Analysis of Soybean Pod Dehiscence Habit Based on Whole Genome Association Analysis and Genetic Diversity

doi:10.13560/j.cnki.biotech.bull.1985.2024-0358

Abstract

Abstract:

Objective Investigating molecular mechanisms and germplasm resources of pod dehiscence resistance would provide evidence for uncovering the genetic and domestication mechanism of pod dehiscence resistance in soybean as well as accelerating the breeding of new soybean varieties with pod dehiscence resistance on southern China. Method With genome-wide association studies (GWAS) and genetic diversity analysis between wild and cultivated soybean populations, the genes related to soybean pod dehiscence habit were explored. The phenotype determination of 302 soybean varieties were conducted, and GWAS was performed using 95 ‍744 single nucleotide polymorphism markers in 2 years. And analysis of genetic diversity in QTL segment was carried, with the resequencing data of 1 308 cultivated soybeans and 203 wild soybeans. Result Through GWAS, three QTL loci that explained greater than 10% of the observed phenotypic variance were detected, namely qPdh-Chr08 (Gm08: 3048312), qPdh-Chr15 (Gm15: 312814), and qPdh-Chr16 (Gm16: 29951529). Among them, qPdh-Chr16 was known gene pdh1 (Pod dehiscence habit 1). Combining the resequencing data of wild and cultivated soybeans, it was found that there were population differentiation sequences caused by artificial selection in regions of qPdh-Chr08 and qPdh-Chr15. And two important candidate genes Glyma.08G038600 and Glyma.15G003600 were identified based on population differentiation sequences analysis. Through functional annotation, it was found that these two genes were involved in the metabolism of auxin and lignin, respectively. Conclusion Two new QTL loci qPdh-Chr08 and qPdh-Chr15 of soybean pod dehiscence habit were detected using two-year’s data. Differential genes between wild and cultivated soybean are identified within the QTL region, and two important candidate genes are ultimately identified.

Key words: soybeans, pod dehiscence habit, whole genome association analysis, genetic diversity, crop domestication

SONG Ying-pei, WANG Can, ZHOU Hui-wen, KONG Ke-ke, XU Meng-ge, WANG Rui-kai. Analysis of Soybean Pod Dehiscence Habit Based on Whole Genome Association Analysis and Genetic Diversity[J]. Biotechnology Bulletin, 2025, 41(2): 97-106.

Figures/Tables 5

References 28

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QTL名称 QTL name	SNP名称 SNP name	染色体 Chromosome	位置 Position/bp	最小等位基因频率 MAF	P值 P value	表型解释率 R²/%
qPdh-Chr08	Gm08_3048312	8	3 048 312	0.24	3.50E-06	13.2
qPdh-Chr15	Gm15_312814	15	312 814	0.18	1.32E-06	10.7
qPdh-Chr16（qPdh1）	Gm16_29951529	16	29 951 529	0.36	3.20E-17	36.6
qPdh-Chr13	Gm13_13702059	13	13 702 059	0.37	1.32E-07	0.5
qPdh-Chr18	Gm18_55699653	18	55 699 653	0.43	2.42E-06	1.8

QTL名称 QTL name	SNP名称 SNP name	染色体 Chromosome	位置 Position/bp	最小等位基因频率 MAF	P值 P value	表型解释率 R²/%
qPdh-Chr08	Gm08_3048312	8	3 048 312	0.24	3.50E-06	13.2
qPdh-Chr15	Gm15_312814	15	312 814	0.18	1.32E-06	10.7
qPdh-Chr16（qPdh1）	Gm16_29951529	16	29 951 529	0.36	3.20E-17	36.6
qPdh-Chr13	Gm13_13702059	13	13 702 059	0.37	1.32E-07	0.5
qPdh-Chr18	Gm18_55699653	18	55 699 653	0.43	2.42E-06	1.8

