小麦苗期根系性状的全基因组关联分析与优异位点挖掘

doi:10.3864/j.issn.0578-1752.2023.05.001

Abstract

Abstract:

【Objective】Plant roots are critical for water and nutrient acquisition, crop growth and development as well as yield formation. Exploring SNP loci significantly associated with root traits in wheat at seedling stage and mining candidate genes, will lay a foundation for understanding the genetic mechanism of wheat root system architecture and breeding wheat elite varieties with better root architecture.【Method】In this study, 189 diverse wheat cultivars were assembled as an association-mapping panel, five root traits including total root length (TRL), total root area (TRA), total root volume (TRV), average root diameter (ARD) and root dry weight (RDW) were investigated by growing in two culture conditions (Hoagland nutrient solution and pure water), and the experiments were repeated twice. Then, genome-wide association studies (GWAS) were performed for the five root traits with genotypic data derived from Wheat 660K SNP Array. Candidate genes were predicted by sequence alignment, domain analysis, and annotation information. Futhermore, kompetitive allele specific PCR (KASP) markers were developed for root traits. 【Result】The root traits varied greatly among the 189 cultivars, and the roots were thick and short cultured under Hoagland nutrient solution, while slender seminal roots and more lateral roots were observed under pure water. A total of 95 QTLs significantly associated with root traits cultured in two conditions (P<10^-3) were identified by genome-wide association studies with four models of BLINK (bayesian-information and linkage-disequilibrium iteratively nested keyway), CMLM (compressed mixed linear model), FarmCPU (fixed and random model circulating probability unification) and MLM (mixed linear model). Among them, 18 QTLs were detected in both culture conditions and distributed on chromosomes of 7A, 1B, 2B, 3B, 7B, 1D, 2D, and 3D, which explained 8.68%-14.07% of phenotypic variation. Of those significant loci, 4 QTLs were similar or consistent with that reported previously, and the rest were novel ones. Haplotype analysis conducted for co-localization QTLs of 10 SNPs revealed significant differences in root traits between the two haplotypes of wheat cultivars. Based on these SNPs, KASP markers XNR7143 and XNR3707 were developed for total root volume and root dry weight, respectively. In addition, 12 candidate genes possibly regulating root development were found by mining the genes within the interval of co-localization significant SNPs. Of them, TraesCS7A02G160600, encoding 3-oxoacyl-[acyl-carrier-protein] synthase, is involved in the synthesis of root fatty acids; TraesCS1B02G401800, encoding syntaxin, plays an important role in plant tropism; TraesCS7B02G417900, encoding aldehyde oxidase, contributes to the synthesis of abscisic acid and regulation of crop root development. 【Conclusion】The root traits of wheat varied significantly among the wheat genotypes. Genome-wide association studies detected 18 significant QTLs linked with root traits simultaneously in two culture conditions, two KASP markers were developed for root traits, and 12 candidate genes related to root development were screened, which might provide reference for understanding the regulation mechanism of wheat root traits and molecular marker-assisted breeding for wheat improvement.

Key words: wheat, root traits, genome-wide association study, co-localization SNPs, KASP (kompetitive allele specific PCR) markers, candidate genes

WANG Mai, DONG QingFeng, GAO ShenAo, LIU DeZheng, LU Shan, QIAO PengFang, CHEN Liang, HU YinGang. Genome-Wide Association Studies and Mining for Favorable Loci of Root Traits at Seedling Stage in Wheat[J].Scientia Agricultura Sinica, 2023, 56(5): 801-820.

