小麦胚芽鞘长度QTL定位和GWAS分析

doi:10.3724/SP.J.1006.2024.31034

作物学报 ›› 2024, Vol. 50 ›› Issue (3): 590-602.doi: 10.3724/SP.J.1006.2024.31034

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

小麦胚芽鞘长度QTL定位和GWAS分析

郝倩琳¹(), 杨廷志¹, 吕新茹¹, 秦慧敏¹, 王亚林¹, 贾晨飞¹, 夏先春², 马武军¹, 徐登安¹^,^*()

¹青岛农业大学农学院, 山东青岛 266109
²中国农业科学院作物科学研究所, 北京 100081

收稿日期:2023-05-18 接受日期:2023-09-13 出版日期:2024-03-12 网络出版日期:2023-09-27
通讯作者: *徐登安, E-mail: xudengan200@126.com
作者简介:E-mail: haoqianlin_0211@163.com
基金资助:
青岛农业大学高层次人才科研启动基金(663/1122023);山东省自然科学基金项目(ZR202103020229);国家自然科学基金青年科学基金项目(32101733)

QTL mapping and GWAS analysis of coleoptile length in bread wheat

HAO Qian-Lin¹(), YANG Ting-Zhi¹, LYU Xin-Ru¹, QIN Hui-Min¹, WANG Ya-Lin¹, JIA Chen-Fei¹, XIA Xian-Chun², MA Wu-Jun¹, XU Deng-An¹^,^*()

¹College of Agronomy, Qingdao Agricultural University, Qingdao 266109, Shandong, China
²Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Received:2023-05-18 Accepted:2023-09-13 Published:2024-03-12 Published online:2023-09-27
Contact: *E-mail: xudengan200@126.com
Supported by:
High-level Talents Project of Qingdao Agricultural University(663/1122023);Shandong Provincial Natural Science Foundation(ZR202103020229);National Natural Science Foundation of China(32101733)

摘要/Abstract

摘要：

在干旱条件下, 小麦(Triticum aestivum L.)适当深播可提高出苗率, 胚芽鞘长度决定了小麦播种的最大深度, 因此培育长胚芽鞘小麦品种至关重要。为了挖掘控制小麦胚芽鞘长度相关的数量性状位点(quantitative trait loci, QTL), 本研究以275份豆麦/石4185重组自交系(recombinant inbred lines, RIL)群体和186份自然群体为材料, 根据90K SNP芯片的分型结果, 利用3个环境下小麦胚芽鞘长度表型数据进行QTL鉴定。采用完备区间作图法(inclusive composite interval mapping, ICIM)在RIL群体中鉴定到2个稳定的QTL位点, 分别位于4BS (30.17~40.59 Mb)和6BL (700.08~703.53 Mb)染色体上, 解释表型变异率(PVE)分别为26.29%~28.46%和4.16%~4.36%; 全基因组关联分析(GWAS)采用混合线性模型(Mixed linear model, MLM)方法, 共鉴定到36个稳定的QTL位点, 分别位于1A (3)、1B (3)、1D (2)、2A (1)、3A (2)、3B (2)、4B (11)、5A (1)、5B (3)、6B (4)、7A (2)、7B (2)染色体上, 在3个环境中重复检测到的显著关联位点有7个, 其中3个位点与已报道的位点重叠或邻近, 其他4个位点推测为新位点, 分别位于1A (499.03 Mb)、3A (73.06 Mb)、4B (648.74~648.87 Mb)、7A (36.31 Mb)染色体上, 预测了5个候选基因(TraesCS1A03G0748300、Rht1、TraesCS4B03G0110000、TraesCS4B03G0112200和TraesCS7A03G0146600)。在两个群体中均鉴定到位于4BS (30.17~40.59 Mb)染色体上的主效QTL位点, 该位点的候选基因Rht1已被证实能降低小麦胚芽鞘长度。该研究结果为挖掘控制小麦胚芽鞘长度的基因以及胚芽鞘长度相关性状分子标记辅助选择育种奠定了基础。

关键词: 小麦, 胚芽鞘长度, QTL定位, 全基因组关联分析

Abstract:

Under drought conditions, the emergence rate of wheat (Triticum aestivum L.) can be improved by proper deep sowing. The maximum sowing depth of wheat is determined by the length of the coleoptile, so it is very important to cultivate wheat varieties with long coleoptile. In this study, a recombinant inbred line (RIL) population consisting of 275 lines derived from the cross of Doumai and Shi 4185, and 186 natural population materials were used as the experimental materials. Genotyping results of 90K SNP chip were used to identify QTL for wheat coleoptile length in three different environments. The results showed that two stable QTL sites were identified by inclusive composite interval mapping in the RIL population. The two QTL located on Chromosome 4BS (30.17-40.59 Mb) and 6BL (700.08-703.53 Mb), respectively, and explained 26.29%-28.46% and 4.16%- 4.36% of the phenotypic variance, respectively. A total of 36 stable QTL were identified in the genome-wide association study (GWAS) using the mixed linear model. They were located on Chromosome 1A (3), 1B (3), 1D (2), 2A (1), 3A (2), 3B (2), 4B (11), 5A (1), 5B (3), 6B (4), 7A (2), and 7B (2), respectively. Seven significant association loci were repeatedly detected in the three environments, three of which overlapped or were adjacent to reported loci, and the other four loci were presumed to be new loci. They were located on Chromosomes 1A (499.03 Mb), 3A (73.06 Mb), 4B (648.74-648.87 Mb), and 7A (36.31 Mb), respectively. Five candidate genes (TraesCS1A03G0748300, Rht1, TraesCS4B03G0110000, TraesCS4B03G0112200, and TraesCS7A03G0146600) were predicted. A major QTL locus on Chromosome 4BS (30.17-40.59 Mb) was identified in both RIL and natural populations, and the candidate gene Rht1 at this locus had been shown to reduce the length of wheat coleoptile. The results of this study lay a foundation for the identification of genes controlling the length of coleoptile in wheat and the maker-assisted selection breeding.

Key words: wheat, coleoptile length, QTL mapping, GWAS

郝倩琳, 杨廷志, 吕新茹, 秦慧敏, 王亚林, 贾晨飞, 夏先春, 马武军, 徐登安. 小麦胚芽鞘长度QTL定位和GWAS分析[J]. 作物学报, 2024, 50(3): 590-602.

HAO Qian-Lin, YANG Ting-Zhi, LYU Xin-Ru, QIN Hui-Min, WANG Ya-Lin, JIA Chen-Fei, XIA Xian-Chun, MA Wu-Jun, XU Deng-An. QTL mapping and GWAS analysis of coleoptile length in bread wheat[J]. Acta Agronomica Sinica, 2024, 50(3): 590-602.

图/表 12

表1

图1

图2

表2

图3

表3

表4

图4

图5

表5

基于MLM模型在至少2个环境下检测到的CL关联位点"

环境^a Environment ^a	标记名称 Marker name	基因型^b Allele ^b	物理位置^c Physical position (Mb) ^c	P最小值^d P-value min. ^d	P最大值^d P-value max. ^d
E1/BLUE	IWB30674	G/A	1A:48.36	1.59E-04	3.16E-05
E1/E2/E3/BLUE	IWB50788	G/A	1A:499.03	6.07E-04	1.40E-04
E3/BLUE	IWA7871	G/A	1A:505.76	5.98E-04	1.23E-04
E1/E3/BLUE	IWB21039	G/A	1B:30.67	9.25E-04	1.99E-04
E3/BLUE	IWB53874	G/A	1B:588.25	2.83E-04	2.28E-04
E3/BLUE	IWB74028	G/A	1B:690.58	8.03E-04	7.03E-04
E1/BLUE	IWB18554	G/A	1D:42.77	1.00E-03	4.68E-04
E1/BLUE	IWA830	G/A	1D:43.07	1.00E-03	4.68E-04
E1/E2/BLUE	IWB64018	G/A	2A:757.65	3.83E-04	1.30E-05
E2/E3/BLUE	IWB2733	G/A	3A:72.88	8.60E-04	6.15E-04
E1/E2/E3/BLUE	IWB53051	G/A	3A:73.06	5.40E-04	1.52E-04
E1/E2/E3/BLUE	IWB24605	G/A	3B:19.95	2.26E-04	1.17E-04
E1/BLUE	IWB39644	G/A	3B:75.98	7.11E-04	5.20E-04
E1/E2/E3/BLUE	IWB49875	G/A	4B:24.28	8.57E-04	5.50E-05
E1/E2/E3/BLUE	IWB70449	G/A	4B:40.43	7.36E-04	9.01E-05
E1/E2/E3/BLUE	IWB54814	G/A	4B:40.59	3.42E-05	7.35E-06
E1/BLUE	IWA6850	G/A	4B:40.76	9.74E-04	8.55E-04
E1/E3/BLUE	IWB4719	G/A	4B:40.77	5.04E-04	1.79E-04
E1/E3/BLUE	IWB25737	G/A	4B:41.02	5.55E-04	2.55E-04
E1/BLUE	IWB40899	G/A	4B:574.98	7.29E-04	5.86E-04
E1/BLUE	IWB59718	G/A	4B:577.08	8.58E-04	8.18E-04
E1/BLUE	IWB71859	G/A	4B:578.54	9.42E-04	7.17E-04
E1/E2/E3/BLUE	IWB53155	G/A	4B:648.74	3.86E-04	5.06E-05
E1/E2/E3/BLUE	IWB42023	G/A	4B:648.87	5.14E-04	6.61E-05
E1/E3	IWB35845	G/A	5A:710.07	5.69E-04	5.66E-04
E1/BLUE	IWA6527	G/A	5B:211.64	7.49E-04	2.81E-04
E1/BLUE	IWB71849	G/A	5B:607.90	9.62E-04	2.43E-04
E/E2	IWB63425	G/A	5B:75.60	9.64E-04	9.60E-04
E2/E3	IWB62054	G/A	6B:123.26	7.01E-04	6.74E-04
E2/BLUE	IWB56800	G/A	6B:128.10	6.75E-04	4.32E-04
E2/E3	IWB68130	G/A	6B:146.70	9.96E-04	5.02E-04
E2/E3	IWB65561	G/A	6B:683.94	8.99E-04	7.31E-04
E2/E3	IWB22879	G/A	7A:31.41	7.50E-04	5.52E-04
E1/E2/E3/BLUE	IWB11001	G/A	7A:36.31	8.74E-04	4.53E-05
E3/BLUE	IWB72566	G/A	7B:203.84	9.80E-04	4.88E-04
E1/E3/BLUE	IWB11945	G/A	7B:204.38	7.06E-04	1.98E-04

