基于MAGIC群体的水稻抽穗期和产量相关性状全基因组 关联分析

doi:10.16819/j.1001-7216.2020.0107

中国水稻科学 ›› 2020, Vol. 34 ›› Issue (4): 325-331.DOI: 10.16819/j.1001-7216.2020.0107

基于MAGIC群体的水稻抽穗期和产量相关性状全基因组关联分析

魏秀彩¹^,^#, 刘金栋³^,^#, 刘利成^2,⁴, 黎用朝^1,^2,⁴, 潘孝武^1,^2,⁴, 董铮^2,⁴, 刘文强^1,^2,⁴, 熊海波^2,⁴, 闵军^2,⁴, 李小湘^1,^2,^4,^*()

¹湖南大学研究生院隆平分院, 长沙 410125
²湖南省农业科学院水稻研究所, 长沙 410125
³中国农业科学院农业基因组研究所, 深圳 518124
⁴农业部长江中下游籼稻遗传育种重点实验室, 长沙 410125

收稿日期:2020-01-19 修回日期:2020-03-04 出版日期:2020-07-10 发布日期:2020-07-10
通讯作者: 李小湘
作者简介:
^#共同第一作者

Genome-wide Association Analysis of Rice Heading Date and Yield-related Traits Based on MAGIC Population

Xiucai WEI¹^,^#, Jindong LIU³^,^#, Licheng LIU^2,⁴, Yongchao LI^1,^2,⁴, Xiaowu PAN^1,^2,⁴, Zheng DONG^2,⁴, Wenqiang LIU^1,^2,⁴, Haibo XIONG^2,⁴, Jun MIN^2,⁴, Xiaoxiang LI^1,^2,^4,^*()

¹Longping Branch, Graduate School of Hunan University, Changsha 410125, China
²Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China
³Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
⁴Key Laboratory of indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture, Changsha 410125, China

Received:2020-01-19 Revised:2020-03-04 Online:2020-07-10 Published:2020-07-10
Contact: Xiaoxiang LI
About author:
^#These authors contributed equally to the work

摘要/Abstract

摘要：

【目的】挖掘水稻抽穗期和产量相关性状新基因,并筛选携带有利等位基因的优良株系,为分子标记辅助育种提供新基因和优异种质。【方法】以多亲本重组自交系群体MAGIC-Hei群体为材料,分别于2017和2018年连续两年种植于湖南长沙开展抽穗期和产量性状表型调查,基于基因分型（genotyping by sequencing,GBS）技术进行全基因组关联分析发掘影响水稻抽穗期、单株有效穗数、每穗粒数、结实率、千粒重和单株产量性状QTL。【结果】在两个环境下共计检测到26个控制抽穗期和产量相关性状的QTL,分布于除第10染色体外的其他染色体上。其中,11个位点为新位点,1个新位点（qNTP9）在两年均被检测到,该位点受环境影响较小,可用于进一步的精细定位和基因克隆。根据抽穗期和产量性状表型数据,结合SNP基因型筛选到5个携带有利等位基因的优良株系,可用于将来的水稻高产育种。【结论】本研究发掘一批新的水稻抽穗期和产量相关性状QTL位点,可有效加速水稻遗传研究和高产育种进程。

关键词: 多亲本重组自交系群体, 抽穗期, 全基因组关联分析

Abstract:

【Objective】The objective of the study is to identify new genes related to heading date and yield related traits in rice, and to screen the elite rice lines carrying favorable alleles, therefore providing new genes and excellent germplasm for molecular marker-assisted (MAS) breeding.【Method】The multi-parent generation inter-crosses (MAGIC) population MAGIC-Hei was planted in 2017 and 2018 in Changsha, Hunan Province. Genome-wide association analysis was performed to detect the quantitative trait loci associated with heading date, number of tillers per plant, grain number per panicle, seed setting rate, 1000-grain weight and grain yield per plant based on genotyping by sequencing (GBS).【Results】Totally, 26 QTLs that control heading date and yield related traits were identified on all the chromosomes except chromosome 10 in the two years. Of these, 11 are new and qNTP9, associated with the number of effective panicles, was detected in the two years. qNTP9 was less affected by environment and could be used for further fine mapping and gene cloning. Based on the phenotypic and the SNP genotypes five elite lines carrying favorable alleles were selected, which could be used for future high-yielding rice breeding. 【Conclusion】The loci associated with heading date and yield related traits could be used for rice breeding.

