4.9 Chr.14: 4908776 14 4,908,776 1.69E-06 NJ21 开花时间 Flowering time
14_30.3 Chr.14: 30334422 14 30,334,422 9.52E-06 NJ21 开花时间 Flowering time
14_48.4 Chr.14: 48432986 14 48,432,986 6.47E-06 BLUP 开花时间 Flowering time
14_48.4 Chr.14: 48432986 14 48,432,986 3.56E-06 NJ19 开花时间 Flowering time
15_1.6 Chr.15: 1649953 15 1,649,953 2.83E-06 BLUP 开花时间 Flowering time
15_1.7 Chr.15: 1650236 15 1,650,236 9.40E-06 BLUP 开花时间 Flowering time
15_17.9 Chr.15: 17862246 15 17,862,246 3.73E-06 BLUP 开花时间 Flowering time
15_17.9 Chr.15: 17862246 15 17,862,246 4.67E-07 NJ22 开花时间 Flowering time
15_37.6 Chr.15: 37562128 15 37,562,128 7.23E-06 NJ21 开花时间 Flowering time
15_39.5 Chr.15: 39496561 15 39,496,561 1.71E-07 NJ19 开花时间 Flowering time
16_4.6 Chr.16: 4620056 16 4,620,056 2.95E-06 BLUP 开花时间 Flowering time FT5a Glyma.16G044100 4,135,885 4,137,742
16_5.3 Chr.16: 5275907 16 5,275,907 1.13E-06 BLUP 开花时间 Flowering time
16_5.3 Chr.16: 5275907 16 5,275,907 7.70E-06 NJ21 开花时间 Flowering time
16_5.4 Chr.16: 5357573 16 5,357,573 3.15E-06 BLUP 开花时间 Flowering time
16_5.4 Chr.16: 5363834 16 5,363,834 1.05E-06 NJ21 开花时间 Flowering time
16_5.7 Chr.16: 5719462 16 5,719,462 7.64E-06 NJ21 开花时间 Flowering time
16_5.7 Chr.16: 5748536 16 5,748,536 2.87E-06 BLUP 开花时间 Flowering time
16_22.2 Chr.16: 22180805 16 22,180,805 8.54E-06 BLUP 开花时间 Flowering time
16_24.9 Chr.16: 24918284 16 24,918,284 3.86E-06 NJ21 开花时间 Flowering time
16_29.8 Chr.16: 29817877 16 29,817,877 1.47E-06 NJ21 开花时间 Flowering time
16_32.5 Chr.16: 32485435 16 32,485,435 4.40E-06 BLUP 开花时间 Flowering time
17_6.6 Chr.17: 6600113 17 6,600,113 1.78E-06 NJ21 开花时间 Flowering time MDE17 Glyma.17G081200 6,312,563 6,321,583
17_15.3 Chr.17: 15293172 17 15,293,172 1.01E-07 NJ21 开花时间 Flowering time
17_15.4 Chr.17: 15392244 17 15,392,244 7.11E-07 NJ21 开花时间 Flowering time
17_15.5 Chr.17: 15476791 17 15,476,791 2.01E-06 NJ21 开花时间 Flowering time
17_15.6 Chr.17: 15628996 17 15,628,996 3.97E-06 NJ21 开花时间 Flowering time
17_15.7 Chr.17: 15716574 17 15,716,574 1.18E-07 NJ21 开花时间 Flowering time
17_15.8 Chr.17: 15819838 17 15,819,838 8.27E-08 NJ21 开花时间 Flowering time
17_15.9 Chr.17: 15859190 17 15,859,190 7.81E-08 NJ21 开花时间 Flowering time
17_16.1 Chr.17: 16053819 17 16,053,819 6.26E-08 NJ21 开花时间 Flowering time
17_16.2 Chr.17: 16182668 17 16,182,668 1.67E-06 NJ21 开花时间 Flowering time
17_16.3 Chr.17: 16341492 17 16,341,492 1.51E-06 NJ21 开花时间 Flowering time
17_16.4 Chr.17: 16444519 17 16,444,519 1.28E-06 NJ21 开花时间 Flowering time
17_16.5 Chr.17: 16526522 17 16,526,522 6.02E-07 NJ21 开花时间 Flowering time
17_16.6 Chr.17: 16631273 17 16,631,273 6.19E-07 NJ21 开花时间 Flowering time
17_16.7 Chr.17: 16680555 17 16,680,555 1.28E-06 NJ21 开花时间 Flowering time