QTL名称 QTL name	基因 Gene	基因注释 Gene annotation	基因位置 Gene location
qPdh-Chr08	Glyma.08G037400	Tesmin/TSO1样CXC结构域，富含半胱氨酸的结构域 Tesmin/TSO1-like CXC domain， and cysteine-rich domain	Chr.8：29 50 964-2 957 163
qPdh-Chr08	Glyma.08G037500	-	Chr.8：2 959 084-2 961 115
qPdh-Chr08	Glyma.08G037600	-	Chr.8：2 962 310-2 966 347
qPdh-Chr08	Glyma.08G037700	-	Chr.8：2 967 634-2 971 428
qPdh-Chr08	Glyma.08G037800	-	Chr.8：2 973 386-2 977 716
qPdh-Chr08	Glyma.08G037900	动力蛋白轻链1型 Dynein light chain type 1	Chr.8：2 978 411-2 979 627
qPdh-Chr08	Glyma.08G038000	无注释 No annotation	Chr.8：2 987 443-2 988 562
qPdh-Chr08	Glyma.08G038100	S26信号肽酶，S26肽酶 S26 signal peptidase， peptidase S26	Chr.8：2 988 728-2 991 924
qPdh-Chr08	Glyma.08G038200	PPR重复序列 PPR repeat	Chr.8：2 992 820-2 996 514
qPdh-Chr08	Glyma.08G038300	-	Chr.8：2 997 737-2 999 328
qPdh-Chr08	Glyma.08G038400	转录抑制因子 Transcriptional repressor	Chr.8：3 012 183-3 013 602
qPdh-Chr08	Glyma.08G038500	-	Chr.8：3 018 702-3 019 975
qPdh-Chr08	Glyma.08G038600	黄素结合单加氧酶 Flavin-binding monooxygenase-like	Chr.8：3 029 349-3 032 467
qPdh-Chr08	Glyma.08G038700	MVB通路中Vps4活性的调节因子 Regulator of Vps4 activity in the MVB pathway	Chr.8：3 038 024-3 042 749
qPdh-Chr08	Glyma.08G038800	-	Chr.8：3 043 080-3 044 565
qPdh-Chr08	Glyma.08G038900	Ras基因家族 Ras family	Chr.8：3 046 616-3 047 930
qPdh-Chr08	Glyma.08G039000	-	Chr.8：3 053 220-3 053 733
qPdh-Chr08	Glyma.08G039100	Frigida样蛋白 Frigida-like protein	Chr.8：3 057 438-3 060 816
qPdh-Chr08	Glyma.08G039200	乙醛脱氢酶家族 Aldehyde dehydrogenase family	Chr.8：3 067 517-3 072 472
qPdh-Chr08	Glyma.08G039300	乙醛脱氢酶家族 Aldehyde dehydrogenase family	Chr.8：3 073 843-3 078 936
qPdh-Chr08	Glyma.08G039400	富含亮氨酸的重复N-末端结构域 Leucine rich repeat N-terminal domain	Chr.8：3 085 136-3 088 000
qPdh-Chr08	Glyma.08G039500	丝氨酸激酶（Serinc） Serine incorporator （Serinc）	Chr.8：3 101 025-3 107 162
qPdh-Chr08	Glyma.08G039600	Arf的GTP酶激活蛋白 Putative GTPase activating protein for Arf	Chr.8：3 107 698-3 116 601
qPdh-Chr08	Glyma.08G039700	重金属伴生域 Heavy-metal-associated domain	Chr.8：3 129 407-3 131 827
qPdh-Chr08	Glyma.08G039800	纤维连接蛋白Ⅲ型结构域 Fibronectin type Ⅲ domain	Chr.8：3 139 067-3 148 954
qPdh-Chr15	Glyma.15G002100	MULE转座酶结构域 MULE transposase domain	Chr.15：213 887-219 265
qPdh-Chr15	Glyma.15G002200	细胞色素P450 Cytochrome P450	Chr.15：220 497-223 162
qPdh-Chr15	Glyma.15G002300	真核天冬氨酸蛋白酶 Eukaryotic aspartyl protease	Chr.15：224 303-226 574
qPdh-Chr15	Glyma.15G002400	-	Chr.15：233 459-238 218
qPdh-Chr15	Glyma.15G002500	-	Chr.15：240 793-241 445
qPdh-Chr15	Glyma.15G002600	转移酶家族 Transferase family	Chr.15：248 742-253 777
qPdh-Chr15	Glyma.15G002700	CorA样Mg²⁺转运蛋白 CorA-like Mg²⁺ transporter protein	Chr.15：256 675-262 022
qPdh-Chr15	Glyma.15G002800	PPR重复 PPR repeat	Chr.15：262 741-265 142
qPdh-Chr15	Glyma.15G002900	蛋白激酶结构域 Protein kinase domain	Chr.15：267 776-270 825
qPdh-Chr15	Glyma.15G003000	-	Chr.15：274 385-276 541
qPdh-Chr15	Glyma.15G003100	3-氧乙酰基-［酰基载体蛋白（ACP）］合酶Ⅲ 4-3-Oxoacyl-［acyl-carrier-protein （ACP）］ synthase Ⅲ	Chr.15：276 702-278 479
qPdh-Chr15	Glyma.15G003200	-	Chr.15：280 413-286 646
qPdh-Chr15	Glyma.15G003300	WRKY DNA结合结构域 WRKY DNA-binding domain	Chr.15：290 145-292 323
qPdh-Chr15	Glyma.15G003400	NAF结构域 NAF domain	Chr.15：309 074-311 683
qPdh-Chr15	Glyma.15G003500	天然抗性相关巨噬细胞蛋白 Natural resistance-associated macrophage protein	Chr.15：324 025-331 370
qPdh-Chr15	Glyma.15G003600	NAD依赖性差向异构酶/脱水酶家族 DAD dependent epimerase/dehydratase family	Chr.15：332 065-337 381
qPdh-Chr15	Glyma.15G003700	核糖体蛋白L7Ae/L30e/S12e/Gadd45家族 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	Chr.15：343 771-345 651
qPdh-Chr15	Glyma.15G003800	光系统I反应中心亚基Ⅷ Photosystem I reaction centre subunit Ⅷ	Chr.15：351 123-351 227
qPdh-Chr15	Glyma.15G003900	主要内在蛋白质 Major intrinsic protein	Chr.15：356 131-360 422
qPdh-Chr15	Glyma.15G004000	-	Chr.15：359 275-361 686
qPdh-Chr15	Glyma.15G004100	-	Chr.15：368 686-372 503
qPdh-Chr15	Glyma.15G004200	AP2结构域 AP2 domain	Chr.15：385 421-386 513
qPdh-Chr15	Glyma.15G004300	卤代酸脱卤酶样水解酶；阳离子转运蛋白/ATP酶；N端 Haloacid dehalogenase-like hydrolase； cation transporter/ATPase； N-terminus	Chr.15：390 297-394 072
qPdh-Chr15	Glyma.15G004400	-	Chr.15：398 466-399 046
qPdh-Chr15	Glyma.15G004500	双链RNA结合基序 Double-stranded RNA binding motif	Chr.15：401 329-403 329
qPdh-Chr15	Glyma.15G004600	-	Chr.15：403 355-404 122
qPdh-Chr15	Glyma.15G004700	蛋白酪氨酸激酶 Protein tyrosine kinase	Chr.15：405 502-410 429
qPdh-Chr16（qPdh1）	Glyma.16G141400	-	Chr.16：29 943 929-29 944 387