Key words: multi-parent advanced generation inter-crosses population, heading date, genome-wide association study

中图分类号:

Q755
S511.01

魏秀彩, 刘金栋, 刘利成, 黎用朝, 潘孝武, 董铮, 刘文强, 熊海波, 闵军, 李小湘. 基于MAGIC群体的水稻抽穗期和产量相关性状全基因组关联分析[J]. 中国水稻科学, 2020, 34(4): 325-331.

Xiucai WEI, Jindong LIU, Licheng LIU, Yongchao LI, Xiaowu PAN, Zheng DONG, Wenqiang LIU, Haibo XIONG, Jun MIN, Xiaoxiang LI. Genome-wide Association Analysis of Rice Heading Date and Yield-related Traits Based on MAGIC Population[J]. Chinese Journal OF Rice Science, 2020, 34(4): 325-331.

图/表 5

参考文献 29

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性状 Trait	年份 Year	亲本 Parents								多亲本高世代互交群体 MAGIC population
性状 Trait	年份 Year	A	B	C	D	E	F	G	H	平均值±标准差 Mean±SD	变幅 Range	变异系数 CV /%
抽穗期 Heading date/d	2017	93	79	99	120	84	125	88	95	93.03±5.15	83~106	5.53
抽穗期 Heading date/d	2018	94	80	106	122	90	118	91	96	99.98±8.89 ^**	76~114	8.89
单株有效穗数 No. of effective panicles	2017	15	21	15	12	18	15	18	20	17.25±3.21	10~27	18.58
单株有效穗数 No. of effective panicles	2018	17	18	17	16	11	14	16	16	13.68±2.69^**	7~22	19.68
每穗粒数 Grain number per panicle	2017	166	157	157	110	126	159	114	112	149.7±31.0	81~265	20.72
每穗粒数 Grain number per panicle	2018	198	137	118	117	164	184	117	111	152.2±30.2	88~253	19.82
结实率 Seed setting rate/%	2017	45.85	78.89	67.03	68.51	68.06	78.46	83.14	76.48	62.93±12.72	28.55~88.22	20.22
结实率 Seed setting rate/%	2018	50.41	41.84	55.55	71.56	49.85	73.44	84.05	73.22	61.52±16.50	3.99~89.44	26.82
千粒重 1000-grain weight/g	2017	20.42	15.7	24.65	24.91	26.45	13.2	24.52	22.83	22.23±2.76	15.96~30.89	12.43
千粒重 1000-grain weight/g	2018	22.50	15.66	24.5	24.84	27.29	12.55	25.38	22.5	21.81±2.77 ^**	14.74~32.29	12.68
单株产量 Grain yield per plant/g	2017	24.07	38.88	35.38	23.69	46.49	26.79	34.20	44.83	34.92±9.47	11.56~62.96	27.12
单株产量 Grain yield per plant/g	2018	32.38	26.38	26.66	30.75	25.34	23.52	37.77	30.30	27.81±10.49^**	1.14~67.73	37.70

性状 Trait	年份 Year	亲本 Parents								多亲本高世代互交群体 MAGIC population
性状 Trait	年份 Year	A	B	C	D	E	F	G	H	平均值±标准差 Mean±SD	变幅 Range	变异系数 CV /%
抽穗期 Heading date/d	2017	93	79	99	120	84	125	88	95	93.03±5.15	83~106	5.53
抽穗期 Heading date/d	2018	94	80	106	122	90	118	91	96	99.98±8.89 ^**	76~114	8.89
单株有效穗数 No. of effective panicles	2017	15	21	15	12	18	15	18	20	17.25±3.21	10~27	18.58
单株有效穗数 No. of effective panicles	2018	17	18	17	16	11	14	16	16	13.68±2.69^**	7~22	19.68
每穗粒数 Grain number per panicle	2017	166	157	157	110	126	159	114	112	149.7±31.0	81~265	20.72
每穗粒数 Grain number per panicle	2018	198	137	118	117	164	184	117	111	152.2±30.2	88~253	19.82
结实率 Seed setting rate/%	2017	45.85	78.89	67.03	68.51	68.06	78.46	83.14	76.48	62.93±12.72	28.55~88.22	20.22
结实率 Seed setting rate/%	2018	50.41	41.84	55.55	71.56	49.85	73.44	84.05	73.22	61.52±16.50	3.99~89.44	26.82
千粒重 1000-grain weight/g	2017	20.42	15.7	24.65	24.91	26.45	13.2	24.52	22.83	22.23±2.76	15.96~30.89	12.43
千粒重 1000-grain weight/g	2018	22.50	15.66	24.5	24.84	27.29	12.55	25.38	22.5	21.81±2.77 ^**	14.74~32.29	12.68
单株产量 Grain yield per plant/g	2017	24.07	38.88	35.38	23.69	46.49	26.79	34.20	44.83	34.92±9.47	11.56~62.96	27.12
单株产量 Grain yield per plant/g	2018	32.38	26.38	26.66	30.75	25.34	23.52	37.77	30.30	27.81±10.49^**	1.14~67.73	37.70

