利用陆地棉MAGIC群体定位产量、生育期和株高性状的QTL

doi:10.3724/SP.J.1006.2018.01320

摘要/Abstract

摘要：

棉花的产量、生育期和株高是重要的农艺性状, 决定着棉花的经济效益和生产方式。为了研究这些性状的遗传基础, 利用8个亲本构建的包含960个株系的陆地棉MAGIC (multi-parent advanced generation inter-cross)群体和SSR标记对这些性状进行关联分析。对产量、生育期和株高共8个相关性状进行了3年3个地点共5个环境的田间试验。经过最佳线性无偏预测(BLUP)综合多环境的表型数据, 发现MAGIC群体比亲本有更丰富的表型变异。8个性状的广义遗传力(H ²)变化范围为0.17~0.71。结合284个SSR标记基因型数据, 利用混合线性模型对产量、生育期和株高相关性状进行关联分析, 分别检测到51、27和9个显著关联的位点, 这些位点都表现出微效性, 表明该陆地棉MAGIC群体在性状位点的挖掘方面具有高效性。检测到20个标记位点或区间控制多个性状, 还发现单株有效铃数、单铃皮棉重、第一果枝节位和株高存在染色体热点区域, 对多性状综合研究或单性状深入挖掘具有重要价值。本研究为后续深入利用MAGIC群体进行遗传研究提供参考, 一些表型优良的材料和关联到的位点为育种改良奠定了基础。

关键词: 陆地棉, MAGIC群体, 产量, 生育期, 株高, SSR标记, 关联分析

Abstract:

The yield, growth period and plant height are important agronomic traits that decide the economic value and planting pattern of cotton (Gossypium spp.). In order to dissect the genetic basic of these traits, an 8-way upland cotton MAGIC (multi-parent advanced generation inter-cross) population and SSR markers were used for association mapping. Eight traits of this MAGIC population were phenotyped in five environments (three years and three locations), showing wider variations than these of the founder parents. The broad-sense heritability (H ²) of the eight traits ranged from 0.17 to 0.71. Association analysis based on mix linear model was performed using 284 polymorphic SSR markers. There were 51, 27, and 9 markers significantly associated with yield, growth period and plant height traits respectively. All identified loci had minor effect for controlling the phenotypic variations, showing a higher powerful ability of the MAGIC population in association mapping. Furthermore, 20 loci were found to be associated with multiple traits acting as pleiotropism. In addition, chromosome hot spots were found for effective boll number, lint weight, first fruit spur branch number and plant height, which provided references for deeply genetically studying these loci. The elite MAGIC lines and the valuable SSR loci lay a foundation for the genetic improvement of upland cotton.

Key words: upland cotton, MAGIC population, yield, growth period, plant height, SSR, association mapping

黄聪,李晓方,李定国,林忠旭. 利用陆地棉MAGIC群体定位产量、生育期和株高性状的QTL[J]. 作物学报, 2018, 44(9): 1320-1333.

Cong HUANG,Xiao-Fang LI,Ding-Guo LI,Zhong-Xu LIN. QTL Mapping for Yield, Growth Period and Plant Height Traits Using MAGIC Population in Upland Cotton[J]. Acta Agronomica Sinica, 2018, 44(9): 1320-1333.

图/表 10

表1

表2

表3

图1

图2

图3

表4

检测到与8个性状显著关联的SSR标记"

