Crops ›› 2021, Vol. 37 ›› Issue (3): 8-18.doi: 10.16035/j.issn.1001-7283.2021.03.002

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Whole Genome Discovery and Analysis of Genes Related to 100-Seed Weight in Soybean

Su Yang1(), Yang Jing2, Guo Yong2(), Du Weijun1(), Qiu Lijuan2()   

  1. 1College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/The National Key Facility for Crop Gene Resources and Genetic Improvement/MOA Key Laboratory of Soybean Biology (Beijing), Beijing 100081, China
  • Received:2021-04-29 Revised:2021-05-11 Online:2021-06-15 Published:2021-06-22
  • Contact: Guo Yong,Du Weijun,Qiu Lijuan E-mail:sxhq2275@163.com;guoyong@caas.cn;duweijun68@126.com;qiulijuan@caas.cn

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Abstract:

100-seed weight is an important trait related to yield in soybean breeding. Therefore, identification of genes related to seed size/weight by using forward and reverse genetic methods had important theoretical and practical significance. Functional genes regulating seed size/weight in Arabidopsis thaliana and rice had been obtained from published literatures and a total of 175 homologous genes were identified from whole soybean genome based on the principle of sequence similarity and domain identity. Gene expression profile analysis showed that 22 genes were specifically expressed in soybean seeds. Using the resequencing data of 56 germplasm resources, a total of 2769 SNPs were identified in these genes and 121 SNPs had co-relationship between wild and cultivated soybean. Sixteen SNPs with non-synonymous variations were verified by PCR based sequencing in 26 soybean accessions and the results showed that five SNPs was related to seed size, and had the different variations in wild and cultivated soybean. The genotypes of four SNPs were obtained from the resequencing data of 2368 soybean accessions and genotype-phenotype association analysis suggested that there was a very significant difference in 100-seed weight phenotype between accessions with wild type and mutant variations corresponding to each SNP. The 100-seed weight of majority accessions with WT-genotype was more than 12g while that of accessions with Mut-genotype was less than 12g. Therefore, the four genes harboring these four SNPs may be related to the regulation of soybean seed size/weight. Four candidate genes related to 100-seed weight were obtained in soybean, which provided a reference for fine mapping and functional marker development of soybean 100-seed weight and the functional study of genes regulating soybean seed size/weight.

Key words: Soybean, 100-seed weight, Homologous gene, SNP, Resequencing

Table 1

Functional genes related to seed size/weight in plants"