QTL名称 QTL name	基因 Gene	基因注释 Gene annotation	基因位置 Gene location
qPdh-Chr08	Glyma.08G037400	Tesmin/TSO1样CXC结构域，富含半胱氨酸的结构域 Tesmin/TSO1-like CXC domain， and cysteine-rich domain	Chr.8：29 50 964-2 957 163
qPdh-Chr08	Glyma.08G037500	-	Chr.8：2 959 084-2 961 115
qPdh-Chr08	Glyma.08G037600	-	Chr.8：2 962 310-2 966 347
qPdh-Chr08	Glyma.08G037700	-	Chr.8：2 967 634-2 971 428
qPdh-Chr08	Glyma.08G037800	-	Chr.8：2 973 386-2 977 716
qPdh-Chr08	Glyma.08G037900	动力蛋白轻链1型 Dynein light chain type 1	Chr.8：2 978 411-2 979 627
qPdh-Chr08	Glyma.08G038000	无注释 No annotation	Chr.8：2 987 443-2 988 562
qPdh-Chr08	Glyma.08G038100	S26信号肽酶，S26肽酶 S26 signal peptidase， peptidase S26	Chr.8：2 988 728-2 991 924
qPdh-Chr08	Glyma.08G038200	PPR重复序列 PPR repeat	Chr.8：2 992 820-2 996 514
qPdh-Chr08	Glyma.08G038300	-	Chr.8：2 997 737-2 999 328
qPdh-Chr08	Glyma.08G038400	转录抑制因子 Transcriptional repressor	Chr.8：3 012 183-3 013 602
qPdh-Chr08	Glyma.08G038500	-	Chr.8：3 018 702-3 019 975
qPdh-Chr08	Glyma.08G038600	黄素结合单加氧酶 Flavin-binding monooxygenase-like	Chr.8：3 029 349-3 032 467
qPdh-Chr08	Glyma.08G038700	MVB通路中Vps4活性的调节因子 Regulator of Vps4 activity in the MVB pathway	Chr.8：3 038 024-3 042 749
qPdh-Chr08	Glyma.08G038800	-	Chr.8：3 043 080-3 044 565
qPdh-Chr08	Glyma.08G038900	Ras基因家族 Ras family	Chr.8：3 046 616-3 047 930
qPdh-Chr08	Glyma.08G039000	-	Chr.8：3 053 220-3 053 733
qPdh-Chr08	Glyma.08G039100	Frigida样蛋白 Frigida-like protein	Chr.8：3 057 438-3 060 816
qPdh-Chr08	Glyma.08G039200	乙醛脱氢酶家族 Aldehyde dehydrogenase family	Chr.8：3 067 517-3 072 472
qPdh-Chr08	Glyma.08G039300	乙醛脱氢酶家族 Aldehyde dehydrogenase family	Chr.8：3 073 843-3 078 936
qPdh-Chr08	Glyma.08G039400	富含亮氨酸的重复N-末端结构域 Leucine rich repeat N-terminal domain	Chr.8：3 085 136-3 088 000
qPdh-Chr08	Glyma.08G039500	丝氨酸激酶（Serinc） Serine incorporator （Serinc）	Chr.8：3 101 025-3 107 162
qPdh-Chr08	Glyma.08G039600	Arf的GTP酶激活蛋白 Putative GTPase activating protein for Arf	Chr.8：3 107 698-3 116 601
qPdh-Chr08	Glyma.08G039700	重金属伴生域 Heavy-metal-associated domain	Chr.8：3 129 407-3 131 827
qPdh-Chr08	Glyma.08G039800	纤维连接蛋白Ⅲ型结构域 Fibronectin type Ⅲ domain	Chr.8：3 139 067-3 148 954
qPdh-Chr15	Glyma.15G002100	MULE转座酶结构域 MULE transposase domain	Chr.15：213 887-219 265
