冀北坝上大豆结瘤相关性状全基因组关联分析

doi:10.3864/j.issn.0578-1752.2024.11.005

Abstract

Abstract:

【Objective】Exploring efficient nodulation soybean germplasm adapted to the ecological conditions of the Bashang area, identifying genetic loci and candidate genes regulating soybean-rhizobium symbiotic nodulation, and improving soybean symbiotic nitrogen fixation efficiency.【Method】This study utilized a natural population of 260 soybean germplasms as the research object, rhizobium strain USDA110 was inoculated under outdoor potted conditions in the Bashang of Hebei Province. The single plant nodule number and single plant nodule dry weight data were used as phenotypic values. Combined with genotype data of the 260 germplasms, a genome-wide association analysis was conducted to explore genes related to soybean-rhizobium symbiotic nodulation.【Result】A total of 18 SNPs significantly associated with soybean nodule number were detected, located on chromosomes 2, 7, 8, 13, 18, and 19. Among them, the significant associated locus BARC_2.01_Chr02_43161654_A_G on chromosome 2 was identified as the main locus controlling soybean nodule number (LOD=3.89). Linkage disequilibrium analysis within the 200 kb interval upstream and downstream of this locus containing BARC_2.01_Chr02_43161654_A_G identified 10 candidate genes regulating soybean nodule number. There was a significant difference in the number of nodules among the materials corresponding to different haplotypes of Glyma.02G243200 (P<0.05), the expression pattern of this gene was queried in the SoyBase database, and it was expressed in root hairs, indicating that Glyma.02G243200 may be a key gene influencing soybean nodule number. Additionally, six SNPs significantly associated with soybean nodule dry weight were identified, located on chromosomes 6, 18, and 20. Among them, the significant associated loci BARC_2.01_Chr06_6069381_G_A and BARC_2.01_Chr06_6192925_T_C on chromosome 6 were identified as the main loci controlling soybean nodule dry weight (LOD=3.49 and LOD=3.35, respectively). Linkage disequilibrium analysis within the 100 kb interval upstream of BARC_2.01_ Chr06_6069381_G_A and downstream of BARC_2.01_Chr06_6192925_T_C identified 14 candidate genes regulating soybean nodule dry weight. Haplotype analysis revealed significant differences in nodule dry weight for the genes Glyma.06G079600 and Glyma.06G079900 between different haplotype materials (P<0.01, P<0.001), the expression pattern of this gene was queried in the SoyBase database, and they were expressed in roots, indicating that these two genes may be key genes influencing soybean nodule dry weight.【Conclusion】This study identified a candidate gene significantly associated with nodule number on chromosome 2 and two candidate genes significantly associated with nodule dry weight on chromosome 6, providing new genetic resources and references for genetic improvement of soybean nodulation traits.

Key words: soybean, rhizobium, genome-wide association study (GWAS), soybean nodules number, soybean nodules dry weight

SHOU XinYue, LIU Zhi, CHEN YueHan, LI ChenHui, SUN BinCheng, SUN RuJian, HAN DeZhi, LU WenCheng, SHEN YongHui, WANG XiaoBo, YAN Long. Genome-Wide Association Analysis of Soybean Nodulation-Related Traits in the Northern Hebei[J].Scientia Agricultura Sinica, 2024, 57(11): 2102-2113.

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Figures/Tables 6

Table 1

Fig. 1

Table 2

The SNPs significantly associated with the number and the dry weight of nodules identified in 2023"

