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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (12): 2978-2986.doi: 10.3724/SP.J.1006.2022.14226

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

QTL mapping and candidate gene prediction of soybean 100-seed weight based on high-density bin map

GE Tian-Li(), TIAN Yu, ZHANG Hao, LIU Zhang-Xiong, LI Ying-Hui(), QIU Li-Juan()   

  1. National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Soybean Biology in Beijing, Ministry of Agriculture and Rural Affairs / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-12-02 Accepted:2022-02-25 Online:2022-12-12 Published:2022-03-12
  • Contact: LI Ying-Hui,QIU Li-Juan E-mail:2030587001@qq.com;liyinghui@caas.cn;qiulijuan@caas.cn
  • About author:First author contact:

    **Contributed equally to this work

  • Supported by:
    National Key Research and Development Program of China for Crop Breeding “Evaluation, Innovation, and Excellent Gene Excavation for Elite Soybean Cultivars between China and Europe”(2019YFE0105900)

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Abstract:

The 100-seed weight is a critical factor for soybean yield. Identifying QTLs/genes related to 100-seed weight paves a way for breeding a new type of high-yielding and large-seed cultivar through modern molecular design. In this study, combined with the high-density Bin map and the phenotype of 100-seed weight, two environmentally stable QTLs were detected on chromosomes 12 and 18 in six environments in a RILs population derived from cross of Zhonghuang 13 × Zhongpin 03-5373 (ZH13 × ZP03-5373), respectively. Among them, qSW12-2, could explain 7.31% to 11.03% the observed phenotypic variation and 0.52 to 0.91 g of the additive effect, and its positive allele was derived from ZH13. The physical interval of qSW12-2 was 0.19 Mb that harbored 20 annotated genes. Among them, Glyma.12G195500 carried a large-effect site involved in the biosynthesis of brassinosteroids. According to the gene expression pattern, Glyma.12G195500 preferentially expressed in the developing seeds, suggesting that Glyma.12G195500 was the candidate gene for qSW12-2. Three haplotypes were observed in Glyma.12G195500 in 385 soybean germplasm resources using re-sequencing data. Among them, there was significantly higher in 100-seed weight of ZH13-type H2 haplotype than H1, which was selected during soybean domestication. These results provide genetic loci for revealing the genetic mechanism controlling soybean seed weight and breeding high-yielding cultivars.

Key words: soybean, 100-seed weight, Bin map, candidate genes, haplotype analysis

Table 1

Phenotypic performance of ZH13/ZP03-5373 RIL population and parents for 100-seed weight"

环境
Environment		 亲本 Parents 群体 Population
中黄13
Zhonghuang 13		 中品03-5373
Zhongpin 03-5373		 最小值
Min.		 最大值
Max.		 平均值
Mean		 标准差
SD		 偏斜度
Skewness		 峰度
Kurtosis
CP09 23.8±1.8 18.9±1.2 15.0 26.2 20.37 2.14 0.19 -0.10
SYa09 26.5±1.2 20.2±1.4 13.5 32.0 22.22 3.29 0.26 0.12
CP10 28.9±1.9 22.0±1.5 16.3 31.4 23.24 2.69 0.27 -0.14
SYa10 27.2±1.0 19.3±0.5 15.0 32.1 22.79 3.31 0.41 -0.12
SYi10 30.3±1.7 20.7±1.0 14.9 34.2 23.79 3.00 0.23 0.38
CP11 27.7±1.4 20.4±1.4 15.8 31.6 22.66 2.50 0.31 0.37
BLUP 27.4±2.2 20.3±1.1 16.3 27.7 22.30 1.97 0.23 -0.05

Fig. 1

Distribution of 100-seed weight for Zhonghuang 13/Zhongpin 03-5373 RIL population and parent"

Table 2

QTLs for 100-seed weight mapped in the Zhonghuang 13/Zhongpin 03-5373 RIL population in multiple environments"

