Genome-wide Association Analysis of Cadmium Content in Rice Based on MAGIC Population

doi:10.16819/j.1001-7216.2022. 210504

Chinese Journal OF Rice Science ›› 2022, Vol. 36 ›› Issue (1): 35-42.DOI: 10.16819/j.1001-7216.2022. 210504

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Genome-wide Association Analysis of Cadmium Content in Rice Based on MAGIC Population

DONG Zheng¹^,²^,^#, WANG Yamei³^,^#, LI Yongchao¹^,², XIONG Haibo¹^,², XUE Canhui¹, PAN Xiaowu¹^,², LIU Wenqiang¹^,², WEI Xiucai¹^,², LI Xiaoxiang¹^,²^,^*()

¹Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China
²Key Laboratory of indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, Changsha 410125, China
³Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

Received:2021-05-24 Revised:2021-08-16 Online:2022-01-10 Published:2022-01-10
Contact: LI Xiaoxiang
About author:First author contact:
^#These authors contributed equally to the work;

基于MAGIC群体的水稻镉含量全基因组关联分析

董铮¹^,²^,^#, 王雅美³^,^#, 黎用朝¹^,², 熊海波¹^,², 薛灿辉¹, 潘孝武¹^,², 刘文强¹^,², 魏秀彩¹^,², 李小湘¹^,²^,^*()

¹湖南省农业科学院水稻研究所, 长沙 410125
²农业部长江中下游籼稻遗传育种重点实验室, 长沙 410125
³中国农业科学院农业基因组研究所, 深圳 518120

通讯作者: 李小湘
作者简介:第一联系人：
^#共同第一作者;
基金资助:
国家重点研发计划资助项目(2016YFD0100101-12);国家现代农业产业技术体系建设专项(CARS-01-14);湖南省农业科技创新资金项目(2019LS05-2);湖南省农业科技创新资金项目(2020CX17)

Abstract

Abstract:

【Objective】Based on the MAGIC-Hei (Multi parent advanced generation inter cross) population of rice, we explored new loci/genes related to cadmium (Cd) content in multiple environments, and screened excellent lines with low Cd alleles to provide new genes and germplasm resources for breeding low Cd varieties.【Method】MAGIC-Hei, which is composed of eight parents, was planted in Changsha, Hunan Province in 2017-2020, and the Cd content was measured. Based on genotypic data by using genotyping-by-sequencing, we carried out genome wide association analysis (GWAS) on Cd content and explored QTLs to analyze their genetic mechanism. 【Results】Fourteen QTLs controlling Cd accumulation were detected. Except for chromosome 8, the 14 QTLs distribute on the other 11 chromosomes. Among them, six loci were consistent with reported genes, and eight loci were newly found. In addition, the eight loci on chromosomes 2, 4, 7, 9 and 12, can be detected in two or more environments and the effects are relatively stable, which can be used for further fine mapping and functional research. According to the results of gene annotation and gene expression analysis, LOC_ Os02g37160, LOC_ Os02g49560, LOC_ Os04g39010 and LOC_ Os06g46310 are candidate genes for Cd content related sites, which are related to heavy metal transport. In addition, we screened 10 excellent lines carrying favorable alleles, which can be used to create low Cd rice materials. 【Conclusion】Eight new QTLs for Cd accumulation related traits and excellent materials with low Cd content in rice were found in this study, which is of great significance for the genetic study of Cd accumulation and the breeding of low Cd varieties by marker assisted selection (MAS).