基因名称
Gene name		 物种
Species		 基因编号
Gene ID		 生物学功能
Biological function		 大豆中基因拷贝数
Copy number in soybean		 参考文献
Reference
激素信号转导Hormone signal transduction
KLU Arabidopsis AT1G13710 Cytochrome P450 5 [20]
SOB7 Arabidopsis AT1G17060 Cytochrome p450 72C1 13 [21]
AHK3 Arabidopsis AT1G27320 Histidine kinase 3 2 [20]
CKX5 Arabidopsis AT1G75450 Cytokinin oxidase 5 2 [22]
AHK4 Arabidopsis AT2G01830 Histidine kinase: cytokinin-binding receptor 5 [20]
DET2 Arabidopsis AT2G38050 Brassinolide biosynthetic 2 [20]
CKX1 Arabidopsis AT2G41510 Cytokinin oxidase/dehydrogenase 1 2 [22]
EOD3 Arabidopsis AT2G46660 Cytochrome P450 3 [21]
DWF4 Arabidopsis AT3G50660 Cytochrome P450 superfamily protein 3 [5]
CYP78A9 Arabidopsis AT3G61880 Cytochrome P450 78a9 3 [21]
AP2 Arabidopsis AT4G36920 Integrase-type DNA-binding superfamily protein 4 [7]
ATMYB56 Arabidopsis AT5G17800 Myb domain protein 56 2 [22]
AGG3 Arabidopsis AT5G20635 Atypical heterotrimeric G-protein gamma-subunit 4 [23]
AHK2 Arabidopsis AT5G35750 Histidine kinase AHK2 2 [20]
ABA2 Arabidopsis AT1G52340 Xanthoxin dehydrogenase 2 [21]
ABI5 Arabidopsis AT2G36270 Basic-leucine zipper (bZIP) transcription factor family protein 3 [21]
BRI1 Arabidopsis AT4G39400 Protein BRASSINOSTEROID INSENSITIVE 1 2 [21]
ARF2 Arabidopsis AT5G62000 Auxin response factor 2 4 [5]
DWARF 61 Rice OS01G0718300 Receptor serine/threonine kinase 2 [23]
OsBZR1 Rice OS07G0580500 Brassinosteroid (BR) regulated growth response 6 [21]
GSK2 Rice OS05G0207500 GSK3/SHAGGY-like kinase 1 [21]
BG1 Rice Os03g0175800 Positive regulator of auxin response and transport 1 [21]
DWARF 11 Rice OS04G0469800 Brassinosteroid (BR) biosynthesis 1 [21]
GE Rice OS07G0603700 Cytochrome P450 78A5 5 [23]
泛素代谢途径Ubiquitin pathway
GW2 Rice OS02G0244100 RING-type E3 ubiquitin ligase 2 [8]
UBP15 Arabidopsis AT1G17110 Ubiquitin-specific protease 15 2 [24]
DA1 Arabidopsis AT1G19270 Ubiquitin receptors 2 [25]
DA2 Arabidopsis AT1G78420 E3 ubiquitin-protein ligase DA2 2 [26]
EOD1 Arabidopsis AT3G63530 E3 ubiquitin ligase 2 [21]
DAR1 Arabidopsis AT4G36860 Ubiquitin binding protein 6 [23]
其他Others
SAMBA Arabidopsis AT1G32310 Valine-tRNA ligase 2 [23]
MINI3 Arabidopsis AT1G55600 Member of WRKY Transcription Factor 2 [2]
IKU1 Arabidopsis AT2G35230 VQ motif-containing protein 5 [20]
TTG2 Arabidopsis AT2G37260 WRKY family transcription factor 2 [20]
SOD7 Arabidopsis AT3G11580 AP2/B3-like transcriptional factor 4 [21]
IKU2 Arabidopsis AT3G19700 Leucine-rich repeat protein kinase 1 [20]
FER Arabidopsis AT3G51550 Malectin/receptor-like protein kinase 2 [21]
STK Arabidopsis AT4G09960 MADS box transcription factor 2 [22]
基因名称
Gene name		 物种
Species		 基因编号
Gene ID		 生物学功能
Biological function		 大豆中基因拷贝数
Copy number in soybean		 参考文献
Reference
RPT2A Arabidopsis AT4G29040 Regulatory particle AAA-ATPase 2A 4 [23]
ANT Arabidopsis AT4G37750 Integrase-type DNA-binding superfamily protein 8 [20]
DPA4 Arabidopsis AT5G06250 AP2/B3-like transcriptional factor 4 [21]
MET1 Arabidopsis AT5G49160 Methyltransferase 1 2 [23]
AGL62 Arabidopsis AT5G60440 AGAMOUS-like 62 24 [20]
SHB1 Arabidopsis At4G25350 Acts in cryptochrome signaling 1 [20]
GS2 Rice Os02G0701300 Growth-regulating factor 4-like 1 [21]
SMG1 Rice OS02G0787300 Mitogen-activated protein kinase kinase 5 2 [23]
GS3 Rice OS03G0407400 Keratin-associated protein 5-5 4 [21]
qGL3 Rice Os03G0646900 Serine/threonine phosphatase 1 [21]
RGB1 Rice OS03G0669100 Deoxyuridine 5'-triphosphate nucleotidohydrolase-like 2 [23]
OsGIF1 Rice OS03G0733600 GRF1-interacting factor 1 4 [23]
GS5 Rice OS05G0158500 Serine carboxypeptidase-like 26 3 [23]
RGA1 Rice OS05G0333200 Guanine nucleotide-binding protein alpha-1 subunit 4 [23]
OsMAPK6 Rice OS06G0154500 Mitogen-activated protein kinase 1-like 2 [27]
TGW6 Rice OS06G0623700 Protein STRICTOSIDINE SYNTHASE-LIKE 10 6 [28]
GW6a Rice OS06G0650300 Probable N-acetyltransferase HLS1 2 [23]
GLW7 Rice Os07G0505200 Plant-specific transcription factor 1 [23]
GW7 Rice OS07G0603300 Protein LONGIFOLIA 1 8 [29]
GW8 Rice OS08G0531600 Squamosa promoter binding like protein 16 2 [30]
DEP1 Rice OS09G0441900 Keratin-associated protein 5-5 4 [31]