17_16.8 Chr.17: 16814325 17 16,814,325 4.77E-06 NJ21 开花时间 Flowering time
17_16.9 Chr.17: 16931162 17 16,931,162 1.38E-06 NJ21 开花时间 Flowering time
17_17 Chr.17: 17028485 17 17,028,485 1.28E-06 NJ21 开花时间 Flowering time
17_17.2 Chr.17: 17158996 17 17,158,996 4.90E-06 NJ21 开花时间 Flowering time
17_17.3 Chr.17: 17292001 17 17,292,001 1.28E-06 NJ21 开花时间 Flowering time
17_17.4 Chr.17: 17352058 17 17,352,058 1.28E-06 NJ21 开花时间 Flowering time
17_17.5 Chr.17: 17494501 17 17,494,501 1.38E-06 NJ21 开花时间 Flowering time
17_17.6 Chr.17: 17584756 17 17,584,756 1.38E-06 NJ21 开花时间 Flowering time
17_17.7 Chr.17: 17683919 17 17,683,919 1.28E-06 NJ21 开花时间 Flowering time
17_18 Chr.17: 17963083 17 17,963,083 1.67E-06 NJ21 开花时间 Flowering time
18_0.7 Chr.18: 687088 18 687,088 1.23E-06 NJ21 开花时间 Flowering time
18_0.8 Chr.18: 841400 18 841,400 5.18E-07 NJ21 开花时间 Flowering time
18_0.8 Chr.18: 843464 18 843,464 4.83E-07 NJ19 开花时间 Flowering time
18_0.9 Chr.18: 861675 18 861,675 4.13E-07 NJ19 开花时间 Flowering time
18_0.9 Chr.18: 879311 18 879,311 2.63E-06 NJ21 开花时间 Flowering time
18_1.6 Chr.18: 1628084 18 1,628,084 1.65E-06 NJ21 开花时间 Flowering time
18_1.7 Chr.18: 1707431 18 1,707,431 3.47E-06 NJ21 开花时间 Flowering time
18_1.8 Chr.18: 1844386 18 1,844,386 8.14E-06 NJ21 开花时间 Flowering time
18_1.9 Chr.18: 1925015 18 1,925,015 4.75E-07 NJ21 开花时间 Flowering time
18_2 Chr.18: 2029511 18 2,029,511 9.73E-07 NJ21 开花时间 Flowering time
18_36.4 Chr.18: 36385829 18 36,385,829 4.91E-06 NJ21 开花时间 Flowering time
18_50.3 Chr.18: 50275974 18 50,275,974 5.27E-06 NJ19 开花时间 Flowering time
18_51.6 Chr.18: 51622787 18 51,622,787 4.53E-06 NJ21 开花时间 Flowering time SOC1a Glyma.18G224500 51,203,136 51,222,128
18_52.7 Chr.18: 52659743 18 52,659,743 4.41E-07 NJ21 开花时间 Flowering time
18_52.9 Chr.18: 52944567 18 52,944,567 9.39E-06 BLUP 开花时间 Flowering time
18_53.7 Chr.18: 53676491 18 53,676,491 3.36E-06 NJ21 开花时间 Flowering time
18_53.8 Chr.18: 53808169 18 53,808,169 9.33E-06 NJ21 开花时间 Flowering time
19_18.1 Chr.19: 18069101 19 18,069,101 4.91E-06 NJ22 开花时间 Flowering time
19_44.9 Chr.19: 44925371 19 44,925,371 8.80E-06 NJ22 开花时间 Flowering time
19_45.4 Chr.19: 45368289 19 45,368,289 1.86E-06 NJ22 开花时间 Flowering time
19_45.5 Chr.19: 45456935 19 45,456,935 2.71E-06 NJ22 开花时间 Flowering time
20_15.1 Chr.20: 15061974 20 15,061,974 2.70E-06 NJ21 开花时间 Flowering time
20_34.9 Chr.20: 34852481 20 34,852,481 1.14E-06 BLUP 开花时间 Flowering time
20_34.9 Chr.20: 34852481 20 34,852,481 5.46E-06 NJ21 开花时间 Flowering time
1_53.5 Chr.01: 53455419 1 53,455,419 9.52E-06 NJ22 成熟期 Maturity date
3_24.9 Chr.03: 24877913 3 24,877,913 3.16E-06 NJ21 成熟期 Maturity date
