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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (11): 2121-2133.doi: 10.3724/SP.J.1006.2021.04249


Utilization of dynamic transcriptomics analysis for candidate gene mining of 100-seed weight in soybean

ZENG Jian(), XU Xian-Chao, XU Yu-Fei, WANG Xiu-Cheng, YU Hai-Yan, FENG Bei-Bei, XING Guang-Nan*()   

  1. Soybean Research Institute, Nanjing Agricultural University / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General), Ministry of Agriculture and Rural Affairs / National Key Laboratory for Crop Genetic and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, Jiangsu, China
  • Received:2020-11-20 Accepted:2021-03-19 Online:2021-11-12 Published:2021-04-01
  • Contact: XING Guang-Nan E-mail:2019101129@njau.edu.cn;xinggn@njau.edu.cn
  • Supported by:
    National Key Research and Development Program of China(2016YFD0100201);National Natural Science Foundation of China(31571694);Fundamental Research Funds for Central Universities(KYT201801);MOE Program for Changjiang Scholars and Innovative Research Team in University(PCSIRT_17R55);Project of Intellectual Base for Discipline Innovation in Colleges and Universities(B08025);China Agriculture Research System(CARS-04);iangsu Higher Education PAPD Program, and the Jiangsu JCIC-MCP Program


100-seed weight of soybean is an important agronomic trait that affects yield, and it is of great significance to reveal its molecular basis and discover key candidate genes for soybean improvement breeding. In this study, weighted gene co-expression network analysis (WGCNA) was performed on the transcriptome data of 36 samples from 12 soybean varieties at three stages of seed development, and 20 gene co-expression modules were obtained. After correlating with 100-seed weight and four-seed shape traits, the green module was found to be most correlated with the phenotypes. Then 13 hub genes of green module were screened based on the Gene Significance (GS) and Eigengene Connectivity (kME) value. Gene differential expression of two groups of soybean varieties with extremely significant differences in 100-seed weight showed that the MAPK signaling pathway in the early and mid-term of seed development might regulate the 100-seed weight in soybean. According to SNPs/InDels calling and Gene Ontology (GO) annotation, Glyma.14G043900 and Glyma.15G217400 in the green module caused synonymous and non-synonymous coding mutations due to SNP mutations, and there were GO Terms and zinc finger domains related to gene expression regulation. These results suggested that they might regulate the 100-seed weight and seed shape of soybeans by regulating the hub gene and differentially expressed genes. Furthermore, Glyma.15G217400 was located in four reported QTLs of 100-seed weight, while Glyma.14G043900 was located in a reported seed protein content QTL and an oil content QTL. Compared with soybean public database, the increasing 100-seed weight alleles of the two genes were artificially selected and their frequency was gradually increased from wild accessions to landraces, resulting in the improved cultivars. These results provide new ideas for further discovering 100-seed weight candidate gene in soybean and its expression regulation mechanism.

Key words: soybean, 100-seed weight, transcriptomics, WGCNA, candidate gene

Fig. 1

Determination of soft threshold β The ordinate represents the index of scale free network model in figure A, the red line represents that R2 is equal to 0.85. The ordinate represents the average link degree of each soft threshold in figure B. The abscissa in both figures A and B represent the soft threshold β."

Table 1

SNPs/InDels filter standards"

SNPs filter standards
InDels filter standards
QualByDepth (QD) > 2.0 QualByDepth (QD) > 2.0
RMSMappingQuality (MQ) > 40.0
FisherStrand (FS) < 60.0 FisherStrand (FS) < 200.0
StrandOddsRatio (SOR) < 3.0 StrandOddsRatio (SOR) < 10.0
MappingQualityRankSumTest (MQRankSum) > -12.5 MappingQualityRankSumTest (MQRankSum) > -12.5
ReadPosRankSumTest (ReadPosRankSum) > -8.0 ReadPosRankSumTest (ReadPosRankSum) > -8.0

Fig. 2

Box diagram of 100-seed weight of 12 soybean varieties The abscissa represents 12 soybean varieties, and the ordinate represents the 100-seed weight. One point represents one observation. Soybean varieties with different uppercase letters are significantly different in 100-seed weight at P = 0.01 by Duncan’s new multiple-range test."

Fig. 3

Histogram of the number of genes in modules The abscissa represents the module and the ordinate represents the number of genes in the module."