位点
QTL		 标记区间
Marker internal		 物理位置
Physical position		 阈值LOD 表型贡献率
PVE (%)		 加性效应
Add		 环境
Environment		 已报道的区间
Reported QTLs
qSW2 mk258-mk259 7850001-8317538 4.24 5.70 0.71a SYi10 Liu et al. 2013[12]
4.25 4.35 0.40a BLUP
qSW5 mk1027-mk1028 41520254-41629890 5.09 7.62 0.83a SYa10 Specht et al. 2001[23]
4.15 4.25 0.40a BLUP
qSW11 mk2301-mk2302 28333312-28950000 3.07 4.19 0.61a SYi10 Li et al. 2008[24]
4.94 5.11 0.43a BLUP
qSW12-1 mk2516-mk2519 34887226-35322974 5.99 4.64 0.56b CP09 Liu et al. 2013[12]
4.74 6.21 0.86b SYa09
qSW12-2 mk2522-mk2523 35526715-35712060 6.44 11.03 0.85b CP10 Liu et al. 2013[12]
6.59 9.19 0.91b SYi10
6.87 7.31 0.52b BLUP
qSW18 Gm18-551.5-Gm18-552.5 55141446-55293847 3.08 5.10 0.58b CP10 Liu et al. 2013[12]
4.56 6.26 0.75b SYi10
8.00 8.64 0.56b BLUP
qSW19 mk4377-mk4378 42546296-44734953 6.26 8.56 0.89b SYi10 Stombaugh et al. 2004[17]
7.76 8.27 0.56b BLUP

Table S1

Large-effect SNP and InDel mutation sites of candidate genes between parents in qSW12-2"

基因
Gene		 位置
Position		 变异类型
Variation type		 参考碱基
REF		 变异碱基
ALT		 中品03-5373
Zhongpin 03-5373		 中黄13
Zhonghuang 13
Glyma.12G193900 35561419 Nonsynonymous SNP C T TT CC
Glyma.12G194100 35578344 Nonsynonymous SNP A G GG AA
Glyma.12G194100 35578375 Nonsynonymous SNP G A AA GG
Glyma.12G194100 35583338 Nonsynonymous SNP T G GG TT
Glyma.12G194100 35583347 Nonsynonymous SNP G A AA GG
Glyma.12G194200 35593338 Nonsynonymous SNP G A AA GG
Glyma.12G194200 35593393 Nonsynonymous SNP T C CC TT
Glyma.12G194200 35595213 Nonsynonymous SNP A T TT AA
Glyma.12G194200 35595382 Nonsynonymous SNP G A AA GG
Glyma.12G194300 35603012 Nonsynonymous SNP A C CC AA
Glyma.12G194400 35608860 Nonsynonymous SNP T A AA TT
Glyma.12G194600 35644029 Nonsynonymous SNP C T TT CC
Glyma.12G195100 35667870 Nonsynonymous SNP T G GG TT
Glyma.12G195200 35671604 Nonsynonymous SNP C T TT CC
Glyma.12G195300 35677690 Nonsynonymous SNP A G GG AA
Glyma.12G195300 35677929 Nonsynonymous SNP G A AA GG
Glyma.12G195300 35677965 Nonsynonymous SNP T C CC TT
Glyma.12G195300 35678251 Nonsynonymous SNP C A AA CC
Glyma.12G195300 35677627 Stopgain SNP C G GG CC
Glyma.12G195400 35681037 Nonsynonymous SNP T C CC TT
Glyma.12G195400 35681173 Nonsynonymous SNP C T TT CC
Glyma.12G195400 35681196 Nonsynonymous SNP A C CC AA
Glyma.12G195400 35681366 Nonsynonymous SNP C G GG CC
Glyma.12G195400 35681492 Nonsynonymous SNP T A AA TT
Glyma.12G195500 35691745 Nonsynonymous SNP T C TT CC
Glyma.12G195500 35692321 Nonsynonymous SNP A G GG AA

Fig. 2

Relative expression profiling of candidate genes for 100-seed weight trait during seed development period in soybean Genes in red font: the candidate gene for 100-seed weight of soybean. Data are obtained from the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA, USA."

Table 3

Large-effect SNP and InDel mutation sites of Glyma.12G195500 between parents"

基因
Gene		 位置
Position		 变异类型
Variation type		 中黄13
Zhonghuang 13		 中品03-5373
Zhongpin 03-5373
Glyma.12G195500 Gm12_35691745** Nonsynonymous SNP C T
Glyma.12G195500 Gm12_35692321** Nonsynonymous SNP A G

Fig. 3

Differences of 100-seed weight of different genotype materials in Glyma.12G195500 in RIL population"

Fig. 4

Haplotype analysis of Glyma.12G195500 in 385 soybean accessions A: the genome structure and haplotypes of the Glyma.12G195500 gene; the linear gene structure in the top panel displays the UTRs (black rectangles), CDS region (teal rectangles), and introns (horizontal solid black lines). The SNPs highlighted in red are the functional ones in 385 soybean samples; B: the structures of proteins encoded by three haplotypes. The amino acid abbreviations before and after slashes represent the reference and the alternative amino acids, respectively; C: frequency of haplotypes in G. soja, landrace and improved cultivar; D: significant analysis of the difference in 100-seed weight between haplotypes; the letter above the bar graph represents the P-value."

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