3_38.2 Chr.03: 38239475 3 38,239,475 7.23E-06 NJ22 成熟期 Maturity date
3_40.6 Chr.03: 40648275 3 40,648,275 6.21E-06 NJ21 成熟期 Maturity date
4_13.3 Chr.04: 13315724 4 13,315,724 4.66E-06 BLUP 成熟期 Maturity date
5_7.8 Chr.05: 7788997 5 7,788,997 4.09E-06 BLUP 成熟期 Maturity date
5_39.9 Chr.05: 39904246 5 39,904,246 2.86E-06 NJ21 成熟期 Maturity date
6_15.2 Chr.06: 15190257 6 15,190,257 7.35E-06 BLUP 成熟期 Maturity date
6_31.6 Chr.06: 31617314 6 31,617,314 7.32E-06 NJ19 成熟期 Maturity date
6_31.6 Chr.06: 31628655 6 31,628,655 7.33E-06 NJ22 成熟期 Maturity date
6_32.7 Chr.06: 32672780 6 32,672,780 7.58E-06 NJ19 成熟期 Maturity date
6_51.3 Chr.06: 51320491 6 51,320,491 6.32E-08 NJ21 成熟期 Maturity date
7_20.3 Chr.07: 20259235 7 20,259,235 5.12E-06 BLUP 成熟期 Maturity date
8_24 Chr.08: 23981243 8 23,981,243 1.96E-06 BLUP 成熟期 Maturity date
8_38.8 Chr.08: 38794063 8 38,794,063 4.41E-06 BLUP 成熟期 Maturity date
8_38.9 Chr.08: 38878988 8 38,878,988 3.73E-06 NJ21 成熟期 Maturity date
8_38.9 Chr.08: 38884153 8 38,884,153 1.09E-06 BLUP 成熟期 Maturity date
9_32.5 Chr.09: 32534471 9 32,534,471 8.01E-06 NJ22 成熟期 Maturity date
10_4 Chr.10: 3977824 10 3,977,824 7.76E-06 BLUP 成熟期 Maturity date
10_4 Chr.10: 4023746 10 4,023,746 4.71E-06 NJ22 成熟期 Maturity date
10_43.4 Chr.10: 43371195 10 43,371,195 4.43E-08 BLUP 成熟期 Maturity date
11_24.6 Chr.11: 24616338 11 24,616,338 5.72E-06 BLUP 成熟期 Maturity date
11_25.4 Chr.11: 25447626 11 25,447,626 3.71E-06 NJ22 成熟期 Maturity date
11_25.4 Chr.11: 25448017 11 25,448,017 4.33E-07 BLUP 成熟期 Maturity date
11_25.5 Chr.11: 25452041 11 25,452,041 1.93E-06 BLUP 成熟期 Maturity date
11_25.5 Chr.11: 25452041 11 25,452,041 7.79E-06 NJ22 成熟期 Maturity date
11_25.9 Chr.11: 25916809 11 25,916,809 2.96E-06 NJ22 成熟期 Maturity date
11_25.9 Chr.11: 25937388 11 25,937,388 1.75E-06 BLUP 成熟期 Maturity date
11_26 Chr.11: 25950712 11 25,950,712 7.50E-06 BLUP 成熟期 Maturity date
11_26 Chr.11: 25971580 11 25,971,580 1.41E-06 NJ22 成熟期 Maturity date
11_26 Chr.11: 25992150 11 25,992,150 4.75E-06 NJ21 成熟期 Maturity date
12_20.7 Chr.12: 20727547 12 20,727,547 6.38E-06 NJ19 成熟期 Maturity date
12_28.5 Chr.12: 28523263 12 28,523,263 7.51E-06 NJ22 成熟期 Maturity date
12_35.6 Chr.12: 35626973 12 35,626,973 2.72E-06 NJ19 成熟期 Maturity date
12_35.7 Chr.12: 35655153 12 35,655,153 2.10E-06 BLUP 成熟期 Maturity date
12_35.7 Chr.12: 35666432 12 35,666,432 2.60E-06 NJ19 成熟期 Maturity date
13_11 Chr.13: 10977075 13 10,977,075 9.32E-06 BLUP 成熟期 Maturity date
13_16.3 Chr.13: 16348650 13 16,348,650 7.87E-07 NJ19 成熟期 Maturity date
13_23.9 Chr.13: 23897160 13 23,897,160 7.14E-06 NJ21 成熟期 Maturity date
13_33 Chr.13: 33044518 13 33,044,518 3.72E-06 NJ21 成熟期 Maturity date
13_44.5 Chr.13: 44471214 13 44,471,214 9.06E-06 NJ21 成熟期 Maturity date