性状 Trait	SSR标记 SSR marker	染色体 Chromosome	遗传位置 Position (cM)	P值 P-value	解释率 R²(%)	环境 Environment
开花期	NBRI_HQ527566	1	150.22	4.24E-03 ^{(*, #)}	1.45	BLUP
FT	MON_CGR5525	6	49.08	3.91E-03 ^{(*, #)}	1.20	BLUP
	MON_DC20094	8	101.49	1.33E-03 ^(**)	1.12	BLUP
	MON_CER0167	10	101.22	9.83E-03 ^{(*, #)}	0.81	BLUP
	MON_CGR5113	11	10.25	1.38E-03 ^{(**, #)}	5.44	BLUP
	MON_CGR5390	13	55.20	7.07E-03 ^{(*, #)}	1.10	BLUP
	MON_DPL0522	21	16.34	1.35E-03 ^{(**, #)}	1.52	BLUP
	MON_DC30015	23	85.25	1.04E-05 ^{(**, #)}	7.23	BLUP
	DPL0461	24	63.21	6.98E-03 ^{(*, #)}	0.78	BLUP, E5
	MON_SHIN0607	26	137.12	2.09E-03 ^{(**, #)}	1.52	BLUP
第一果枝节位	NBRI_HQ527566	1	150.22	5.85E-03 ^(*)	1.28	BLUP
FFSBN	MON_CGR5534	2	17.30	5.68E-03 ^{(*, #)}	1.24	BLUP
性状 Trait	SSR标记 SSR marker	染色体 Chromosome	遗传位置 Position (cM)	P值 P-value	解释率 R²(%)	环境 Environment
	NAU2858	2	133.14	1.64E-03 ^{(**, #)}	2.03	BLUP
	MON_CER0086b	6	106.70	5.23E-05 ^{(**, #)}	2.48	BLUP
	MON_CGR5001b	7	22.05	8.69E-03 ^{(*, #)}	0.73	BLUP
	MON_DC20094	8	101.49	6.08E-03 ^{(*, #)}	0.80	BLUP, E2
	BNL3442	11	31.48	6.41E-03 ^{(*, #)}	0.79	BLUP
	HAU2489	15	44.81	5.03E-03 ^(*)	0.84	BLUP
	MUSS422b	15	115.63	2.58E-08 ^{(**, #)}	3.33	BLUP
	MON_CGR5001a	16	39.66	1.26E-03 ^{(**, #)}	1.10	BLUP
	HAU3069	19	206.66	3.92E-03 ^{(*, #)}	1.18	BLUP, E3
	NAU7153	21	59.03	9.20E-05 ^{(**, #)}	1.97	BLUP
	BNL3171	21	72.70	4.07E-03 ^(*)	1.89	BLUP
	MON_DC30015	23	85.25	8.21E-08 ^{(**, #)}	7.27	BLUP
	MON_CGR5423	24	10.95	2.18E-03 ^{(**, #)}	1.43	BLUP
	HAU3812	24	43.09	5.18E-03 ^{(*, #)}	1.12	BLUP
	MON_CER0086a	25	86.68	1.69E-03 ^{(**, #)}	1.49	BLUP
株高	miR393-Me4	8	67.26	9.45E-03 ^(*)	0.71	BLUP
PH	MON_CGR5113	11	10.25	8.72E-03 ^{(*, #)}	4.02	BLUP
	MON_CGR6580a	11	78.45	7.93E-03 ^{(*, #)}	1.21	BLUP
	MON_SHIN1343	17	40.41	6.26E-03 ^{(*, #)}	1.11	BLUP
	HAU3069	19	206.66	7.38E-03 ^{(*, #)}	1.04	BLUP, E3
	MON_DPL0522	21	16.34	1.61E-03 ^{(**, #)}	1.40	BLUP
	DPL0461	24	63.21	7.63E-05 ^{(**, #)}	1.66	BLUP
	MON_DC20035	24	198.85	1.49E-03 ^{(**, #)}	1.36	BLUP
	MON_DPL0811a	25	113.14	6.02E-03 ^{(*, #)}	0.79	BLUP
单株有效铃数	MON_DC40052	1	51.96	5.92E-03 ^{(*, #)}	1.69	BLUP
EBN	NBRI_HQ527566	1	150.22	2.93E-03 ^(**)	1.52	BLUP
	CIR381	2	38.87	3.97E-04 ^{(**, #)}	1.68	BLUP
	CCRI523	5	39.95	9.49E-03 ^(*)	0.72	BLUP
	BNL584	6	17.52	7.51E-03 ^{(*, #)}	1.26	BLUP
	MON_CER0086b	6	106.70	1.34E-03 ^{(**, #)}	1.61	BLUP
