基于高密度Bin图谱的大豆百粒重QTL定位和候选基因分析

doi:10.3724/SP.J.1006.2022.14226

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()

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()

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)

摘要/Abstract

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

葛天丽, 田宇, 张皓, 刘章雄, 李英慧, 邱丽娟. 基于高密度Bin图谱的大豆百粒重QTL定位和候选基因分析[J]. 作物学报, 2022, 48(12): 2978-2986.

GE Tian-Li, TIAN Yu, ZHANG Hao, LIU Zhang-Xiong, LI Ying-Hui, QIU Li-Juan. QTL mapping and candidate gene prediction of soybean 100-seed weight based on high-density bin map[J]. Acta Agronomica Sinica, 2022, 48(12): 2978-2986.

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环境 Environment	亲本 Parents		群体 Population
环境 Environment	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

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	0.71^a	SYi10	Liu et al. 2013^[12]
			4.25	4.35	0.40^a	BLUP
qSW5	mk1027-mk1028	41520254-41629890	5.09	7.62	0.83^a	SYa10	Specht et al. 2001^[23]
			4.15	4.25	0.40^a	BLUP
qSW11	mk2301-mk2302	28333312-28950000	3.07	4.19	0.61^a	SYi10	Li et al. 2008^[24]
			4.94	5.11	0.43^a	BLUP
qSW12-1	mk2516-mk2519	34887226-35322974	5.99	4.64	0.56^b	CP09	Liu et al. 2013^[12]
			4.74	6.21	0.86^b	SYa09
qSW12-2	mk2522-mk2523	35526715-35712060	6.44	11.03	0.85^b	CP10	Liu et al. 2013^[12]
			6.59	9.19	0.91^b	SYi10
			6.87	7.31	0.52^b	BLUP
qSW18	Gm18-551.5-Gm18-552.5	55141446-55293847	3.08	5.10	0.58^b	CP10	Liu et al. 2013^[12]
			4.56	6.26	0.75^b	SYi10
			8.00	8.64	0.56^b	BLUP
qSW19	mk4377-mk4378	42546296-44734953	6.26	8.56	0.89^b	SYi10	Stombaugh et al. 2004^[17]
			7.76	8.27	0.56^b	BLUP

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

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

基于高密度Bin图谱的大豆百粒重QTL定位和候选基因分析

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

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