水稻RIL群体高密度遗传图谱构建及粒型QTL定位

doi:10.3864/j.issn.0578-1752.2021.24.001

摘要/Abstract

摘要：

【目的】水稻粒型是与产量直接相关的重要农艺性状,影响稻米的外观品质和商品价值。挖掘新的水稻粒型相关基因,对揭示水稻粒型调控的遗传机理研究有重要意义,同时可为水稻粒型分子育种提供新的基因资源。【方法】以极端粒型差异的粳稻TD70和籼稻Kasalath,以及杂交构建的186个家系的重组自交系群体为研究材料,利用高通量测序技术对亲本和RIL株系进行深度测序。统计186个RIL基因型数据,利用滑动窗法（SNP/InDel数目为15）,将窗口内SNP/InDel信息转换成窗口的基因型,预测染色体上的重组断点构建RIL群体的BinMap遗传图谱,结合2年的粒长、粒宽、粒厚和千粒重的表型数据,运用QTL IciMapping软件,采用复合区间作图法对RIL群体的4个性状进行QTL定位。【结果】构建了一张包含12 328个Bin标记的高密度遗传图谱,该图谱各染色体Bin标记数为763—1 367个,标记间平均物理距离为30.26 kb。粒长、粒宽、粒厚和千粒重4个性状在RIL群体中呈近正态连续分布,且2年间的变化趋势相似,符合QTL作图要求。2018年对粒长、粒宽、粒厚及千粒重进行QTL分析,共检测到40个粒型QTL,其中,粒长12个,粒宽9个,粒厚8个,千粒重11个,2019年对粒长、粒宽、粒厚及千粒重进行QTL分析,检测到56个籽粒相关的QTL,粒长15个,粒宽11个,粒厚13个,千粒重17个。分析定位到的96个粒型QTL位点,连续2年都能检测到的QTL位点有11个,其中7个为已克隆的粒型基因位点,4个为未知的新位点,分别分布于第1、3、4、5染色体上,分别为粒长qGL-1-2和qGL5-2、粒厚qGT-3-2、粒宽qGW-4-1。【结论】构建了一张包含12 328个Bin标记的分子遗传连锁图谱,解析大粒粳稻资源的粒型基因,获得了qGW-4-1、qGL5-2、qGT-3-2、qGL-1-2等4个新的粒型QTL,可用于后续粒型调控基因的精细定位及克隆研究。

关键词: 水稻, Bin图谱, 粒型, QTL定位

Abstract:

【Objective】Rice grain shape is an important agronomic trait directly related to yield, which affects the appearance quality and commercial value of rice. Research on new rice grain shape genes is of great value for revealing the genetic mechanism of rice grain shape, and it can provide some new genetic resources for molecular breeding. 【Method】In the present study, a RIL population which constructed by an extra-large grain japonica rice variety TD70 and a small-grain indica rice variety Kasalath was used as the research material. The phenotypic data of grain shape, such as grain length, grain width, grain thickness and thousand grain weight were investigated. Using the Genotyping-By-Sequencing approach to re-sequence the parents and RILs to obtain SNP information. The sliding window method (the number of SNP/InDel is 15) was used for genotype calling and recombination breakpoint determination. Based on these results, a high-density Bin map was constructed. Meanwhile, the compound interval mapping method of QTL IciMapping software was used to map the QTLs related to grain shape. 【Result】A high-density genetic map containing 12 328 Bin markers was constructed. The number of Bin markers on each chromosome is 763 to 1367, and the average physical distance between markers was 30.26 kb. The frequency distribution of each trait for RIL population was continuous, which were consistent with the characteristics of quantitative characters, so it was suitable for the detection of QTL. QTL analysis of RIL population in 2018 showed that 40 grain-shape QTL were detected, including 12 grain length QTL, 9 grain width QTL, 8 grain thickness QTL, and 11 thousand-grain weight QTL. QTL analysis was performed of RIL population in 2019, and 56 grain-related QTL were detected, including 15 grain length QTL, 11 grain width QTL, 13 grain thickness QTL, and 17 thousand-grain weight QTL. Based on the two-year mapping results, we have mapped a total of 96 grain shape QTL. We found that 11 QTL could be detected for two consecutive years; among them, 7 QTL have been cloned and 4 new QTL were distributed on 1, 3, 4 and 5 chromosomes. Among the 4 new QTL, qGL-1-2 and qGL-5-2 was related to grain length, qGT-3-2 related grain thickness and qGW-4-1 related to grain width. 【Conclusion】We constructed a molecular genetic linkage map containing 12 328 Bin markers and used the map to analyze the grain shape loci of extra-large grain rice resources. Four new QTLs related to grain shape were obtained, which can be used for subsequent fine mapping, cloning and functional studies.