qPdh-Chr15	Glyma.15G002200	细胞色素P450 Cytochrome P450	Chr.15：220 497-223 162
qPdh-Chr15	Glyma.15G002300	真核天冬氨酸蛋白酶 Eukaryotic aspartyl protease	Chr.15：224 303-226 574
qPdh-Chr15	Glyma.15G002400	-	Chr.15：233 459-238 218
qPdh-Chr15	Glyma.15G002500	-	Chr.15：240 793-241 445
qPdh-Chr15	Glyma.15G002600	转移酶家族 Transferase family	Chr.15：248 742-253 777
qPdh-Chr15	Glyma.15G002700	CorA样Mg²⁺转运蛋白 CorA-like Mg²⁺ transporter protein	Chr.15：256 675-262 022
qPdh-Chr15	Glyma.15G002800	PPR重复 PPR repeat	Chr.15：262 741-265 142
qPdh-Chr15	Glyma.15G002900	蛋白激酶结构域 Protein kinase domain	Chr.15：267 776-270 825
qPdh-Chr15	Glyma.15G003000	-	Chr.15：274 385-276 541
qPdh-Chr15	Glyma.15G003100	3-氧乙酰基-［酰基载体蛋白（ACP）］合酶Ⅲ 4-3-Oxoacyl-［acyl-carrier-protein （ACP）］ synthase Ⅲ	Chr.15：276 702-278 479
qPdh-Chr15	Glyma.15G003200	-	Chr.15：280 413-286 646
qPdh-Chr15	Glyma.15G003300	WRKY DNA结合结构域 WRKY DNA-binding domain	Chr.15：290 145-292 323
qPdh-Chr15	Glyma.15G003400	NAF结构域 NAF domain	Chr.15：309 074-311 683
qPdh-Chr15	Glyma.15G003500	天然抗性相关巨噬细胞蛋白 Natural resistance-associated macrophage protein	Chr.15：324 025-331 370
qPdh-Chr15	Glyma.15G003600	NAD依赖性差向异构酶/脱水酶家族 DAD dependent epimerase/dehydratase family	Chr.15：332 065-337 381
qPdh-Chr15	Glyma.15G003700	核糖体蛋白L7Ae/L30e/S12e/Gadd45家族 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	Chr.15：343 771-345 651
qPdh-Chr15	Glyma.15G003800	光系统I反应中心亚基Ⅷ Photosystem I reaction centre subunit Ⅷ	Chr.15：351 123-351 227
qPdh-Chr15	Glyma.15G003900	主要内在蛋白质 Major intrinsic protein	Chr.15：356 131-360 422
qPdh-Chr15	Glyma.15G004000	-	Chr.15：359 275-361 686
qPdh-Chr15	Glyma.15G004100	-	Chr.15：368 686-372 503
qPdh-Chr15	Glyma.15G004200	AP2结构域 AP2 domain	Chr.15：385 421-386 513
qPdh-Chr15	Glyma.15G004300	卤代酸脱卤酶样水解酶；阳离子转运蛋白/ATP酶；N端 Haloacid dehalogenase-like hydrolase； cation transporter/ATPase； N-terminus	Chr.15：390 297-394 072
qPdh-Chr15	Glyma.15G004400	-	Chr.15：398 466-399 046
qPdh-Chr15	Glyma.15G004500	双链RNA结合基序 Double-stranded RNA binding motif	Chr.15：401 329-403 329
qPdh-Chr15	Glyma.15G004600	-	Chr.15：403 355-404 122
qPdh-Chr15	Glyma.15G004700	蛋白酪氨酸激酶 Protein tyrosine kinase	Chr.15：405 502-410 429
qPdh-Chr16（qPdh1）	Glyma.16G141400	-	Chr.16：29 943 929-29 944 387

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