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作物学报 ›› 2022, Vol. 48 ›› Issue (12): 2978-2986.doi: 10.3724/SP.J.1006.2022.14226

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于高密度Bin图谱的大豆百粒重QTL定位和候选基因分析

葛天丽(), 田宇, 张皓, 刘章雄, 李英慧(), 邱丽娟()   

  1. 农作物基因资源与基因改良国家重大科学工程 / 农业农村部北京大豆生物学重点实验室 / 中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2021-12-02 接受日期:2022-02-25 出版日期:2022-12-12 网络出版日期:2022-03-12
  • 通讯作者: 李英慧,邱丽娟
  • 作者简介:葛天丽, E-mail: 2030587001@qq.com第一联系人：

    **同等贡献

  • 基金资助:
    “十三五”国家重点研发计划项目“中欧大豆品种联合鉴定、创新及优异基因源发掘”(2019YFE0105900)

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 Published:2022-12-12 Published online:2022-03-12
  • Contact: LI Ying-Hui,QIU Li-Juan
  • 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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摘要：

百粒重是决定大豆产量的关键因子, 鉴定百粒重相关的QTL和候选基因, 进而利用现代分子设计育种技术改良粒大小, 是培育大粒高产品种的重要途径。本研究以中黄13和中品03-5373为亲本所构建的重组自交系(recombinant inberd lines, RIL)群体为材料, 利用前期构建的高密度Bin图谱和3年6个环境下的百粒重表型, 检测到2个在环境间稳定的百粒重相关QTL, 分别位于12号和18号染色体。其中qSW12-2表型贡献率为7.31%~11.03%, 加性效应为0.52~0.91 g, 增效等位基因来自中黄13。qSW12-2区间长度为0.19 Mb, 覆盖20个注释基因, 进一步根据候选区间内各基因的组织表达量、注释和双亲多态性分析结果, 推测参与油菜素类固醇的生物合成、在籽粒发育期高度表达且携带大效应遗传位点的Glyma.12G195500为百粒重功能基因。基于全基因组重测序数据, 多态性分析表明Glyma.12G195500在385份大豆种质资源形成3种单倍型, 其中以中黄13为代表的携带H2单倍型的种质资源的百粒重显著高于以中品03-5373为代表的携带H1单倍型的种质资源, H2单倍型在大豆驯化过程中被选择。本研究挖掘的新位点可为进一步揭示大豆百粒重的遗传机制和培育高产大豆新品种奠定基础。

关键词: 大豆, 百粒重, Bin图谱, 候选基因, 单倍型分析

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

表1

中黄13/中品03-5373重组自交系及亲本的百粒重性状表型"

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

图1

中黄13/中品03-5373重组自交系及亲本的百粒重表型分布特征"

表2

中黄13/中品03-5373 RIL群体中在多环境定位到的百粒重QTL"

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

附表1

qSW12-2内候选基因在亲本间的大效应SNP变异位点"

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

图2

种子发育不同时期大豆百粒重相关候选基因特异性表达分析 红色字体基因: 大豆百粒重候选基因。数据信息来源于SoyBase中大豆参考基因组Wm82.a2.v1 (var. Williams 82)提供的RNA-Seq。"

表3

Glyma.12G195500在亲本间的大效应SNP变异位点"

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

图3

RIL群体中携带Glyma.12G195500不同基因型材料的百粒重差异"

图4

Glyma.12G195500在385份大豆种质资源中的单倍型分析 A: Glyma.12G195500的基因结构和单倍型; 线性基因结构显示了UTR (黑色矩形)、CDS区域(青色矩形)和内含子(水平黑色实线)。红色垂直实线代表385个大豆资源中的功能SNP位点; B: 3种单倍型编码的蛋白质的结构; 斜线前后的氨基酸缩写代表参考和替代氨基酸; C: 单倍型在野生大豆、地方品种和选育品种中的发生频率; D: 单倍型间百粒重差异显著性分析; 条形图上方的字母表示P值。"

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