13_44.9 Chr.13: 44921511 13 44,921,511 6.89E-07 NJ21 成熟期 Maturity date
13_45 Chr.13: 45026819 13 45,026,819 3.37E-07 NJ21 成熟期 Maturity date
13_45.1 Chr.13: 45057706 13 45,057,706 1.31E-06 NJ21 成熟期 Maturity date
14_36.2 Chr.14: 36158402 14 36,158,402 2.59E-06 NJ21 成熟期 Maturity date
15_16.2 Chr.15: 16178266 15 16,178,266 5.94E-06 NJ21 成熟期 Maturity date
15_48.5 Chr.15: 48503783 15 48,503,783 4.93E-06 NJ21 成熟期 Maturity date
15_51.7 Chr.15: 51674778 15 51,674,778 3.43E-06 NJ22 成熟期 Maturity date
16_29.3 Chr.16: 29264471 16 29,264,471 3.64E-06 BLUP 成熟期 Maturity date
17_15.3 Chr.17: 15293172 17 15,293,172 8.12E-06 NJ21 成熟期 Maturity date
17_15.4 Chr.17: 15392244 17 15,392,244 2.69E-06 NJ21 成熟期 Maturity date
17_15.7 Chr.17: 15716574 17 15,716,574 8.85E-07 NJ21 成熟期 Maturity date
17_15.8 Chr.17: 15819838 17 15,819,838 5.76E-07 NJ21 成熟期 Maturity date
17_15.9 Chr.17: 15859190 17 15,859,190 9.86E-07 NJ21 成熟期 Maturity date
17_16.1 Chr.17: 16053819 17 16,053,819 1.32E-06 NJ21 成熟期 Maturity date
17_16.5 Chr.17: 16526522 17 16,526,522 8.52E-06 NJ21 成熟期 Maturity date
17_18 Chr.17: 18037446 17 18,037,446 7.41E-06 NJ21 成熟期 Maturity date
17_19.4 Chr.17: 19389681 17 19,389,681 8.03E-06 NJ21 成熟期 Maturity date
17_21.3 Chr.17: 21305063 17 21,305,063 1.56E-06 NJ21 成熟期 Maturity date
17_21.7 Chr.17: 21677960 17 21,677,960 7.10E-06 NJ21 成熟期 Maturity date
17_24.1 Chr.17: 24091653 17 24,091,653 3.33E-07 NJ21 成熟期 Maturity date
17_24.3 Chr.17: 24307894 17 24,307,894 3.43E-08 NJ21 成熟期 Maturity date
17_24.4 Chr.17: 24437170 17 24,437,170 2.72E-07 NJ21 成熟期 Maturity date
17_24.5 Chr.17: 24517740 17 24,517,740 6.14E-07 NJ21 成熟期 Maturity date
17_24.6 Chr.17: 24596822 17 24,596,822 2.97E-06 NJ21 成熟期 Maturity date
17_24.7 Chr.17: 24728155 17 24,728,155 2.90E-06 NJ21 成熟期 Maturity date
17_24.9 Chr.17: 24941611 17 24,941,611 1.80E-06 NJ21 成熟期 Maturity date
17_25 Chr.17: 25022937 17 25,022,937 1.06E-07 NJ21 成熟期 Maturity date
17_25.1 Chr.17: 25122017 17 25,122,017 9.61E-08 NJ21 成熟期 Maturity date
17_25.3 Chr.17: 25315919 17 25,315,919 9.81E-08 NJ21 成熟期 Maturity date
17_25.4 Chr.17: 25364731 17 25,364,731 8.51E-08 NJ21 成熟期 Maturity date
17_25.6 Chr.17: 25604042 17 25,604,042 2.97E-06 NJ21 成熟期 Maturity date
17_25.7 Chr.17: 25729099 17 25,729,099 6.43E-08 NJ21 成熟期 Maturity date
17_26.1 Chr.17: 26132875 17 26,132,875 1.50E-07 NJ21 成熟期 Maturity date
17_26.3 Chr.17: 26343874 17 26,343,874 3.43E-06 NJ21 成熟期 Maturity date
17_26.4 Chr.17: 26414971 17 26,414,971 8.51E-08 NJ21 成熟期 Maturity date
17_26.5 Chr.17: 26500711 17 26,500,711 2.97E-06 NJ21 成熟期 Maturity date
17_26.6 Chr.17: 26570104 17 26,570,104 7.37E-06 NJ21 成熟期 Maturity date
