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

摘要/Abstract

摘要：

【目的】植物根系对水分及营养的获取、作物的生长发育和产量的形成至关重要。挖掘小麦苗期根系性状显著关联的SNP位点，预测相关候选基因，为解析小麦根系建成遗传机制及选育具有优良根系构型的小麦品种奠定基础。【方法】以189份小麦品种组成的自然群体为供试材料，调查2种培养条件（霍格兰营养液和去离子水）下培育21 d的苗期根系总长度（TRL）、根系总表面积（TRA）、根系总体积（TRV）、根系平均直径（ARD）及根系干重（RDW）等5个根系性状，试验进行2次重复，同时结合小麦660K SNP芯片的分型结果进行全基因组关联分析（genome-wide association study，GWAS）。此外，通过序列比对、结构域分析和注释信息预测候选基因，并采用竞争性等位基因特异性PCR（kompetitive allele specific PCR，KASP）技术开发根系性状的分子标记。【结果】霍格兰营养液培养条件下的根系性状变异范围较大，根系整体粗短；而去离子水条件下的根系细长、侧根较多。选用贝叶斯信息与连锁不平衡迭代嵌套式模型（BLINK）、压缩式混合线性模型（CMLM）、固定随机循环概率模型（FarmCPU）以及混合线性模型（MLM）4个模型，结合2种培养条件下的根系性状进行全基因关联分析，共检测到95个与小麦苗期根系性状显著关联的QTL位点（P<10^-3），其中，有18个QTL在2个条件下同时被检测到，分布在7A、1B、2B、3B、7B、1D、2D及3D染色体，可解释8.68%—14.07%的表型变异。筛选获得的显著性位点中，有4个与前人的研究相近或一致，其余为新发现QTL位点。对共定位的SNP进行单倍型分析，有10个SNP能够将供试材料分为2种单倍型，且单倍型间的根系性状具有显著差异，同时，基于这些SNP开发KASP标记，筛选到与根系总体积及根系干重相关的2个KASP标记（XNR7143和XNR3707）。进一步挖掘共定位SNP位点上下游区间内的基因，筛选到12个可能与根系发育相关的候选基因，其中，TraesCS7A02G160600编码酰基载体蛋白合成酶，参与根系脂肪酸的合成；TraesCS1B02G401800编码突触融合蛋白，对植物重力向性具有重要作用；TraesCS7B02G417900编码醛脱氢酶，参与脱落酸的合成，从而调控作物根系发育。【结论】小麦根系性状在不同基因型间差异显著，在2个条件下同时检测到18个显著QTL位点，开发了2个根系分子标记（XNR7143和XNR3707），并筛选出12个与根系性状相关的候选基因。

关键词: 小麦, 根系性状, 全基因组关联分析, 共定位SNP位点, KASP标记, 候选基因

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

王脉, 董清峰, 高珅奥, 刘德政, 卢山, 乔朋放, 陈亮, 胡银岗. 小麦苗期根系性状的全基因组关联分析与优异位点挖掘[J]. 中国农业科学, 2023, 56(5): 801-820.

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