小麦旗叶形态相关性状全基因组关联分析

doi:10.3724/SP.J.1006.2023.21085

Abstract

Abstract:

The flag leaf of wheat is the primary functional leaf for photosynthesis and contributes significantly to yield. Therefore, it is essential to investigate the genetic process of flag leaf morphology and identify the candidate genes for flag leaf morphology-related features. We combined 90K SNP gene chips and 300 wheat varieties (lines) for genome-wide association analysis of flag leaf length, width, and area under normal irrigation (NI), and drought stress (DS) conditions in five environments. The results showed that flag leaf length, width, and area exhibited significant differences between the two moisture treatments and displayed rich phenotypic variation with the coefficients of variation ranging from 0.07-0.23 in different environments (P<0.05). Moreover, genome-wide association study (GWAS) revealed that a total of 37 stable genetic loci were significantly associated with flag leaf length, width, and area. These loci were distributed on chromosomes 1D, 2A, 2B, 3A, 3D, 4A, 5A, 5B, 6A, 6B, 7A, and 7B, with individual SNP loci explaining 3.70%-9.05% of the genetic variation, including 22 stable genetic loci detected under normal irrigation and 15 stable genetic loci detected under drought stress. Eight stable genetic loci at the same time detected under both water treatments were discovered on chromosomes 2B, 3A, 5A, 6A, 7A, and 7B, while the five stable genetic loci related by several traits were simultaneously detected on chromosomes 2B, 3A, 6A, and 7A. By analyzing haplotypes at markers with stable inheritance and high contribution, it was found that the Kukri_c1406_275 (R²=9.05%) marker was significantly associated with flag leaf length, with three haplotypes of FLL-Hap1, FLL-Hap2, and FLL-Hap3, and the wsnp_bq170165A_Ta_1_1 (R²=7.88%) marker was also detected in three haplotypes, FLA-Hap1, FLA-Hap2, and FLA-Hap3. In combination with phenotypic analysis, the flag leaf length of 300 winter wheat varieties (lines) containing FLL-Hap1 (77.78% frequency of occurrence) or FLL-Hap2 (18.89%) haplotypes was significantly higher than that of FLL-Hap3 (3.33%) haplotypes. The flag leaf area was significantly higher in haplotypes containing FLA-Hap1 (48.19%) than in haplotypes containing FLA-Hap2 (30.80%) or FLA-Hap3 (21.01%) (P<0.05). Different haplotypes were distributed differently in different winter wheat varieties (lines). Haplotype FLL-Hap1 was more frequently distributed in foreign varieties (lines), while haplotypes FLL-Hap2 and FLL-Hap3 were more frequently distributed in the northern winter wheat region and the southwestern winter wheat region, respectively. Haplotypes FLA-Hap1 and FLA-Hap2 were more frequently distributed in the southwestern winter wheat region and the northern winter wheat region, respectively, while haplotypes FLA-Hap3 were no more frequently distributed in all winter wheat regions. Searching for stable genetic loci under both water treatments yielded and screening of five candidate genes associated with flag leaf morphology, which could be used as the important genes for flag leaf-related traits.

Key words: wheat, morphological characters of flag leaf, genome-wide association analysis, haplotype, candidate genes

WANG Rui, REN Yi, CHENG Yu-Kun, WANG Wei, ZHANG Zhi-Hui, GENG Hong-Wei. Genome-wide association analysis of morphological traits of flag leaf in wheat[J].Acta Agronomica Sinica, 2023, 49(11): 2886-2901.