性状 Trait	染色体 Chromosome	标记名称 SNP	位置 Position (bp)	LOD值 -log₁₀(P)	贡献率 R²(%)	均值±标准差 Mean±SD
根瘤数量 Nodule number	2	BARC_2.01_Chr02_2559614_A_G	2559614	3.20	1.22	11.19±2.17	9.53±2.64
		BARC_2.01_Chr02_2576535_G_A	2576535	3.08	1.16	11.07±2.14	9.66±2.58
		BARC_2.01_Chr02_43119820_T_C	43119820	3.34	1.24	10.50±2.27	11.65±2.20
		BARC_2.01_Chr02_43152909_T_C	43152909	3.05	1.12	10.52±2.23	11.30±2.22
		BARC_2.01_Chr02_43160129_T_C	43160129	3.62	1.37	10.52±2.15	11.21±1.96
		BARC_2.01_Chr02_43161654_A_G	43161654	3.89	1.49	10.50±2.23	11.15±2.39
		BARC_2.01_Chr02_43230817_G_T	43230817	3.03	1.11	10.72±2.08	11.56±2.51
	7	BARC_2.01_Chr07_37781401_T_C	37781401	3.13	1.15	10.30±2.14	11.86±2.30
	7	BARC_2.01_Chr07_37867888_G_A	37867888	3.09	1.14	10.51±2.16	12.12±2.08
	8	BARC_2.01_Chr08_19418262_A_G	19418262	3.04	1.11	10.66±1.91	11.88±2.52
		BARC_2.01_Chr08_19440300_C_T	19440300	3.06	1.12	10.35±2.11	11.74±2.66
		BARC_2.01_Chr08_19460867_T_C	19460867	3.16	1.16	10.22±2.12	11.46±2.32
		BARC_2.01_Chr08_19664993_C_T	19664993	3.13	1.15	10.50±2.01	11.94±2.31
		BARC_2.01_Chr08_19781668_T_G	19781668	3.84	1.47	10.29±2.02	11.92±2.47
		BARC_2.01_Chr08_19790967_C_T	19790967	3.38	1.26	10.44±2.03	12.18±2.70
	13	BARC_2.01_Chr13_33815541_C_A	33815541	3.15	1.16	10.48±2.11	11.67±2.31
	18	BARC_2.01_Chr18_11323656_G_A	11323656	3.24	1.21	10.56±2.26	10.89±2.21
	19	BARC_2.01_Chr19_38414793_A_G	38414793	3.45	1.34	11.26±2.25	10.23±1.96
根瘤干重 Nodule dry weight	6	BARC_2.01_Chr06_6069381_G_A	6069381	3.49	0.31	0.04±0.01	0.04±0.01
	6	BARC_2.01_Chr06_6192925_T_C	6192925	3.35	0.25	0.04±0.01	0.04±0.01
	18	BARC_2.01_Chr18_56401752_T_G	56401752	3.22	0.35	0.04±0.01	0.04±0.01
	20	BARC_2.01_Chr20_36618731_G_A	36618731	3.05	0.31	0.04±0.01	0.05±0.01
		BARC_2.01_Chr20_38571066_A_G	38571066	3.34	0.38	0.04±0.01	0.05±0.01
		BARC_2.01_Chr20_38608664_A_C	38608664	3.42	0.40	0.04±0.01	0.05±0.02

Table 2

Table 3

The number of nodules and dry weight of nodules are potential related candidate genes"

候选基因 Candidate genes	功能描述 Description	表达模式 Expression pattern	候选基因 Candidate genes	功能描述 Description	表达模式 Expression pattern
Glyma.02G242700	跨膜激酶1 Transmembrane kinase 1	-	Glyma.06G079300	-	根 Root
Glyma.02G242800	跨膜激酶1 Transmembrane kinase 1	-	Glyma.06G079400	-	根 Root
Glyma.02G242900	CYS、MET、PRO和GLY蛋白1 CYS, MET, PRO, and GLY protein 1	根 Root	Glyma.06G079500	功能未知的蛋白质，DUF599 Protein of unknown function, DUF599	花 Flower
Glyma.02G243000	PLATZ转录因子家族蛋白 PLATZ transcription factor family protein	-	Glyma.06G079600	非ATP酶亚基9 Non-ATPase subunit 9	根 Root
Glyma.02G243100	PLATZ转录因子家族蛋白 PLATZ transcription factor family protein	-	Glyma.06G079700	-	根 Root
Glyma.02G243200	RING/FYVE/PhD锌指超家族蛋白 RING/FYVE/PHD zinc finger superfamily protein	花 Flower	Glyma.06G079800	碱性亮氨酸拉链 9 basic leucine zipper 9	根 Root
Glyma.02G243300	-	根 Root	Glyma.06G079900	类钙调蛋白42 Calmodulin like 42	根 Root
Glyma.02G243400	STELAR K+外向整流器 STELAR K+outward rectifier	根和花 Root and flower	Glyma.06G080000	-	根 Root
Glyma.02G243500	五肽重复（PPR）超家族蛋白 Pentatricopeptide repeat (PPR) superfamily protein	根和叶 Root and leaf	Glyma.06G080100	肌球蛋白重链相关 Myosin heavy chain-related	根 Root
Glyma.02G243600	真核天冬氨酰蛋白酶家族蛋白 Eukaryotic aspartyl protease family protein	花和叶 Flower and leaf	Glyma.06G080200	含NAC结构域的蛋白质 38 NAC domain containing protein 38	根 Root
Glyma.06G079100	-	根 Root	Glyma.06G080300	tRNA（鸟嘌呤-N-7）甲基转移酶 tRNA (guanine-N-7) methyltransferase	根 Root
Glyma.06G079200	SAUR样生长素反应蛋白家族 SAUR-like auxin-responsive protein family	根 Root	Glyma.06G080400	线粒体编辑因子21 Mitochondrial editing factor 21	根 Root

Table 3

Fig. 2

Fig. 3

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性状 Trait	平均值 Mean	最大值 Max	最小值 Min	标准差 SD	变异系数 CV (%)	偏度 Skew	峰度 Kurt	遗传力 h²_b
根瘤数量Nodules number	10.62	17.00	6.00	2.24	21.09	0.43	0.15	0.75
根瘤干重Nodules dry weight (g/plant)	0.04	0.08	0.02	0.01	25.00	0.85	1.07	0.70

Genome-Wide Association Analysis of Soybean Nodulation-Related Traits in the Northern Hebei

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