Key words: rice (Oryza sativa L.), Bin genetic map, grain shape, QTL mapping

张亚东,梁文化,赫磊,赵春芳,朱镇,陈涛,赵庆勇,赵凌,姚姝,周丽慧,路凯,王才林. 水稻RIL群体高密度遗传图谱构建及粒型QTL定位[J]. 中国农业科学, 2021, 54(24): 5163-5176.

ZHANG YaDong,LIANG WenHua,HE Lei,ZHAO ChunFang,ZHU Zhen,CHEN Tao,ZHAO QingYong,ZHAO Ling,YAO Shu,ZHOU LiHui,LU Kai,WANG CaiLin. Construction of High-Density Genetic Map and QTL Analysis of Grain Shape in Rice RIL Population[J]. Scientia Agricultura Sinica, 2021, 54(24): 5163-5176.

图/表 7

图1

表1

图2

表2

图3

图4

表3

粒型性状QTL分析"

性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	LOD值 LOD score		贡献率PVE (%)		加性效应 Additive
性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	2018	2019	2018	2019	2018	2019
粒长 GL
qGL-1-1	1	RBN0626—RBN0627			3.32		1.41		-0.14
qGL-1-2*	1	RBN0752—RBN0746		3.60		3.15		-0.29
qGL-2-2	2	RBN2285—RBN2286	TGW2	7.47	8.27	4.26	3.69	-0.22	-0.23
qGL-2-1	2	RBN1612—RBN1613			4.47		2.00		-0.16
qGL-2-3	2	RBN2346—RBN2347			3.31		1.50		0.62
qGL-3-1	3	RBN2661—RBN2665		10.97		6.66		0.87
qGL-3-2	3	RBN2808—RBN2809	GS3	27.88	27.05	20.94	15.44	-0.48	-0.46
qGL-3-3	3	RBN2901—RBN2900		11.36		6.77		-0.29
qGL-3-4	3	RBN2915—RBN2916			12.62		5.79		-0.29
qGL-3-5	3	RBN3000—RBN2997	qGL3/GL3.1	27.50	22.49	21.26	12.55	-0.52	-0.44
qGL-4	4	RBN4252—RBN4253	XIAO	10.85	8.37	6.66	3.86	-0.27	-0.22
qGL-5-1	5	RBN4645—RBN4646			7.43		3.36		0.21
qGL-5-2**	5	RBN5163—RBN5167		5.81	4.31	5.13	4.55	-0.29	-0.24
性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	LOD值 LOD score		贡献率PVE (%)		加性效应 Additive
性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	2018	2019	2018	2019	2018	2019
qGL-7-1	7	RBN6899—RBN6900			3.22		1.48		0.56
qGL-7-2	7	RBN7397—RBN7393			15.55		7.44		0.31
qGL-7-3	7	RBN7400—RBN7402	GL7/GW7	10.13	33.76	5.99	21.17	0.26	0.53
qGL-8	8	RBN8430—RBN8434	GW8	7.30		4.13		-0.25
qGL-9	9	RBN8628—RBN8629			2.58		1.02		0.39
qGL-11	11	RBN11026—RBN11027		3.99		2.21		-0.16
qGL-12-1	12	RBN11481—RBN11482	LARGE2	5.36		3.00		0.18
qGL-12-2	12	RBN11605—RBN11608			4.99		2.14		0.17
粒宽 GW
qGW-2-1	2	RBN1385—RBN1387			7.16		4.55		-0.08
qGW-2-2	2	RBN1564—RBN1566	GW2	35.15	32.03	28.82	30.07	-0.20	-0.21
qGW-2-3	2	RBN2138—RBN2136			8.47		5.61		-0.09
qGW-2-4	2	RBN2203—RBN2204	GS2	3.05		1.61		-0.05
qGW-4-1**	4	RBN3403—RBN3404		5.17	3.22	3.05	3.65	0.13	-0.38
qGW-4-2	4	RBN4252—RBN4253	XIAO	4.40		2.50		0.06
qGW-4-3	4	RBN4420—RBN4421		12.66		7.73		-0.10
qGW-4-4	4	RBN4427—RBN4428			5.45		3.48		-0.07
qGW-5	5	RBN4641—RBN4642	GW5	32.44	22.82	25.59	18.31	-0.18	-0.16
qGW-7-1	7	RBN7188—RBN7189	GLW7	7.20		4.11		-0.07
qGW-7-2	7	RBN7481—RBN7482		5.03		2.78		-0.09
qGW-8-1	8	RBN7840—RBN7842			3.51		2.71		-0.41
qGW-8-2	8	RBN8134—RBN8135			3.98		2.54		-0.06
qGW-9-1	9	RBN8981—RBN8988		4.87		3.07		0.06
qGW-10-1	10	RBN9497—RBN9501			2.53		1.60		-0.23