Figures/Tables 8

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Flag leaf shape activity related Stable loci detected by SNP-GWAS"

性状 Trait	标记名称 Marker name	环境 Environment	处理Treatment	染色体 Chr.	位置 Position (Mb）	P值 P-value	贡献率 R²(%)	先前已报道位点 Previously reported QTL
FLL	BS00067711_51	E1/E2/BLUE	NI	2A	36.93	2.61E^‒04-5.69E^‒04	4.09-4.57
	Tdurum_contig82812_213	E3/E4	NI	2A	74.11-78.33	2.17E^‒04-9.46E^‒04	3.81-4.72	Qfll2A-1^[31]
	Excalibur_c11863_289	E1/E2/BLUE	DS	2B	157.69	2.45E^‒04-8.93E^‒04	6.87-8.40
	IACX6324	E1/BLUE	DS	2B	747.18	1.37E^‒04-4.85E^‒04	4.26-4.96	qFll-2B.1^[11]
	wsnp_Ex_c18747_27625264	E1/E2//E4/BLUE	NI	3A	645.09-652.03	4.43E^‒04-8.60E^‒04	4.57-6.84
	wsnp_Ex_c18747_27625264	E2/E3/BLUE	DS	3A	645.09-646.85	4.02E^‒04-8.05E^‒04	3.94-4.28
	RAC875_c10194_673	E1/E2/BLUE	NI	3A	683.07-686.13	1.12E^‒04-7.50E^‒04	3.90-5.04	Qfla-3A^[26]
	wsnp_Ku_c42416_50159250	E3/E2/BLUE	NI	5A	610.22-617.98	2.51E^‒04-7.17E^‒04	5.15-5.72	EPQFll.nau-5A^[12]
	BS00022378_51	E1/E2/BLUE	NI	5A	663.91-664.48	4.76E^‒06-9.50E^‒04	4.71-7.17
	BS00022378_51	E1/E2/ BLUE	DS	5A	663.91-664.48	4.76E^‒06-9.69E^‒04	3.74-7.17
	BobWhite_c8266_227	E2/BLUE	NI	5A	698.51	8.40E^‒06-5.90E^‒04	4.12-6.75
	BobWhite_c8266_227	E2 /BLUE	DS	5A	698.51	5.31E^‒05-2.61E^‒04	4.66-5.75
	RFL_Contig2206_1694	E4/ BLUE	DS	6A	600.45-608.12	2.25E^‒05-9.64E^‒04	3.87-6.45
	tplb0059j12_800	E1/E2 /BLUE	DS	6B	186.70-188.19	1.94E^‒04-7.95E^‒04	3.94-4.71
	Kukri_c1406_275	E1/E2/BLUE	NI	7A	538.69-546.04	6.50E^‒07-7.75E^‒04	3.95-9.05
	Kukri_c1406_275	E3/BLUE	DS	7A	546.04	1.63E^‒04-4.01E^‒04	4.40-6.13
	GENE-4898_208	E1/E2/BLUE	NI	7A	567.58-572.87	1.67E^‒05-7.72E^‒04	3.78-6.42
	CAP7_rep_c5949_55	E1/BLUE	NI	7A	709.12-709.89	3.27E^‒04-4.89E^‒04	4.27-4.52
	BS00067530_51	E3/E4/	NI	7B	648.92-648.93	2.70E^‒05-9.32E^‒04	5.00-7.72
	BS00067530_51	E1/BLUE	DS	7B	648.11-648.93	2.40E^‒04-4.70E^‒04	4.10-5.60
	BobWhite_c14966_231	E1/BLUE	NI	7B	693.00	1.23E^‒04-4.36E^‒04	4.36-5.20	Qfll7B-1^[31]
FLW	CAP12_c46_333	E3/BLUE	NI	1D	15.32	8.92E^‒06-7.96E^‒04	4.14-7.45
	Ra_c19501_1510	E2/BLUE	NI	2B	11.19-14.83	7.15E^‒04	3.96-5.02
	Kukri_c783_1833	E1/BLUE	DS	3D	418.39	4.35E^‒05-3.65E^‒04	4.38-5.79
	BS00023151_51	E1/E2/BLUE	NI	4A	606.59	2.74E^‒04-7.94E^‒04	3.97-4.82
	Tdurum_contig29319_256	E3/BLUE	NI	5B	558.41-558.42	1.99E^‒05-6.10E^‒04	4.11-6.56
	BS00023192_51	E1/E2/BLUE	NI	6A	13.81-18.71	3.90E^‒04-9.76E^‒04	3.79-5.82
	RFL_Contig2206_1694	E2//BLUE	NI	6A	600.45-602.71	3.36E^‒04-9.64E^‒04	3.87-4.45
	RFL_Contig2206_1694	E2/BLUE	DS	6A	600.45	2.25E^‒05-1.31E^‒04	5.17-6.45
	tplb0024a09_2028	E1/BLUE	NI	7A	42.50-46.97	7.89E^‒04-8.19E^‒04	3.90-4.13
	Tdurum_contig66023_89	E3/E4	DS	7A	719.58-724.12	8.43E^‒06-7.80E^‒04	4.23-7.30	Qfla7A-1^[31]
FLA	Ra_c19501_1510	E1/BLUE	DS	2B	7.91-11.19	5.92E^‒05-7.84E^‒04	3.94-6.77
	wsnp_Ex_c18747_27625264	E1/E2/BLUE	NI	3A	645.09-646.85	2.26E^‒05-8.13E^‒04	3.85-6.42
	RAC875_c10194_673	E1/E2/BLUE	NI	3A	683.07	4.93E^‒04-9.55E^‒04	3.70-4.13	Qfla-3A^[26]
	wsnp_bq170165A_Ta_1_1	E1/E2/BLUE	NI	7A	553.39-553.99	9.01E^‒05-8.84E^‒04	3.81-7.88
	wsnp_bq170165A_Ta_1_1	E4/BLUE	DS	7A	553.39-553.99	2.11E^‒04-2.96E^‒04	4.50-4.80
	Tdurum_contig66023_89	E3/E4	DS	7A	721.92	3.32E^‒06-1.22E^‒04	5.29-7.62	Qfla7A-1^[31]