Fig. 4

Heat map of module-trait relationships (A) and gene expression count of 2904 genes in green module (B) The horizontal axis represents 100-seed weight and seed shape traits, and each column represents the co-expression module in the figure A; red color of each box represents the positive correlation between module and trait, blue color of each box represents the negative relationships between module and trait. B: 2904 genes in the green module are mapped after normalization of the expression levels by row of 12 soybean varieties in three stages. G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively."

Fig. 5

GO enrichment of 2904 genes in green module The abscissa (each column) represents the proportion of enriched genes to input genes, and the ordinate (each row) corresponds to GO Terms. The size of the dot represents the number of enriched genes, and the color of the dot represents the corrected Padjust value by the Fisher exact test."

Fig. 6

Gene expression differences in different stages of seed development between two panels of soybean varieties with extremely significant differences in 100-seed weight (A) and KEGG pathway enrichment map of down-regulated genes in small 100-seed weight varieties (B) G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively. Down-regulated genes represent down-regulated genes in small 100-seed weight varieties, and up-regulated genes represent up-regulated genes in small 100-seed weight varieties."

Fig. 7

Histogram of GS and kME value of hub gene in green module (A) and cluster heat map of differentially expressed genes among soybean varieties with different 100-seed weight (B) 100-SW: 100-seed weight; SA: seed area; SL: seed length; SP: seed perimeter; SW: seed width. G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively. Large and Small represent large soybean varieties and small soybean varieties panel at P = 0.01, respectively. Gene in bold represents the first expression pattern in figure B."

Fig. 8

Distribution map of SNPs/InDels and DEGs on soybean chromosomes A: SNPs density; B: InDels density; C: log2 (Fold Change) of DEGs. The inner circle represents significantly up-regulated genes in small 100-seed weight varieties, and the outer circle represents significantly down-regulated genes in small 100-seed weight varieties."

Table 2

SNPs/InDels distributed region"

Variation region
SNPs InDels
Percentage (%)
Percentage (%)
DOWNSTREAM 41,636 23.67 5788 26.22
EXON 72,950 41.48 3028 13.72
INTERGENIC 2100 1.19 424 1.92
INTRON 8576 4.88 1625 7.36
SPLICE_SITE_ACCEPTOR 31 0.02 11 0.05
SPLICE_SITE_DONOR 31 0.02 12 0.05
SPLICE_SITE_REGION 334 0.19 69 0.31
UPSTREAM 29,780 16.93 4128 18.70
UTR_3_PRIME 14,683 8.35 4400 19.94
UTR_5_PRIME 5749 3.27 2586 11.72

Table 3

Ten genes with non-synonymous_coding SNP mutants between the large and small 100-seed weight varieties panels in green module"

Allele of small 100-SW
Allele of large 100-SW
Glyma.02G139500 Gm02 14480344 G A
Glyma.02G140100 Gm02 14531600 T C
Glyma.06G179600 Gm06 15246959 A G
Glyma.07G018200 Gm07 1456246 A G
Glyma.12G057100 Gm12 4156207 T C
Glyma.14G043900 Gm14 3335050 T C
Glyma.15G217400 Gm15 35930038 A T
Glyma.17G071400 Gm17 5580413 A G
Glyma.17G076400 Gm17 5974992 C T
Glyma.18G237000 Gm18 52573168 T C

Table 4

GO annotations of candidate genes Glyma.14G043900 and Glyma.15G217400"

GO type
Annotation description
Glyma.14G043900 GO:0006355 生物过程
Biological process
Regulation of transcription, DNA-templated
GO:0008270 分子功能
Molecular function
Zinc ion binding
Glyma.15G217400 GO:0061158 生物过程
Biological process
3'-UTR-mediated mRNA destabilization
GO:0005829 细胞组分
Cellular component
GO:0003730 分子功能
Molecular function
mRNA 3'端非翻译区结合
mRNA 3'-UTR binding
GO:0046872 分子功能
Molecular function
Metal ion binding

Fig. 9

Co-expression network of candidate genes, hub genes, and differentially expressed genes in the green module Red dots represent candidate genes, yellow dots represent hub genes, green dots represent DEGs, and blue dot represents both DEG and hub gene. The color of the line represents the weight value between genes. Black line represents the weight between genes greater than 0.1, and gray line represents the weight less than 0.1 but greater than 0.01."

Fig. 10

Allele percentage line chart of two non-synonymous_coding SNP mutant of Glyma.14G043900 and Glyma.15G217400 in different soybean types The dots represent the positive effect alleles of 100-seed weight, and the triangles represent the negative effect alleles of 100-seed weight."

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