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标记名称 KASP name		引物序列 Primer sequence (5′-3′)
XNR7143	F-P	GAAGGTGACCAAGTTCATGCTgtgacatggaggacgctgc
	V-P	GAAGGTCGGAGTCAACGGATTgtgacatggaggacgctgt
	R-P	tcgtggagaacatcttgcgt
XNR3707	F-P	GAAGGTGACCAAGTTCATGCTtgcatcatagtacataccactgc
	V-P	GAAGGTCGGAGTCAACGGATTtgcatcatagtacataccactgt
	R-P	aattggcgacattgggagac

培养条件 Environment	性状 Traits	变异范围 Range	均值 Mean	标准差 SD	变异系数 CV (%)
霍格兰营养液 HL	根系总长度TRL (cm)	8.42—141.54	43.73	23.57	52.69
	根系总表面积TRA (cm²)	2.09—33.15	12.53	6.47	51.62
	根系总体积TRV (cm³)	0.03—1.37	0.41	0.27	66.38
	根系平均直径ARD (mm)	0.43—1.40	0.95	0.21	22.13
	根系干重RDW (g)	0.0010—0.0180	0.0061	0.0025	40.31
去离子水 PW	根系总长度TRL (cm)	49.45—348.24	211.01	51.68	24.49
	根系总表面积TRA (cm²)	10.20—39.22	25.27	5.62	22.26
	根系总体积TRV (cm³)	0.13—0.61	0.32	0.08	25.52
	根系平均直径ARD (mm)	0.33—1.09	0.4304	0.07	15.43
	根系干重RDW (g)	0.0088—0.0244	0.0171	0.0030	17.76

性状 Traits	基因型 Genotype		处理 Treatment		基因型×处理 Genotype×Treatment		广义遗传力（H²） Broad-sense heritability (%)
性状 Traits	F	<BOLD>P</BOLD>	<BOLD>F</BOLD>	<BOLD>P</BOLD>	<BOLD>F</BOLD>	<BOLD>P</BOLD>	广义遗传力（H²） Broad-sense heritability (%)
根系总长度 TRL (cm)	7.35	4.79E-79***	10443.99	5.35E-45***	6.74	3.99E-72***	62.40
根系总表面积 TRA (cm²)	6.19	1.47E-65***	2328.39	1.61E-220***	5.26	4.72E-54***	64.24
根系总体积 TRV (cm³)	4.55	9.65E-45***	83.44	7.64E-19***	4.15	2.06E-39***	62.88
根系平均直径 ARD (mm)	5.14	1.59E-52***	5089.04	3.69E-56***	5.07	1.35E-51***	60.41
根系干重 RDW (g)		24.51	5.27E-221***	33559.75	4.19E-40***	18.23	2.19E-183***	65.30

染色体 Chromosome	标记数目 No. of markers	长度 Length (Mb)	标记密度 Density of markers	遗传多样性 Genetic diversity	多态信息含量 PIC
1A	19003	594.10	0.03	0.3251	0.2642
1B	16540	689.99	0.04	0.3851	0.3036
1D	7935	495.45	0.06	0.3349	0.2713
2A	22510	780.80	0.03	0.3567	0.2892
2B	19755	801.26	0.04	0.3651	0.2906
2D	7174	651.85	0.09	0.3689	0.2930
3A	12754	750.84	0.06	0.3687	0.2927
3B	36612	830.83	0.02	0.3518	0.2870
3D	4883	615.55	0.13	0.3463	0.2802
4A	12345	744.59	0.06	0.3522	0.2836
4B	10959	673.62	0.06	0.3449	0.2799
4D	2408	509.86	0.21	0.3654	0.2900
5A	17658	709.77	0.04	0.3912	0.3083
5B	26618	713.15	0.03	0.3743	0.2972
5D	5628	566.08	0.10	0.3430	0.2747
6A	12934	618.08	0.05	0.3799	0.3004
6B	17890	720.99	0.04	0.3635	0.2911
6D	4997	473.59	0.09	0.3378	0.2728
7A	18490	736.71	0.04	0.3287	0.2639
7B	12260	750.62	0.06	0.3776	0.2985
7D	6758	638.69	0.09	0.3359	0.2706
A基因组A genome	115694	4934.89	0.04	0.3575	0.2860
B基因组B genome	140634	5180.46	0.04	0.3660	0.2926
D基因组D genome	39783	3951.07	0.10	0.3475	0.2789
总计Total	296111	14066.42	0.05	0.3570	0.2858