Table 3

Fig. 3

Table 4

Table 5

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性状 Trait	环境 Environment	处理 Treatment	最小值 Min.	最大值 Max.	平均数 Mean	标准差 SD	变异系数 CV	偏度 Skewness	峰度 Kurtosis
旗叶长 FLL (cm)	E1	NI	11.27	23.87	17.51 a	2.37	0.14	0.12	‒0.32
		DS	10.76	24.08	16.54 b	2.27	0.14	0.40	0.17
	E2	NI	9.82	24.57	16.82 a	3.02	0.18	0.46	‒0.19
		DS	9.29	26.05	15.90 b	2.79	0.18	0.49	0.41
	E3	NI	14.48	24.41	19.77 a	1.53	0.08	‒0.03	0.17
		DS	13.44	23.37	18.22 b	1.55	0.09	0.20	‒0.05
	E4	NI	12.84	23.12	18.26 a	1.41	0.08	‒0.22	0.69
		DS	12.08	22.55	17.07 b	1.71	0.10	0.20	‒0.53
	BLUE	NI	14.09	25.92	18.85 a	1.97	0.10	0.43	0.19
		DS	12.61	22.74	16.93 b	1.75	0.10	0.51	0.17
旗叶宽 FLW (cm)	E1	NI	0.89	1.81	1.43 a	0.14	0.10	‒0.20	0.26
		DS	0.86	1.79	1.38 b	0.13	0.09	‒0.06	0.72
	E2	NI	0.87	1.69	1.32 a	0.13	0.10	0.17	0.04
		DS	0.93	1.65	1.30 b	0.13	0.10	0.00	‒0.07
	E3	NI	1.28	2.08	1.73 a	0.13	0.07	‒0.45	0.62
		DS	1.23	2.00	1.66 b	0.12	0.08	‒0.21	0.64
	E4	NI	1.20	2.01	1.59 a	0.11	0.07	‒0.05	0.45
		DS	1.17	2.00	1.57 b	0.13	0.08	0.28	0.74
	BLUE	NI	1.19	1.84	1.51 a	0.10	0.07	‒0.13	0.41
		DS	1.19	1.83	1.48 b	0.10	0.07	0.06	0.05
旗叶面积 FLA (cm²)	E1	NI	10.58	28.30	19.38 a	3.50	0.18	0.12	‒0.36
		DS	9.53	28.68	17.62 b	3.28	0.19	0.56	0.27
	E2	NI	8.99	29.59	17.01 a	3.99	0.23	0.71	0.28
		DS	8.30	28.89	15.99 b	3.65	0.23	0.72	0.56
	E3	NI	15.62	35.55	26.41 a	2.98	0.11	0.12	0.71
		DS	12.76	31.29	23.35 b	2.92	0.13	0.04	0.44
	E4	NI	14.96	30.80	22.36 a	2.59	0.12	0.13	0.26
		DS	11.91	32.90	20.67 b	3.65	0.18	0.48	0.31
	BLUE	NI	14.75	29.77	21.29 a	2.56	0.12	0.40	0.21
		DS	13.90	27.45	19.40 b	2.64	0.14	0.58	0.14