17_26.8 Chr.17: 26766840 17 26,766,840 1.61E-06 NJ21 成熟期 Maturity date
17_27.1 Chr.17: 27112154 17 27,112,154 9.17E-07 NJ21 成熟期 Maturity date
17_27.3 Chr.17: 27303504 17 27,303,504 8.51E-08 NJ21 成熟期 Maturity date
17_27.4 Chr.17: 27422112 17 27,422,112 2.97E-06 NJ21 成熟期 Maturity date
17_27.6 Chr.17: 27598440 17 27,598,440 2.97E-06 NJ21 成熟期 Maturity date
17_27.7 Chr.17: 27658349 17 27,658,349 3.20E-06 NJ21 成熟期 Maturity date
17_28 Chr.17: 27974644 17 27,974,644 5.78E-06 NJ21 成熟期 Maturity date
17_28.1 Chr.17: 28115569 17 28,115,569 2.84E-06 NJ21 成熟期 Maturity date
17_28.5 Chr.17: 28544029 17 28,544,029 4.05E-06 NJ21 成熟期 Maturity date
17_28.6 Chr.17: 28596114 17 28,596,114 3.51E-06 NJ21 成熟期 Maturity date
17_28.7 Chr.17: 28709764 17 28,709,764 2.97E-06 NJ21 成熟期 Maturity date
17_28.8 Chr.17: 28799844 17 28,799,844 2.97E-06 NJ21 成熟期 Maturity date
17_28.9 Chr.17: 28859690 17 28,859,690 2.97E-06 NJ21 成熟期 Maturity date
17_29 Chr.17: 28959749 17 28,959,749 8.57E-08 NJ21 成熟期 Maturity date
17_29.1 Chr.17: 29098100 17 29,098,100 1.28E-06 NJ21 成熟期 Maturity date
17_29.4 Chr.17: 29392667 17 29,392,667 8.57E-08 NJ21 成熟期 Maturity date
17_29.8 Chr.17: 29823861 17 29,823,861 4.17E-06 NJ21 成熟期 Maturity date
17_30.3 Chr.17: 30343066 17 30,343,066 2.97E-06 NJ21 成熟期 Maturity date
17_30.4 Chr.17: 30361157 17 30,361,157 8.57E-08 NJ21 成熟期 Maturity date
17_30.5 Chr.17: 30472789 17 30,472,789 7.80E-08 NJ21 成熟期 Maturity date
17_30.6 Chr.17: 30610259 17 30,610,259 1.71E-08 NJ21 成熟期 Maturity date
17_30.7 Chr.17: 30654151 17 30,654,151 7.48E-07 NJ21 成熟期 Maturity date
17_31 Chr.17: 31004770 17 31,004,770 5.47E-07 NJ21 成熟期 Maturity date
17_31.2 Chr.17: 31226723 17 31,226,723 1.71E-08 NJ21 成熟期 Maturity date
17_31.3 Chr.17: 31348809 17 31,348,809 7.48E-07 NJ21 成熟期 Maturity date
17_31.4 Chr.17: 31369154 17 31,369,154 7.48E-07 NJ21 成熟期 Maturity date
17_32.9 Chr.17: 32923007 17 32,923,007 2.01E-06 NJ21 成熟期 Maturity date
17_35.5 Chr.17: 35478288 17 35,478,288 3.01E-06 NJ21 成熟期 Maturity date
18_11.9 Chr.18: 11946154 18 11,946,154 7.23E-06 NJ22 成熟期 Maturity date
19_5.8 Chr.19: 5769650 19 5,769,650 7.46E-06 NJ19 成熟期 Maturity date
19_35.6 Chr.19: 35579170 19 35,579,170 6.67E-06 NJ21 成熟期 Maturity date
19_44.7 Chr.19: 44659389 19 44,659,389 5.30E-06 NJ21 成熟期 Maturity date
19_45.1 Chr.19: 45078893 19 45,078,893 3.16E-06 NJ21 成熟期 Maturity date
19_45.2 Chr.19: 45241319 19 45,241,319 7.93E-06 NJ21 成熟期 Maturity date
19_45.3 Chr.19: 45271120 19 45,271,120 2.93E-06 NJ21 成熟期 Maturity date
20_6.7 Chr.20: 6685140 20 6,685,140 9.82E-06 BLUP 成熟期 Maturity date
20_6.7 Chr.20: 6685140 20 6,685,140 4.44E-06 NJ19 成熟期 Maturity date
20_14.3 Chr.20: 14255074 20 14,255,074 8.23E-06 NJ22 成熟期 Maturity date