	HAU2147	10	4.91	4.40E-03 ^(*)	0.87	BLUP
	BNL511	10	59.83	9.83E-03 ^{(*, #)}	0.71	BLUP
	HAU3909	10	63.97	6.86E-06 ^{(**, #)}	2.63	BLUP
	MON_CGR5352b	13	22.19	9.17E-04 ^{(**, #)}	1.85	BLUP
	MON_CGR5390	13	55.20	2.17E-03 ^{(**, #)}	1.36	BLUP
	MON_DC30178	13	90.51	6.32E-03 ^(*)	0.80	BLUP
	MON_DPL0535	13	97.44	2.52E-03 ^{(**, #)}	2.01	BLUP
	MON_CER0157	13	148.92	1.41E-03 ^{(**, #)}	1.09	BLUP
	MON_CGR5001a	16	39.66	7.63E-03 ^(*)	0.76	BLUP
	HAU0197	17	61.97	5.67E-04 ^{(**, #)}	2.04	BLUP
	BNL3875	19	125.78	3.76E-03 ^{(*, #)}	1.45	BLUP
	MON_CGR5845	19	177.05	1.72E-05 ^{(**, #)}	4.55	BLUP
	NAU7153	21	59.03	6.31E-05 ^{(**, #)}	2.05	BLUP
性状 Trait	SSR标记 SSR marker	染色体 Chromosome	遗传位置 Position (cM)	P值 P-value	解释率 R²(%)	环境 Environment
	HAU2959	21	107.97	3.53E-03 ^{(*, #)}	0.89	BLUP
	MUSS298	23	29.08	3.94E-03 ^{(*, #)}	0.86	BLUP, E5
	MON_DPL0524	23	31.92	4.30E-03 ^(*)	1.44	BLUP, E3
	MON_DC30015	23	85.25	6.46E-07 ^{(**, #)}	6.19	BLUP
	HAU4497	24	185.64	5.50E-05 ^{(**, #)}	2.05	BLUP
	MON_DC40117	26	62.97	6.25E-03 ^{(*, #)}	1.05	BLUP, E2
单铃籽棉重	HAU1619a	1	168.64	3.66E-03 ^(*)	0.92	BLUP
BW	CIR381	2	38.87	9.59E-04 ^{(**, #)}	1.48	BLUP
	HAU0800a	2	142.99	9.39E-03 ^(*)	0.73	BLUP
	MON_CER0086b	6	106.70	1.74E-03 ^{(**, #)}	1.74	BLUP
	MUSB0812	8	107.81	7.25E-03 ^{(*, #)}	1.42	BLUP
	HAU0119	17	0.00	4.71E-03 ^{(*, #)}	1.75	BLUP
	HAU3986	17	100.50	3.67E-03 ^{(*, #)}	1.68	BLUP
	MUSB1135a	18	140.00	5.50E-05 ^{(**, #)}	1.73	BLUP
	MON_CGR5845	19	177.05	2.16E-03 ^(**)	3.63	BLUP
	MON_DC40103	20	60.87	3.84E-03 ^{(*, #)}	1.17	BLUP
单铃皮棉重	HAU2959	21	107.97	3.16E-03 ^{(**, #)}	0.91	BLUP
LW	NAU5418	21	108.18	8.76E-04 ^{(**, #)}	1.63	BLUP
	HAU3640	24	175.90	6.59E-03 ^{(*, #)}	1.09	BLUP
	HAU0800a	2	142.99	6.07E-03 ^(*)	0.79	BLUP
	BNL3034	14	66.47	5.81E-03 ^{(*, #)}	1.67	BLUP
	MUSB1135a	18	140.00	2.51E-03 ^{(**, #)}	0.95	BLUP
	HAU3640	24	175.90	1.62E-03 ^{(**, #)}	1.37	BLUP
	MON_DPL0811a	25	113.14	1.75E-03 ^{(**, #)}	1.02	BLUP
衣分	MON_CGR5707	9	61.36	2.37E-03 ^{(**, #)}	1.32	BLUP
LP	MON_DPL0095b	17	78.11	3.67E-03 ^{(*, #)}	1.34	BLUP
	MON_DC30015	23	85.25	8.92E-03 ^{(*, #)}	3.60	BLUP
籽指	CIR381	02	38.87	5.35E-06 ^{(**, #)}	2.60	BLUP
SI	HAU1321	12	29.33	7.26E-03 ^(*)	2.12	BLUP
	MON_SHIN1558	13	54.09	9.94E-03 ^(*)	0.71	BLUP
	MON_C2-0118	14	135.20	7.01E-03 ^{(*, #)}	0.78	BLUP
	NAU6468	16	28.49	8.77E-04 ^{(**, #)}	2.51	BLUP

