冬小麦穗部性状GWAS分析及优异单倍型筛选

doi:10.3864/j.issn.0578-1752.2025.18.002

Abstract

Abstract:

【Objective】Spike-related traits constitute a key factor influencing wheat yield. This study conducted a genome-wide association study (GWAS) on wheat spike-related traits to identify significant loci controlling these traits, thereby providing theoretical references for research on genetic improvement of wheat spike-related traits. 【Method】Using a panel of 261 winter wheat varieties (lines), we measured spike-related phenotypic traits and performed genome-wide association studies (GWAS) with the wheat 90K SNP array, employing the Fixed and Random Model Circulating Probability Unification (Farm CPU) model. Stable and significant loci identified through this analysis were further subjected to haplotype analysis. 【Result】Under three environmental conditions, all 11 panicle-related traits exhibited extensive phenotypic variation, with coefficients of variation (CV) ranging from 3.63 to 64.29. The heritability estimates for these traits varied between 0.42 and 0.84. Highly significant differences (P<0.001) were observed among genotype, environment, and genotype × environment interactions. Genome-wide association study (GWAS) identified 171 loci significantly associated with the 11 traits (P<0.001), including 20 pleiotropic loci detected in two or more environments. These loci were associated with eight panicle traits: panicle length (3 loci), peduncle length (7 loci), sterile spikelet number (1 locus), fertile spikelet number (2 loci), total spikelet number (2 loci), grains per panicle (1 locus), grain weight per panicle (2 loci), and thousand-grain weight (2 loci). The phenotypic contribution rates of these loci ranged from 0.95% to 18.54%. A pleiotropic locus (Ra_c10072_677) significantly associated with both grain weight per panicle and grains per panicle was identified on chromosome 7B, demonstrating phenotypic contribution rates ranging from 2.62% to 6.16%. The marker wsnp_Ex_rep_c69639_68590556, which showed consistent association with peduncle length across two or more environmental conditions (explaining 5.94% of the genetic variation), was selected for haplotype analysis. Three haplotypes (Hap1, Hap2, and Hap3) were characterized, with distribution frequencies of 77.40%, 13.70%, and 8.80%, respectively. Phenotypic analysis revealed that 261 winter wheat cultivars (lines) carrying haplotype Hap3 (30.58 cm) exhibited significantly greater peduncle length (P<0.001) compared to those with Hap1 (28.67 cm) and Hap2 (27.49 cm). The haplotype distribution frequencies showed significant geographic divergence: Hap1 predominated in the Northern Winter Wheat Region, Hap2 was more prevalent in the Huang-Huai Winter Wheat Region, while Hap3 displayed no substantial frequency (>5%) across all winter wheat regions. For stably detected loci across three environments, candidate gene mining identified four genes associated with panicle development. These genes, functionally annotated as encoding MYB transcription factors and F-box domain-containing proteins, represent key candidates influencing panicle architecture. 【Conclusion】The spike traits of wheat exhibited significant variation across different genotypes. A total of twenty stably associated loci were identified across two or more environments. Three distinct haplotypes significantly associated with the peduncle length were detected on chromosome 7B, and four candidate genes potentially related to spike traits were screened out.

Key words: wheat, spike architecture traits, genome-wide association study (GWAS), SNP markers, haplotype blocks

LI Ming, CHENG YuKun, BAI Bin, LEI Bin, GENG HongWei. Genome-Wide Association Study on Spike Architecture Traits and Elite Haplotype Mining in Winter Wheat[J].Scientia Agricultura Sinica, 2025, 58(18): 3583-3597.