Table 1

Flowering-related trait association signals detected across multiple environments or traits"

关联信号
Signal
最显著位点
Peak loci
染色体
Chr.
位置
Position (bp)
P
P-value
环境
Environment
性状
Trait
2_0.2 Chr.02: 198739 02 198,739 9.87E-06 NJ22, NJ21 开花时间 Flowering time
3_40.6 Chr.03: 40635793 03 40,635,793 5.59E-06 NJ19, NJ21 开花时间 Flowering time
6_31.6 Chr.06: 31617314 06 31,617,314 7.32E-06 NJ19, NJ22 成熟期 Maturity date
6_51.3 Chr.06: 51320491 06 51,320,491 6.32E-08 NJ21 开花时间, 成熟期
Flowering time, maturity date
8_38.9 Chr.08: 38878988 08 38,878,988 3.73E-06 NJ21, BLUP 成熟期 Maturity date
10_4 Chr.10: 3977824 10 3,977,824 7.76E-06 NJ22, BLUP 成熟期 Maturity date
11_25.4 Chr.11: 25447626 11 25,447,626 3.71E-06 NJ22, BLUP 成熟期 Maturity date
11_26 Chr.11: 25950712 11 25,950,712 7.50E-06 NJ22, NJ21, BLUP 成熟期 Maturity date
12_35.7 Chr.12: 35655153 12 35,655,153 2.10E-06 NJ19, BLUP 成熟期 Maturity date
14_48.4 Chr.14: 48432986 14 48,432,986 6.47E-06 NJ19, BLUP 开花时间 Flowering time
15_17.9 Chr.15: 17862246 15 17,862,246 3.73E-06 NJ22, BLUP 开花时间 Flowering time
16_5.3 Chr.16: 5275907 16 5,275,907 1.13E-06 NJ21, BLUP 开花时间 Flowering time
16_5.7 Chr.16: 5719462 16 5,719,462 7.64E-06 NJ21, BLUP 开花时间 Flowering time
18_0.8 Chr.18: 841400 18 841,400 5.18E-07 NJ19, NJ21 开花时间 Flowering time
20_6.7 Chr.20: 6685140 20 6,685,140 9.82E-06 NJ19, BLUP 成熟期 Maturity date
20_34.9 Chr.20: 34852481 20 34,852,481 1.14E-06 NJ21, BLUP 开花时间 Flowering time