年份 Year	性状 Trait	抽穗期 Heading date	单株有效穗数 No. of effective panicles(NTP)	每穗粒数 Grain number per panicle(GNPP)	结实率 Seed setting rate (SR)	千粒重 1000-grain weight (GW)
2017	单株有效穗数NTP	-0.16^*
	每穗粒数GNPP	0.08	-0.34^**
	结实率SR	-0.41^**	0.06	-0.18^**
	千粒重GW	-0.08	-0.16^*	-0.30^**	-0.01
	单株产量YD	-0.37^**	0.43^**	0.19^**	0.63^**	0.10
2018	单株有效穗数NTP	-0.25^**
	每穗粒数 GNPP	-0.11	-0.25^**
	结实率SR	-0.23^**	0.15^*	-0.03
	千粒重 GW	-0.20^**	0.46^**	-0.27^**	0.04
	单株产量 YD	-0.42^**	0.46^**	0.25^**	0.77^**	0.16^**

年份 Year	性状 Trait	抽穗期 Heading date	单株有效穗数 No. of effective panicles(NTP)	每穗粒数 Grain number per panicle(GNPP)	结实率 Seed setting rate (SR)	千粒重 1000-grain weight (GW)
2017	单株有效穗数NTP	-0.16^*
	每穗粒数GNPP	0.08	-0.34^**
	结实率SR	-0.41^**	0.06	-0.18^**
	千粒重GW	-0.08	-0.16^*	-0.30^**	-0.01
	单株产量YD	-0.37^**	0.43^**	0.19^**	0.63^**	0.10
2018	单株有效穗数NTP	-0.25^**
	每穗粒数 GNPP	-0.11	-0.25^**
	结实率SR	-0.23^**	0.15^*	-0.03
	千粒重 GW	-0.20^**	0.46^**	-0.27^**	0.04
	单株产量 YD	-0.42^**	0.46^**	0.25^**	0.77^**	0.16^**

QTL	年份 Year	染色体 Chromosome	区间 Interval	等位基因 Allele	峰值SNP Peak SNP	P值 P value	贡献率 R²/%	位点附近已知基因 Known gene near the locus
qHD2	2017	2	491 868-972 602	T/C	rs2_636770	1.97×10^-4	4.60
qHD3	2017	3	1 195 479-1 817 619	A/T	rs3_1777161	1.45×10^-5	6.30	OscpSRP43
qHD3	2018	3	1 777 161-1 817 619	A/T	rs3_1817619	3.24×10^-4	4.29
qHD6	2017	6	1 589 993-3 932 840	C/A	rs6_3582593	3.25×10^-5	5.76	HGW
qHD6	2018	6	3 582 592-3 582 593	C/A	rs6_3582593	2.89×10^-4	4.36	HGW
qHD7	2017	7	29 092 626-29 664 075	A/G	rs7_29285337	3.14×10^-4	4.30	GHD7.1
qHD7	2018	7	29 056 813-29 664 075	T/C	rs7_29571005	1.41×10^-6	7.85	GHD7.1
qHD8	2017	8	4 604 002-7 672 471	T/C	rs8_5217372	1.85×10^-7	9.21	DTH8
qHD8	2018	8	3 955 562-7 672 471	T/C	rs8_5217372	3.81×10^-7	8.74
qHD12	2018	12	6 576 540-6 576 601	G/A	rs12_6576540	9.29×10^-4	3.63

基于MAGIC群体的水稻抽穗期和产量相关性状全基因组关联分析

Genome-wide Association Analysis of Rice Heading Date and Yield-related Traits Based on MAGIC Population