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Figures/Tables 5

Table 1

Statistical analysis of stalk characters of 261 varieties (lines)"

性状 Trait	环境 Environment	范围 Range	平均值±标准差 Mean±SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis	均方值Mean square			遗传力 H²
性状 Trait	环境 Environment	范围 Range	平均值±标准差 Mean±SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis	基因型 Genotype (G)	环境 Environment (E)	G×E互作 G×E	遗传力 H²
穗长 SL (cm)	E1	5.61—11.14	8.39±1.03	12.23	0.12	-0.01	4.80***	33.77***	1.02***	0.81
	E2	6.08—11.97	8.66±1.03	11.93	0.54	0.65
	E3	5.97—12.90	8.9±1.14	12.80	0.58	0.61
	BLUP	6.66—11.14	8.65±0.77	8.86	0.40	0.55
穗下节长 PL (cm)	E1	20.09—45.14	29.48±4.74	16.80	0.43	-0.23	97.01***	5072.93***	16.39***	0.84
	E2	15.58—40.36	25.21±4.42	17.54	0.47	0.14
	E3	20.25—49.29	31.28±4.78	15.29	0.49	0.39
	BLUP	22.80—36.51	28.66±2.88	10.04	0.38	-0.34
不育小穗数 SSN	E1	0.00—4.13	1.49±0.76	51.01	0.59	0.45	365.77***	51.27***	395.34***	0.55
	E2	0.00—4.60	1.05±0.67	64.29	1.33	3.69
	E3	0.00—4.10	1.24±0.66	53.08	0.58	0.58
	BLUP	0.65—1.98	1.26±0.27	21.32	0.29	-0.32
可育小穗数 FSN	E1	12.73—24.77	17.14±1.67	9.75	0.39	1.08	8.62***	88.72***	3.46***	0.66
	E2	13.80—22.30	17.76±1.54	8.69	0.31	-0.32
	E3	12.80—22.80	17.92±1.61	8.99	0.16	0.01
	BLUP	15.78—20.06	17.61±0.82	4.66	0.22	-0.16
小穗结实率 SF (%)	E1	0.75—1.00	0.92±0.04	4.46	-0.60	0.76	0.00***	0.08***	0.00***	0.55
	E2	0.81—1.00	0.94±0.03	3.63	-1.00	1.69
	E3	0.80—1.00	0.93±0.04	3.78	-0.53	0.23
	BLUP	0.89—0.96	0.93±0.01	1.53	-0.24	-0.22
总小穗数 TSN	E1	15.17—25.13	18.63±1.56	8.38	0.22	0.41	8.31***	39.44***	3.14***	0.69
	E2	15.80—24.00	18.81±1.6	8.48	0.36	-0.25
	E3	14.50—24.40	19.17±1.52	7.93	0.15	0.17
	BLUP	16.75—21.07	18.87±0.87	4.60	-0.03	-0.31
穗粒数 GNS	E1	17.00—67.47	40.99±7.07	17.25	0.43	1.39	158.71***	3458.58***	78.16***	0.58
	E2	29.70—70.70	45.32±7.34	16.19	0.59	0.28
	E3	26.60—68.80	45.57±7.33	16.08	0.33	0.06
	BLUP	35.33—51.80	43.97±2.98	6.77	0.22	-0.02
穗粒重 GWPS (g)	E1	0.81—3.05	1.63±0.31	19.27	0.74	1.64	0.37***	25.83***	0.23***	0.53
	E2	1.04—3.47	2.07±0.40*	19.25	0.76	0.72
	E3	0.82—2.85	1.78±0.39	22.08	0.27	-0.30
	BLUP	1.53—2.16	1.83±0.11	6.20	0.26	0.12
千粒重 TGW (g)	E1	27.31—51.72	39.3±4.63	11.77	-0.47	-0.04	91.76***	7452.80***	33.25***	0.72
	E2	33.32—60.15	45.74±4.89	10.69	0.06	-0.30
	E3	18.21—52.64	39.1±5.81	14.87	-0.34	-0.08
	BLUP	34.04—47.27	41.43±2.71	6.54	-0.42	-0.35
小穗着生密度 SD	E1	1.55—3.58	2.26±0.3	13.30	1.02	2.25	0.21***	0.80***	0.08***	0.68
	E2	1.69—3.08	2.21±0.22	9.86	0.37	0.79
	E3	1.52—3.09	2.19±0.23	10.33	0.48	1.33
	BLUP	1.86—2.66	2.22±0.14	6.26	0.38	0.49
每小穗粒数 GNSL	E1	1.03—3.32	2.24±0.3	13.53	-0.11	0.91	0.26***	3.85***	0.19***	0.42
	E2	1.53—3.43	2.41±0.34	14.29	0.22	0.00
	E3	1.52—3.54	2.37±0.33	13.84	0.28	0.18
	BLUP	2.09—2.54	2.34±0.08	3.52	-0.11	-0.23

