Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (11): 2102-2113.doi: 10.3864/j.issn.0578-1752.2024.11.005

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• SPECIAL FOCUS: SOYBEAN DISEASE RESISTANCE, YIELD AND QUALITY CORRELATION • Previous Articles     Next Articles

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

SHOU XinYue1,2(), LIU Zhi2(), CHEN YueHan2, LI ChenHui2, SUN BinCheng3, SUN RuJian3, HAN DeZhi4, LU WenCheng4, SHEN YongHui5, WANG XiaoBo1(), YAN Long2()   

  1. 1 College of Agronomy, Anhui Agricultural University, Hefei 230036
    2 Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/National Soybean Improvement Center Shijiazhuang Sub-Center/Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035
    3 Hulunbuir Institute of Agricultural and Animal Husbandry Sciences, Hulunbuir 162650, Inner Mongolia
    4 Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe 164399, Heilongjiang
    5 Zhengding County Agriculture and Rural Bureau, Shijiazhuang 050800
  • Received:2024-01-19 Accepted:2024-03-26 Online:2024-06-01 Published:2024-06-07
  • Contact: WANG XiaoBo, YAN Long

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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

Table 1

Statistical analysis of the phenotypic variation in the number and dry weight of nodules of 260 soybean germplasm inoculated USDA110 in 2023"

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
h2b
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

Fig. 1

Genome-wide association analysis of nodule number and nodule dry weight a: Manhattan plot, Q-Q plot and LDblock plot of the number of nodules; b: The 65 kb Manhattan plot of the number of nodules associated region on chromosome 2; c: Manhattan plot, Q-Q plot and LDblock plot of nodule dry weight; d: The 84 kb Manhattan plot of the nodule dry weight associated region on chromosome 6"

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
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
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 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

Fig. 2

Haplotype analysis of the candidate genes related to nodule number a: Gene structure and haplotype analysis of Glyma.02G242700; b: Gene structure and haplotype analysis of Glyma.02G242900; c: Gene structure and haplotype analysis of Glyma.02G243000; d: Gene structure and haplotype analysis of Glyma.02G243200; e: Gene structure and haplotype analysis of Glyma.02G243500. * P<0.05. The same as below"

Fig. 3

Haplotype analysis of candidate genes related to nodule dry weight a: Gene structure and haplotype analysis of Glyma.06G079300; b: Gene structure and haplotype analysis of Glyma.06G079600; c: Gene structure and haplotype analysis of Glyma.06G079900; d: Gene structure and haplotype analysis of Glyma.06G080400. **P<0.01, ***P<0.001"

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