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性状 Trait	QTL	年份 Year	染色体 Chr.	区间 Interval/bp	等位基因Allele	峰值SNP Peak SNP	P值 P-value	贡献率 R²/%	位点附近基因 Gene nearby
单株有效穗数 No. of tillers per plant	qNTP2	2018	2	27 342 909–27 866 887	G/A	rs2_27799677	3.49×10^-4	6.08	OsGRF10
	qNTP7	2017	7	19 631 949–28 445 131	G/A	rs7_19631949	1.16×10^-4	6.84
	qNTP9	2017	9	12 265 152–14 127 114	C/T	rs9_12265152	2.16×10^-4	6.28
		2018	9	12 266 970–12 272 116	C/G	rs9_12266970	8.16×10^-4	5.31
每穗粒数 Grain number per panicle	qGNPP1.1	2017	1	6 388 045–6 419 185	G/A	rs1_6388045	7.61×10^-4	5.30	OsSCAR1
	qGNPP1.2	2017	1	42 038 276–42 110 528	A/C	rs1_42038276	7.53×10^-4	5.30
	qGNPP3	2017	3	26 360 129–26 584 753	G/T	rs3_26556040	1.12×10^-5	9.19	RGB1
		2018	3	26 360 129–26 584 753	G/T	rs3_26556040	3.56×10^-5	7.99
	qGNPP4	2017	4	27 568 586–27 724 754	C/A	rs4_27568586	6.61×10^-4	5.42	OsMKKK10, GPX1
结实率 Seed setting rate	qSR2	2017	2	1 576 258–2 042 539	T/C	rs2_2022085	5.00×10^-4	5.71	CAP1
	qSR8	2017	8	6 256 114–8 323 064	G/A	rs8_6256114	2.54×10^-6	10.68	SPL29
		2018	8	5 329 786–8 323 064	G/A	rs8_6256114	6.58×10^-6	9.89
	qSR9	2018	9	14 813 317–15 691 090	G/A	rs9_15627416	6.13×10^-5	7.74
千粒重 1000-grain weight	qGW1	2017	1	7 569 628–9 712 079	C/G	rs1_8577645	1.12×10^-4	6.83	OsDof2, OsSar1c
	qGW3	2017	3	16 975 669–17 039 466	G/A	rs3_16975669	7.49×10^-4	5.16	GS3
		2018	3	13 733 085–17 285 992	T/C	rs3_16842769	1.16×10^-5	8.97
	qGW5	2018	5	5 391 586–6 065 099	T/C	rs5_6065099	8.15×10^-4	5.13	JMJ703
	qGW7	2018	7	20 500 034–28 901 978	G/T	rs7_28901978	8.33×10^-5	7.16
	qGW8	2018	8	26 573 952–27 943 348	C/A	rs8_26573952	2.84×10^-4	6.06	OsOTUB1, OsSPL16
单株产量 Grain yield per plant	qYD1.1	2018	1	216 965–229 285	C/G	rs1_216965	3.96×10^-4	5.90	OsDET1, OsLIR1
	qYD1.2	2017	1	28 576 150–28 596 409	A/G	S1_28576150	9.55×10^-4	5.16
	qYD7	2018	7	5 726 510–5 770 877	G/T	S7_5769445	2.64×10^-4	6.29
	qYD11	2018	11	239 86 604–23 989 090	A/G	rs11_23986604	6.11×10^-4	5.52
	qYD12	2017	12	17 618 079–19 072 396	T/C	rs12_18120406	1.01×10^-4	7.22

品系 Line	性状 Trait	染色体 Chr.	区间 Interval/bp	有利等位基因 Favorable allele	SNP基因型对照 SNP genotype control	2017 2018
GID4170482	单株有效穗数 NTP	9	12 265 152–14 127 114	C/T	TGCGC/TGTGC	27	22
GID4170482	抽穗期 HD / d	6	1 589 993–3 932 840	C/A	TGCCC/CGACC	87	92
GID4172993	每穗粒数 GNPP	3	26 360 129–26 584 753	G/T	AGGGT/CCTCC	249	204
GID4172993	抽穗期 HD / d	8	4 604 002–7 672 471	T/C	GGTGC/GGCGC	90	92
GID4173982	结实率 SR / %	8	5 329 786–8 323 064	G/A	TAGGG/TAACC	84.12	81.27
GID4173982	抽穗期 HD / d	6	1 589 993–3 932 840	C/A	TGCCC/CGACC	85	86
GID4173992	千粒重 GW / g	3	13 733 085–17 285 992	G/A	GCGTT/ATATG	26.88	29.34
GID4173992	抽穗期 HD / d	8	4 604 002–7 672 471	C/T	GGTGC/GGCGC	84	87
GID4171060	单株产量 YD / g	12	17 618 079–19 072 396	T/C	CGTTC/CGCTT	46.90	67.73
GID4171060	抽穗期 HD / d	8	4 604 002–7 672 471	C/T	GGTGC/GGCGC	85	94

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基于MAGIC群体的水稻抽穗期和产量相关性状全基因组 关联分析

Genome-wide Association Analysis of Rice Heading Date and Yield-related Traits Based on MAGIC Population

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基于MAGIC群体的水稻抽穗期和产量相关性状全基因组关联分析