Table 2

Chromosome location of genes related to 100-seed weight in soybean"

染色体
Chromosome		 泛素代谢途径
Ubiquitin
pathway		 激素信号转导途径
Hormone signal
transduction		 其他
Others		 合计
Total
1 1 5 3 9
2 1 4 5 10
3 0 3 4 7
4 0 4 6 10
5 0 5 3 8
6 0 6 6 12
7 0 4 4 8
8 0 4 7 11
9 0 1 2 3
10 1 0 21 22
11 1 6 2 9
12 2 0 0 2
13 3 5 5 13
14 1 2 3 6
15 2 7 0 9
16 1 2 2 5
17 1 4 6 11
18 0 0 3 3
19 0 4 7 11
20 0 0 5 5
Scaffold 0 0 1 1
合计Total 14 66 95 175

Fig. 1

Expression profiling of genes related to 100-seed weight in soybean"

Table 3

Specifically expressed genes in different tissues of soybean"

植物组织
Plant tissue		 泛素代谢途径
Ubiquitin pathway		 激素信号
转导途径
Hormone signal transduction		 其他
Others		 合计
Total
种子Seed 3 6 12 21
花Flower 5 14 16 35
荚Pod 0 4 7 11
根毛Root hairs 0 2 6 8
叶片Leaf 1 5 1 7
根Root 2 5 18 25
根瘤Nodules 1 7 5 13
顶端分生组织SAM 0 17 15 32
茎Stem 2 2 7 11

Table 4

Distribution of non-synonymous variation SNP loci"

基因号Gene ID 染色体Chromosome 区域Region 遗传分化指数Fst 参考碱基Ref 突变碱基Mutant type 氨基酸变异Amino acid variation
Glyma.02G179300 Gm02 CDS 0.45 G T T<->K
Glyma.02G194000 Gm02 CDS 0.49 T C I<->T
Glyma.05G019800 Gm05 CDS 0.52 T C S<->P
Glyma.07G022800 Gm07 CDS 0.51 T C I<->M
Glyma.07G052300 Gm07 CDS 0.56 T A S<->T
Glyma.13G055700 Gm13 CDS 0.48 T C I<->V
Glyma.13G055700 Gm13 CDS 0.47 T C T<->A
Glyma.13G055700 Gm13 CDS 0.51 C A V<->L
Glyma.13G055700 Gm13 CDS 0.62 T C N<->D
Glyma.13G259700 Gm13 CDS 0.58 C T S<->N
Glyma.13G261700 Gm13 CDS 0.69 C T S<->N
Glyma.13G262000 Gm13 CDS 0.52 T G M<->L
Glyma.13G262000 Gm13 CDS 0.57 C T G<->D
Glyma.17G080000 Gm17 CDS 0.58 C T E<->K
Glyma.17G080500 Gm17 CDS 0.65 A G I<->V
Glyma.17G080500 Gm17 CDS 0.46 A G K<->E

Fig.2

Distribution of 16 SNPs in 26 soybean accessions W: Wild soybean accessions; C: Cultivated soybean accessions. “*” represents significant difference (P < 0.05)"

Fig.3

Phenotypic analysis of 100-seed weight corresponding to different types of SNP “**”represents significant difference (P < 0.01)"

Fig.4

Distribution of soybean accessions in different 100-seed weight phenotypic ranges"

Table 5

Functional annotation of candidate genes"

基因号
Gene ID		 拟南芥/水稻中同源基因
Homologous gene in Arabidopsis/rice		 功能注释
Functional annotation
Glyma.05G019800 GW7 单细胞的生长调节
Glyma.07G022800 GW6a N-乙酰基转移酶活性
Glyma.13G259700 UBP15/SOD2 泛素水解酸活性
Glyma.13G261700 SOB7 氧化还原酶活性
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