表4

图4

表5

表6

定位到的位点与已报道的结果比较"

SSR标记 SSR marker	本研究定位到的性状 Associated traits in this study	已报道定位到的性状 Identified traits in reported studies
BNL3034	单铃皮棉重LW	籽壳比重, 籽指, 纤维舒适度, 纤维2.5%跨距长度, 株高 HP, SI, WF, SL2.5, PH
BNL3171	第一果枝节位FFSBN	纤维50%跨距长度, 纤维2.5%跨距长度, 纤维长度, 纤维强度 SL50, SL2.5, FL, FS
BNL3442	第一果枝节位FFSBN	纤维50%跨距长度, 纤维2.5%跨距长度, 纤维长度 SL50, SL2.5, FL
		单株籽棉产量, 单株有效铃数 SY, EBN
BNL3875	单株有效铃数EBN	纤维长度, 纤维强度, 纤维伸长率, 纤维整齐度FL, FU, FE, FS
BNL584	单株有效铃数EBN	衣指, 马克隆值LI, MV
CIR381	单铃籽棉重, 单株有效铃数, 籽指 LW, EBN, SI	纤维周长, 纤维舒适度, 纤维2.5%跨距长度, 纤维强度 PER, WF, SL2.5, FS
HAU0119	单铃籽棉重BW	纤维强度, 耐盐性 FS, ST
HAU1321	籽指SI	单株铃数, 棉籽含油量 EBN, OC
HAU1619a	单铃籽棉重BW	马克隆值 MV
HAU2147	单株有效铃数BW	籽指, 纤维长度 SI, FL
HAU2489	第一果枝节位FFSBN	纤维伸长率, 纤维整齐度 FE, FU
SSR标记 SSR marker	本研究定位到的性状 Associated traits in this study	已报道定位到的性状 Identified traits in reported studies
HAU3069	第一果枝节位, 株高 FFSBN, PH	单铃籽棉重, 籽指, 根系面积 BW, SI, RSA
MON_CGR5001a	单株有效铃数EBN	棉籽含油量, 棉籽蛋白含量 OC, PC
MON_CGR5423	第一果枝节位FFSBN	主根长 RL
MON_CGR5525	开花期FT	果枝长度 FBL
MON_CGR5534	第一果枝节位FFSBN	衣分, 株高, 果枝数, 籽指, 第一果枝长度 LP, PH, FSBN, SI, BFBL
MON_CGR5707	衣分LP	单铃种子数, 衣分 BSN, LP
MON_DC30015	单株有效铃数, 第一果枝节位, 开花期, 衣分 EBN, FFSBN, FT, LP	籽指 SI
MON_DC30178	单株有效铃数EBN	籽指 SI
MON_DC40052	单株有效铃数EBN	棉籽棕榈酸含量 PAC
MON_DC40117	单株有效铃数EBN	腺体 Gl
MON_DPL0095b	衣分LP	衣分, 籽棉产量, 籽指 LP, SY, SI
MON_DPL0522	开花期, 株高FT, PH	第一果枝节位 FFSBN
MON_DPL0524	单株有效铃数EBN	开花期, 果枝始节高 FT, FFSH
MON_DPL0535	单株有效铃数EBN	根系面积, 根系体积 RSA, RV
MUSB0812	单铃籽棉重EBN	枯萎病抗性 FW
MUSS298	单株有效铃数EBN	棉仁蛋白含量, 纤维马克隆值, 纤维强度 EPP, MV, FS
MUSS422b	第一果枝节位FFSBN	株高, 果枝数, 秋桃数, 纤维长度, 纤维强度 PH, FSBN, AB, FL, FS
NAU5418	单铃籽棉重EBN	棉籽含油量 OC
NAU6468	籽指SI	果枝数, 纤维长度 FSBN, FL