显著性标记 SNP	关联性状 Related traits	染色体 Chromosome	位置 Position (Mb)	<BOLD>P</BOLD>值 -log₁₀(<BOLD>P</BOLD>)	贡献率 R² (%)
AX-109555941	TRL	1B	689.00	4.63	14.07
AX-108888527	TRL	2D	556.05	4.12	11.73
AX-108888527	TRA	2D	556.05	4.11	10.64
AX-94581300	TRL	3D	239.36	3.56	10.83
AX-108889829	TRL	2B	85.25	4.15	11.52
AX-111514405	TRL	2B	81.55	3.57	9.33
AX-109029863	RDW	3B	416.69	4.13	11.18
AX-109029863	TRA	3B	416.69	4.28	11.11
AX-108924279	RDW	2B	57.67	3.36	9.02
AX-110371944	RDW	2B	57.68	3.43	9.01
AX-110455550	RDW	2B	57.67	3.43	9.01
AX-110567747	RDW	2B	57.78	3.36	8.68
AX-109933707	RDW	2B	57.68	3.49	9.09
AX-108792070	TRA	7A	638.24	3.79	11.19
AX-108792070	TRV	7A	638.24	3.70	11.13
AX-110097055	TRA	7A	638.52	3.79	11.19
AX-110097055	TRV	7A	638.52	3.70	11.13
AX-110497143	TRV	7A	116.76	4.28	11.19
AX-110491393	TRV	1B	632.00	5.11	13.93
AX-111564445	TRV	3B	757.93	4.10	10.60
AX-94823257	TRV	1D	460.79	4.14	10.75
AX-110122975	TRV	7B	686.14	3.54	9.82

Genome-Wide Association Studies and Mining for Favorable Loci of Root Traits at Seedling Stage in Wheat

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候选基因 Candidate genes	物理位置 Position (bp)	功能注释 Gene annotations
TraesCS7A02G160600	Chr.7A:116650020—116654196	3-氧酰基-酰基载体蛋白质合成酶 3-oxoacyl-[acyl-carrier-protein] synthase
TraesCS1B02G401800	Chr.1B:631998104—632003904	突触融合蛋白 Syntaxin
TraesCS2B02G097600	Chr.2B:57672647—57676616	黄条转运蛋白12 Yellow stripe-like transporter 12
TraesCS2B02G097800	Chr.2B:57679415—57682721	MLO蛋白 MLO-like protein
TraesCS2B02G097900	Chr.2B:57778375—57781675	MLO蛋白 MLO-like protein
TraesCS2B02G117900	Chr.2B:81755546—81758516	WUSCHEL相关同源框蛋白 WUSCHEL-related homeobox
TraesCS2B02G119200	Chr.2B:85320654—85325523	三磷酸腺苷双磷酸酶 Apyrase-like protein
TraesCS3B02G516000	Chr.3B:757920799—757926024	转录起始因子TFIID亚基9 Transcription initiation factor TFIID subunit 9
TraesCS7B02G417900	Chr.7B:686141549—686157029	醛脱氢酶 Aldehyde oxidase
TraesCS1D02G388600	Chr.1D:460789199 - 460794120	解毒蛋白 Detoxification protein
TraesCS2D02G445500	Chr.2D:556053437—556059076	E3泛素蛋白连接酶RNF14 E3 ubiquitin-protein ligase RNF14
TraesCS3D02G201400	Chr.3D:239349590—239362410	分子伴侣 danJ Chaperone protein dnaJ

性状 Traits	标记 Marker	<BOLD>KASP</BOLD>标记 <BOLD>KASP </BOLD>marker	基因型 Genotype	数量 Number	均值 Mean	P值 P value
根系总体积 TRV (cm³)	AX-110497143	XNR7143	CC	165	0.4000	2×10-6**
根系总体积 TRV (cm³)	AX-110497143	XNR7143	TT	6	0.9300	2×10-6**
根系干重 RDW (g)	AX-109933707	XNR3707	CC	94	0.0162	0.001**
根系干重 RDW (g)	AX-109933707	XNR3707	TT	77	0.0180	0.001**

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