qGW-11-1	11	RBN10406—RBN10407	SRS5/TID1/OsTubA2		3.84		2.80		-0.19
qGW-11-2	11	RBN10496—RBN10497			3.40		2.21		0.06
粒厚 GT
qGT-1	1	RBN0651—RBN0652			8.59		6.82		-0.05
qGT-2-1	2	RBN1564—RBN1566	GW2	31.44		33.33		-0.09
qGT-2-2	2	RBN1569—RBN1573			11.80		9.67		-0.05
qGT-2-3	2	RBN1609—RBN1610			17.82		16.27		-0.06
qGT-3-1	3	RBN2565—RBN2566		5.28		4.06		-0.03
qGT-3-2*	3	RBN2710—RBN2711			6.32		5.01		-0.04
qGT-3-3	3	RBN2782—RBN2783		4.43		3.36		0.03
qGT-3-4	3	RBN2901—RBN2900		5.78		4.33		-0.04
qGT-3-5	3	RBN2987—RBN2986			10.68		8.76		-0.05
qGT-4-1	4	RBN3413—RBN3414			5.28		4.14		0.03
qGT-4-2	4	RBN3548—RBN3549		3.56		2.67		0.03
qGT-5-1	5	RBN4661—RBN4663		9.81		7.77		-0.04
性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	LOD值 LOD score		贡献率PVE (%)		加性效应 Additive
性状与位点 Trait and loc	染色体 Chr.	标记区间 Marker interval	关联基因 Cloned gene	2018	2019	2018	2019	2018	2019
qGT-5-2	5	RBN4668—RBN4669			8.16		6.66		-0.04
qGT-7	7	RBN7494—RBN7495		7.86		6.04		0.04
qGT-8	8	RBN7851—RBN7852			3.21		2.51		-0.02
qGT-10-1	10	RBN10072—RBN10074			5.68		4.49		-0.03
qGT-10-2	10	RBN10129—RBN10126		2.88		2.11		-0.02
qGT-11	11	RBN10949—RBN10950			3.43		2.73		0.03
qGT-12-1	12	RBN11790—RBN11791			6.85		5.44		-0.05
qGT-12-2	12	RBN11823—RBN11824			4.22		3.18		0.05
qGT-12-3	12	RBN11866—RBN11879			4.67		3.60		0.03
千粒重 TGW
qTGW-1-1	1	RBN0261—RBN0262		3.99		2.48		-1.03
qTGW-1-2*	1	RBN0752—RBN0746			22.24		11.34		-2.38
qTGW-1-3	1	RBN0767—RBN0766			10.25		4.31		1.46
qTGW-2-1	2	RBN1564—RBN1566	GW2	19.35		14.68		-2.55
qTGW-2-2	2	RBN1630—RBN1631			27.16		14.59		-2.56
qTGW-2-3	2	RBN1917—RBN1918			7.12		2.85		1.21
qTGW-2-4	2	RBN2043—RBN2044			7.52		3.31		-1.32
qTGW-2-5	2	RBN2121—RBN2120		4.43		3.42		-1.28
qTGW-3-1	3	RBN2539—RBN2536			8.19		3.31		-1.55
qTGW-3-2*	3	RBN2710—RBN2711		8.56		6.07		-1.69
qTGW-3-3	3	RBN2827—RBN2828			9.97		4.24		-1.42
qTGW-3-4	3	RBN2901—RBN2900		33.78		31.19		-3.91
qTGW-3-5	3	RBN3000—RBN2997	qGL3/GL3.1		23.36		12.38		-2.50
qTGW-4-1	4	RBN3699—RBN3697		3.30		2.03		0.96
qTGW-4-2	4	RBN4427—RBN4428			5.81		2.31		-1.00
qTGW-5-1	5	RBN4536—RBN4537	OsMKP1/GSN1	3.64		2.26		0.98
qTGW-5-2	5	RBN4618—RBN4620	GS5	9.63		6.55		-1.65
qTGW-5-3	5	RBN4702—RBN4701	GSK2		7.36		2.97		-1.13
qTGW-6-1	6	RBN5529—RBN5530			8.91		4.03		-1.37
qTGW-6-2	6	RBN5538—RBN5539	TGW6		11.92		5.15		1.47
qTGW-7-1	7	RBN7400—RBN7402	GL7/GW7	6.37		4.13		1.32
qTGW-7-2	7	RBN7516—RBN7517			9.62		4.03		-1.30
qTGW-10	10	RBN10129—RBN10126		3.41		2.12		-0.97
qTGW-11-1	11	RBN10406—RBN10407	SRS5/TID1/OsTubA2		2.71		1.17		-1.70
qTGW-11-2	11	RBN10523—RBN10524		5.27		3.73		-1.67
qTGW-11-3	11	RBN11260—RBN11261			4.38		2.14		-1.01
qTGW-12-1	12	RBN11790—RBN11791			10.85		4.63		-1.91
qTGW-12-2	12	RBN11948—RBN11949			5.54		2.19		1.10