表6

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亲本编号 Parent code	杂交编号 Cross code	材料名 Name	品系名称 Strain	农艺性状 Agronomic trait	材料来源 Material sources
PM1	A	GY5	鄂棉15选系 Emian 15 inbred lines	优质, 高产 High yield and fibre quality	长江大学农学院 College of Agriculturel, Yangtze University
PM2	B	KB10	鄂抗棉10号 Ekangmian 10	抗枯萎病、耐黄萎病 Fusarium wilt-resistant and Verticillium wilt-tolerance	中国农业科学院棉花研究所 Cotton Research Institute of Chinese Academy of Agricultural Sciences
PM3	C	GY2	苏棉16 Sumian 16	优质高产 High yield and fibre quality	江苏省太仓农场 Taicang City Cotton Seed Farm in Jiangsu province
PM4	D	KC9	DP410B	抗虫 Pest-resistant	湖北省种子管理中心 Hubei Province Seed Management Station
PM5	E	CQ13	GK-12	抗虫 Pest-resistant	中国农业科学院棉花研究所 Cotton Research Institute of Chinese Academy of Agricultural Sciences
PM6	F	GY6	鄂棉15 Emian 15	优质高产 High yield and fibre quality	长江大学农学院 College of Agriculture, Yangtze University
PM7	G	CQ2	KC160	抗虫 Pest-resistant	湖北省种子管理中心 Hubei Province Seed Management Station
PM8	H	GY4	鄂荆1号选系 Ejing 1 inbred lines	优质高产 High yield and fibre quality	长江大学农学院 College of Agriculture, Yangtze University

性状 Trait	平方和 Sum of squares			均方 Mean of square			P值显著性 Significance by P-value
性状 Trait	G	E	G×E	G	E	G×E	G	E	G×E
开花期FT	28792	276730	9815	30	138365	7		***
第一果枝节位FFSBN	27900	19	11088	29.12	18.92	15.73
株高PH	212681	770794	100555	222	770794	145		***
单株有效铃数EBN	44434	78050	68598	46	39025	37	*	***
单铃籽棉重BW	672.5	1949.1	460.3	0.7	974.6	0.3	***	***	***
单铃皮棉重LW	129.5	435.3	108.8	0.13	217.67	0.06	***	***	***
衣分LP	14719	3611	10178	15.3	1805.4	5.7	***	***	*
籽指SI	1679.2	321.9	502.3	1.7	321.9	0.6	***	***

性状 Trait	均值 Mean		变异范围 Range		标准差 SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis	遗传力 H²
性状 Trait	PMs	MLs	PMs	MLs	MLs	MLs	MLs	MLs	PMs	MLs
开花期FT (d)	76.52	77.93	74.41-78.39	76.71-80.44	0.55	0.70	0.93	1.35	0.87	0.46
第一果枝节位FFSBN	6.03	5.59	5.68-6.32	5.44-5.76	0.06	1.07	0.35	-0.37	0.45	0.20
株高PH (cm)	102.04	104.36	98.22-103.61	98.44-108.96	1.32	1.26	-0.23	0.88	0.59	0.29
单株有效铃数EBN	27.75	24.77	25.16-29.41	23.71-26.29	0.39	1.56	0.37	0.44	0.57	0.17
单铃籽棉重BW (g)	5.04	5.46	4.84-5.36	4.73-6.34	0.21	3.88	-0.02	0.23	0.66	0.64
单铃皮棉重LW (g)	2.17	2.23	2.15-2.20	1.90-2.50	0.08	3.48	-0.21	0.59	0.22	0.54
衣分LP (%)	43.14	40.74	42.34-43.87	35.31-44.49	1.04	2.54	-0.55	2.00	0.56	0.60
籽指SI (g)	10.87	10.63	10.60-11.35	9.23-12.07	0.48	4.48	0.18	0.01	0.62	0.71