小麦胚芽鞘长度QTL定位和GWAS分析

doi:10.3724/SP.J.1006.2024.31034

Abstract

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

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.

Figures/Tables 12

Table 1

Fig. 1

Fig. 2

Table 2

Fig. 3

Table 3

Table 4

Fig. 4

Fig. 5

Table 5

CL-associated loci detected in at least two environments by MLM"

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

Table 5

Fig. 6

Table 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

QTL mapping and GWAS analysis of coleoptile length in bread wheat

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