表3

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性状 Trait	年份 Year	亲本 Parents		重组自交系 RIL populations
性状 Trait	年份 Year	TD70	Kasalath	平均值 Average	变异范围 Range	变异系数 CV (%)
粒长 GL (mm)	2018	13.40	8.04	9.72	7.77—13.00	12.72
粒长 GL (mm)	2019	13.29	8.07	9.58	7.42—12.74	12.57
粒宽 GW (mm)	2018	4.42	2.48	3.12	2.37—4.34	11.52
粒宽 GW (mm)	2019	4.29	2.48	3.11	2.31—4.42	11.88
粒厚 GT (mm)	2018	2.99	1.84	2.10	1.71—2.63	7.35
粒厚 GT (mm)	2019	2.93	1.90	2.17	1.79—2.78	8.12
千粒重 TGW (g)	2018	64.95	17.40	30.60	17.95—55.40	22.58
千粒重 TGW (g)	2019	66.52	17.83	27.99	14.77—49.75	22.68

染色体 Chromosome	Bin个数 Bin number	遗传距离 Genetic distance (cM)	标记平均距离 Mean distance between markers (cM)
1	1367	2173.32	1.589846379
2	991	1290.30	1.302018163
3	948	1158.52	1.222067511
4	1177	2400.93	2.039872557
5	954	1522.71	1.596132075
6	1103	1849.13	1.676455122
7	1032	2198.84	2.130658915
8	1045	2055.74	1.967215311
9	788	1453.83	1.844961929
10	763	1006.01	1.318492792
11	1098	1938.07	1.765091075
12	1062	2248.04	2.116798493