性状 Trait	变异来源 Source of variance	平方和 SS	均方 MS	F值 F-value	P值 P-value	遗传力 h²
FLL	基因型 Genotype (G)	16,768.48	56.08	9.26	1×10^‒5	0.77
	环境 Environment (E)	19,735.89	6578.63	1085.89	1×10^‒5
	基因型×环境 G×E	13,444.44	15.01	2.48	1×10^‒5
FLW	基因型 Genotype (G)	71.96	0.24	10.52	1×10^‒5	0.85
	环境 Environment (E)	198.12	66.04	2886.16	1×10^‒5
	基因型×环境 G×E	35.80	0.04	1.75	1×10^‒5
FLA	基因型 Genotype (G)	42,619.36	142.54	7.11	1×10^‒5	0.75
	环境 Environment (E)	138,568.38	46,189.46	2302.74	1×10^‒5
	基因型×环境 G×E	37,193.72	41.51	2.07	1×10^‒5

性状 Trait	标记名称 Marker name	单倍型 Haplotype	等位基因 Allele	频率 Frequency (%)	平均值 Mean
性状 Trait	标记名称 Marker name	单倍型 Haplotype	等位基因 Allele	频率 Frequency (%)	NI (cm)	DS (cm)
FLL	Kukri_c1406_275	FLL-Hap1	AT	77.78	18.89 a	16.93 a
		FLL-Hap2	AC	18.89	18.94 a	17.16 a
		FLL-Hap3	GC	3.33	17.43 b	15.29 b
FLA	wsnp_bq170165A_Ta_1_1	FLA-Hap1	GA	48.19	22.21 a	20.35 a
		FLA-Hap3	AA	21.01	21.27 b	19.45 b
		FLA-Hap2	GG	30.80	19.80 c	17.73 c

染色体 Chr.	位点 Marker name	处理Treatment	性状 Trait	物理位置 Position (Mb)	基因 Gene	基因注释或编码蛋白 Gene annotation or coding protein
2B	IACX6324	DS	FLL	744.68	TraesCS2B01G548800	2-酮戊二酸(2OG)和Fe(II)依赖性加氧酶超家族蛋白 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
3A	RAC875_c10194_673	NI	FLL, FLA	686.74	TraesCS3A01G446100	F-box家族蛋白 F-box family protein
5B	Tdurum_contig29319_256	NI	FLW	557.70	TraesCS5B01G379500	GDSL酯酶/脂肪酶 GDSL esterase/lipase
6A	RFL_Contig2206_1694	NI/DS	FLL, FLW	603.18	TraesCS6A01G385500	Myb转录因子家族蛋白 Myb family transcription factor family protein
7A	wsnp_bq170165A_Ta_1_1	NI/DS	FLA	554.49	TraesCS7A01G379000	F-box家族蛋白 F-box family protein
7B	BS00067530_51	NI/DS	FLL	648.13	TraesCS7B01G382400	F-box家族蛋白 F-box family protein

Genome-wide association analysis of morphological traits of flag leaf in wheat

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