Table 1

Fig. 1

Fig. 2

Table 2

Fig. 3

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性状 Trait	标记 Marker	染色体 Chr.	位置 Position (Mb)	P值 P-value	贡献率 R²(%)	环境 Environment
穗长SL	wsnp_Ex_c19094_28015035	2B	784.30	1.50E^-04—4.06E^-04	18.00—18.54	E1/BLUP
	Tdurum_contig62138_385	2D	45.80	7.59E^-05—3.20E^-04	5.57—5.89	E2/BLUP
	wsnp_Ex_c26128_35374652	3B	440.89	9.17E^-05—3.28E^-04	5.64—7.15	E1/E2/BLUP
穗下节长PL	Kukri_rep_c87640_135	3A	573.99	6.43E^-05—2.03E^-04	5.81—9.23	E1/E2
	RAC875_c929_170	5B	462.15	6.43E^-05—8.20E^-04	1.53—5.94	E1/E2
	Tdurum_contig42655_1727	6B	12.67	5.42E^-07—3.09E^-04	1.60—5.94	E3/BLUP
	Jagger_c3477_441	6D	20.85	3.34E^-04—3.51E^-04	3.28—5.94	E1/E2
	Kukri_rep_c70199_506	7A	709.41	5.47E^-04—8.35E^-04	5.01—5.64	E1/E2
	wsnp_Ex_rep_c69639_68590556	7B	198.94	3.86E^-04—9.04E^-04	0.95—5.94	E1/E2/BLUP
	wsnp_Ex_c17176_25816766	7B	700.39	3.48E^-04—5.68E^-04	5.94—9.32	E1/E2
不育小穗数SSN	Tdurum_contig42729_242	6A	35.64	6.71E^-04—7.92E^-04	1.45—2.62	E2/BLUP
可育小穗数FSN	Kukri_c7218_1145	3A	504.80	5.11E^-04—5.21E^-04	3.61—3.66	E1/BLUP
可育小穗数FSN	wsnp_Ex_c18318_27140346	4B	12.53	5.90E^-04—9.38E^-04	1.05—3.55	E1/BLUP
总小穗数TSN	wsnp_Ex_c1924_3630519	7A	582.64	3.49E^-04—6.84E^-04	1.60—4.89	E2/BLUP
总小穗数TSN	Excalibur_c87219_204	7B	747.47	2.01E^-04—3.95E^-04	1.00—4.12	E1/BLUP
穗粒数GNS	Ra_c10072_677	7B	295.33	2.65E^-04—6.77E^-04	2.62—3.84	E1/BLUP
穗粒重GWPS	Excalibur_rep_c68296_2217	4A	327.75	5.96E^-04—8.19E^-04	5.13—9.31	E1/BLUP
穗粒重GWPS	Ra_c10072_677	7B	295.33	9.75E^-05—2.60E^-04	2.85—6.16	E2/BLUP
千粒重TGW	BS00076889_51	1B	22.15	3.82E^-05—5.87E^-04	1.16—4.61	E1/BLUP
千粒重TGW	RFL_Contig5418_347	3B	567.25	3.63E^-04—4.64E^-04	1.09—4.30	E1/BLUP

Genome-Wide Association Study on Spike Architecture Traits and Elite Haplotype Mining in Winter Wheat

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