Key words: MAGIC, QTL, cadmium content, MAS breeding, candidate gene

摘要：

【目的】基于水稻MAGIC-Hei（Multi-parent advanced generation inter-cross）群体,在多环境下挖掘镉含量相关新位点/基因,并筛选含有低镉等位基因的优良株系,为选育低镉积累品种提供新的基因和种质资源。【方法】将由8个亲本衍生的MAGIC群体分别于2017、2018、2019和2020年度种植于湖南长沙并开展稻米镉含量表型测试分析。利用GBS（genotyping by sequencing）简化基因组测序获得基因型数据,对稻米镉含量开展全基因组关联分析（genome-wide association analysis,GWAS）,发掘QTL位点,解析其遗传机制。【结果】检测到了14个镉积累相关的QTL位点,除了第8染色体之外,其他11条染色体上均有分布。其中6个位点与已报道基因一致,8个为新发现位点。另外,这8个位点分布在第2、4、7、9和12染色体上,均可以在两个及以上环境中检测到,效应较为稳定,可用于下一步精细定位及功能研究。结合基因注释和基因表达分析结果,推测LOC_Os02g37160、LOC_Os02g49560、LOC_Os04g39010和LOC_Os06g46310为镉含量相关位点候选基因,这些基因与重金属转运和积累等功能相关。另外,我们筛选到10个携带有利等位基因的优良株系,可用于低镉积累水稻材料的创制。【结论】发掘了8个水稻镉积累相关性状的QTL位点和低镉优异材料,对于镉积累相关遗传研究和利用分子标记辅助选育低镉积累品种具有一定意义。

关键词: MAGIC, QTL, 镉含量, 分子标记辅助选择育种, 候选基因

DONG Zheng, WANG Yamei, LI Yongchao, XIONG Haibo, XUE Canhui, PAN Xiaowu, LIU Wenqiang, WEI Xiucai, LI Xiaoxiang. Genome-wide Association Analysis of Cadmium Content in Rice Based on MAGIC Population[J]. Chinese Journal OF Rice Science, 2022, 36(1): 35-42.

董铮, 王雅美, 黎用朝, 熊海波, 薛灿辉, 潘孝武, 刘文强, 魏秀彩, 李小湘. 基于MAGIC群体的水稻镉含量全基因组关联分析[J]. 中国水稻科学, 2022, 36(1): 35-42.

Figures/Tables 7

References 28

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年份 Year	亲本 Parent								多亲本高世代互交群体MAGIC population
	A	B	C	D	E	F	G	H	平均值±标准差 Mean±SD	变幅 Range	变异系数 CV/%
	2017	0.889	0.528	1.070	1.338	0.542	1.412	0.527	0.514	0.651±0.184 a	0.148~1.336	28.26
2018	1.239	0.579	1.667	1.254	0.949	1.140	0.841	0.845	0.672±0.226 ab	0.068~1.516	33.63
2019	0.605	0.291	0.627	0.823	0.491	0.443	0.459	0.509	0.327±0.154 c	0.070~1.188	47.10
2020	0.944	0.509	0.903	0.739	0.288	0.554	0.380	0.532	0.534±0.160 b	0.192~1.125	29.96

年份 Year	亲本 Parent								多亲本高世代互交群体MAGIC population
	A	B	C	D	E	F	G	H	平均值±标准差 Mean±SD	变幅 Range	变异系数 CV/%
	2017	0.889	0.528	1.070	1.338	0.542	1.412	0.527	0.514	0.651±0.184 a	0.148~1.336	28.26
2018	1.239	0.579	1.667	1.254	0.949	1.140	0.841	0.845	0.672±0.226 ab	0.068~1.516	33.63
2019	0.605	0.291	0.627	0.823	0.491	0.443	0.459	0.509	0.327±0.154 c	0.070~1.188	47.10
2020	0.944	0.509	0.903	0.739	0.288	0.554	0.380	0.532	0.534±0.160 b	0.192~1.125	29.96