Table 2

Candidate genes predicted to be involved in the regulation of flowering time and maturity date"

Fig. 2

Identification of candidate genes for the associated loci Chr18: 841400 (a): local Manhattan plot and linkage disequilibrium heatmap of Chr.18: 841400; (b): expression pattern of candidate genes for Chr.18: 841400; (c): haplotypes of three loci, Chr.18: 743337, Chr.18: 850114, and Chr.18: 895954, among soybean natural variations. SAM: shoot apical meristem."

Fig. 3

Identification of candidate genes for the associated loci Chr.03: 40635793 (a): local Manhattan plot and linkage disequilibrium heatmap of Chr.03: 40635793; (b): expression pattern of candidate genes for Chr.03: 40635793; (c): haplotypes among soybean natural variations. SAM: shoot apical meristem."

Fig. 4

Identification of candidate genes for the associated loci Chr.16: 5275907 (a): local Manhattan plot and linkage disequilibrium heatmap of Chr.16: 5275907; (b): expression pattern of candidate genes for Chr.16: 5275907; (c): haplotypes among soybean natural variations. SAM: shoot apical meristem."

Table S2

Expression patterns of candidate genes related to maturity date in multiple tissues"

基因编号
Gene ID

Root
根毛
Root hairs
根瘤
Nodules

Stem

Leaves
茎尖分生组织
SAM

Flower

Pod
种子
Seed
Glyma.10G043300 7.66 7.77 8.50 11.15 28.58 9.85 27.42 12.39 12.55
Glyma.10G043500 0 0 0 0.08 0.04 0.06 0.09 0.05 0.02
Glyma.10G043600 9.71 11.05 10.49 8.77 6.97 8.27 11.12 9.09 9.43
Glyma.10G043700 18.14 2.15 1.65 13.31 14.26 12.31 10.84 4.27 16.52
Glyma.10G043900 0.34 1.35 1.53 1.71 2.45 2.30 1.73 2.37 2.44
Glyma.10G044400 26.50 8.28 9.43 6.40 21.92 3.95 9.31 5.20 2.39
Glyma.10G044800 0.10 0.89 4.63 5.42 0 0.05 21.12 1.24 17.61
Glyma.10G044900 0 0.05 0.09 0.63 0.03 0 1.20 0.02 0.43
Glyma.10G045000 12.59 4.32 3.34 2.29 0.11 3.05 6.19 1.48 9.05
Glyma.10G045100 1.37 1.59 2.83 0.79 0.08 2.31 0.67 0.08 0.07
Glyma.10G045200 1.51 0.33 0.20 0 0 0 0 0 0
Glyma.10G045600 1.82 2.80 5.81 5.92 2.75 4.98 1.64 7.31 10.45
Glyma.10G045700 0.81 0.44 0.15 0.41 0.98 15.00 2.44 7.34 2.52
Glyma.12G194400 1.67 0.73 0.01 1.48 8.26 16.99 10.74 9.34 11.65
Glyma.12G196100 0.35 0.43 0.58 0.12 0 0.59 0.52 0.15 0.82
Glyma.12G196200 1.16 2.74 3.21 1.25 64.15 1.61 84.01 1.84 2.34
Glyma.06G324300 122.59 213.10 98.41 129.56 7.69 68.99 5.38 27.69 89.66
Glyma.06G324500 10.04 8.88 8.39 8.93 9.40 6.93 14.55 6.63 8.30
Glyma.06G324700 6.12 9.86 9.39 8.83 21.79 34.41 6.63 12.94 20.16
Glyma.06G324800 2.60 4.08 3.33 6.50 3.69 5.32 3.93 6.68 4.53
Glyma.06G325000 0 0 0 0 0 0 0 0 0
Glyma.06G325100 0.35 1.16 0.28 1.59 19.50 7.62 2.49 4.93 4.54
Glyma.06G325300 103.78 82.57 48.05 104.96 33.73 67.34 25.18 60.08 16.79
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