表5

图6

表6

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环境 Environment	亲本 Parents		RIL家系 RIL lines
环境 Environment	豆麦 Doumai	石4185 Shi 4185	最小值 Min.	最大值 Max.	均值 Mean	标准差 SD	变异系数 CV (%)
E1	5.41	4.49	2.88	6.33	4.32	0.57	13.31
E2	5.65	4.57	3.23	6.16	4.29	0.56	13.06
E3	5.16	4.54	3.10	6.21	4.27	0.58	13.50
BLUE	5.40	4.54	3.14	6.20	4.29	0.55	12.76

环境 Environment	相关系数 Correlation coefficient			广义遗传力 H²
环境 Environment	E1	E2	E3	广义遗传力 H²
E1	1			0.92
E2	0.89^**	1
E3	0.80^**	0.88^**	1

数量性状位点^a QTL ^a	环境 Environment	侧翼标记 Flanking marker	物理区间^b Physiol interval (Mb) ^b	LOD值^c LOD value ^c	贡献率 PVE (%)	加性效应 Add
QCL.qau-4BS	E1	IWA102-IWB54814	30.17-40.59	18.43	27.84	0.32
	E2	IWA102-IWB54814	30.17-40.59	15.51	26.29	0.30
	E3	IWA102-IWB54814	30.17-40.59	16.99	26.66	0.31
	BLUE	IWA102-IWB54814	30.17-40.59	19.32	28.46	0.31
QCL.qau-6BL	E1	IWB19986-IWB35852	702.16-703.53	3.15	4.16	-0.12
	E3	IWB63870-IWB19986	700.08-702.16	3.02	4.36	-0.12
	BLUE	IWB19986-IWB35852	702.16-703.53	15.03	20.97	-0.25

环境 Environment	均值 Mean	标准差 SD	变异系数 CV (%)	相关系数 Correlation coefficient			遗传力 H²
环境 Environment	均值 Mean	标准差 SD	变异系数 CV (%)	E1	E2	E3	遗传力 H²
E1	3.98	0.55	13.74	1			0.91
E2	4.01	0.56	14.07	0.94^**	1
E3	4.03	0.57	14.25	0.93^**	0.93^**	1
BLUE	4.01	0.55	13.70

标记名称 Marker name	标记物理位置^a Position (Mb)^a	基因名称^b Gene name^b	基因物理位置^c Position (Mb)^c	同源基因^d Homologs ^d	基因功能 Gene function
IWB50788	1A:499.03	1A03G0748300	1A:496.71	OsEXP4^[48]	Alpha-expansin OsEXPA4
IWB70449	4B:40.43	Rht1	4B:33.61		DELLA protein
IWB54814	4B:40.59	4B03G0110000	4B:42.02	AT5G39760^[50]	Zinc finger homeodomain protein
IWB54814	4B:40.59	4B03G0112200	4B:43.56	AT1G09570^[51]	Phytochrome A
IWB11001	7A:36.31	7A03G0146600	7A:32.23	AT5G13320^[52]	Auxin-responsive GH3 protein

小麦胚芽鞘长度QTL定位和GWAS分析

QTL mapping and GWAS analysis of coleoptile length in bread wheat

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