QTL 名称	环境 Environment	染色体Chromosome	优异等位基因 Allele	位置 Position/Mb	峰值SNP Peak SNP	P值 P-value	贡献率 R²/%	参考文献 Reference
qCd1.1	E1/E2/E4	1	G	20.9-22.0	rs1_21942515	5.3×10^-4	8.26	[20]
qCd2.1	E4	2	G	23.8-24.3	S2_23819612	1.7×10^-4	8.53
qCd2.2	E2	2	A	30.1	rs2_30102654	9.4×10^-4	6.62
qCd3.1	E2/E3	3	A	5.8-6.9	S3_5834039	3.4×10^-4	7.40	[21]
qCd4.1	E2/E3/E4	4	T	20.2-24.2	S4_20195543	4.4×10^-4	7.46
qCd5.1	E1/E3	5	C	1.7-2.1	rs5_1811027	2.9×10^-4	7.27	OsMTP1[22]
qCd6.1	E1/E2/E4	6	C	27.0-30.8	S6_27300620	2.6×10^-5	10.57	OsHMA2[23]
qCd7.1	E3/E4	7	C	14.5-17.1	S7_16945471	6.8×10^-5	9.11
qCd9.1	E1/E2	9	C	8.1-9.8	rs9_9777578	6.9×10^-5	9.64
qCd9.2	E1	9	G	12.2-12.8	rs9_12209561	3.0×10^-4	8.00
qCd9.3	E4	9	G	16.6-16.8	S9_16720741	4.1×10^-4	7.53	[24]
qCd10.1	E3	10	C	15.9	S10_15856776	2.7×10^-4	7.66
qCd11.1	E3/E4	11	G	17.6-18.0	S11_17883239	1.3×10^-4	8.77	[25]
qCd12.1	E3	12	G	8.0-8.2	S12_8031425	9.7×10^-5	8.73

QTL 名称	环境 Environment	染色体Chromosome	优异等位基因 Allele	位置 Position/Mb	峰值SNP Peak SNP	P值 P-value	贡献率 R²/%	参考文献 Reference
qCd1.1	E1/E2/E4	1	G	20.9-22.0	rs1_21942515	5.3×10^-4	8.26	[20]
qCd2.1	E4	2	G	23.8-24.3	S2_23819612	1.7×10^-4	8.53
qCd2.2	E2	2	A	30.1	rs2_30102654	9.4×10^-4	6.62
qCd3.1	E2/E3	3	A	5.8-6.9	S3_5834039	3.4×10^-4	7.40	[21]
qCd4.1	E2/E3/E4	4	T	20.2-24.2	S4_20195543	4.4×10^-4	7.46
qCd5.1	E1/E3	5	C	1.7-2.1	rs5_1811027	2.9×10^-4	7.27	OsMTP1[22]
qCd6.1	E1/E2/E4	6	C	27.0-30.8	S6_27300620	2.6×10^-5	10.57	OsHMA2[23]
qCd7.1	E3/E4	7	C	14.5-17.1	S7_16945471	6.8×10^-5	9.11
qCd9.1	E1/E2	9	C	8.1-9.8	rs9_9777578	6.9×10^-5	9.64
qCd9.2	E1	9	G	12.2-12.8	rs9_12209561	3.0×10^-4	8.00
qCd9.3	E4	9	G	16.6-16.8	S9_16720741	4.1×10^-4	7.53	[24]
qCd10.1	E3	10	C	15.9	S10_15856776	2.7×10^-4	7.66
qCd11.1	E3/E4	11	G	17.6-18.0	S11_17883239	1.3×10^-4	8.77	[25]
qCd12.1	E3	12	G	8.0-8.2	S12_8031425	9.7×10^-5	8.73

候选基因 Candidate gene	注释信息 Annotation
LOC_Os02g37160	重金属转运蛋白Heavy metal transport/detoxification protein, putative, expressed
LOC_Os02g49560	bZIP转录因子bZIP transcription factor domain containing protein, expressed
LOC_Os04g39010	重金属相关结构域蛋白Heavy metal associated domain containing protein, expressed
LOC_Os06g46310	重金属转运因子Nramp6 Metal transporter Nramp6, putative, expressed

Genome-wide Association Analysis of Cadmium Content in Rice Based on MAGIC Population

基于MAGIC群体的水稻镉含量全基因组关联分析

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