耐低氮小麦品种的筛选及耐低氮指数的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2025.13.001

摘要/Abstract

摘要： 【目的】氮肥的大量应用造成了生态环境的污染和农业资源的浪费。培育氮高效小麦新品种，提高小麦的氮素利用效率，是实现农业可持续发展和保护环境的有效途径。筛选耐低氮种质资源，挖掘耐低氮性相关遗传位点及候选基因，为氮高效小麦新品种的培育提供材料和奠定理论基础。【方法】以389份小麦品种组成的自然群体为材料，分别在高氮（HN）和低氮（LN）处理下的10个田间环境中测定小麦单株籽粒产量（GYP）。然后，基于GYP计算各品种的耐低氮指数（stress tolerance index，STI），并筛选出具有不同耐低氮性的小麦品种。结合自然群体660K单核苷酸多态性（SNP）标记芯片的基因型分析数据，对STI进行全基因组关联分析（GWAS），鉴定与小麦田间耐低氮性稳定关联的遗传位点。进一步根据候选基因的单倍型分析、表达分析和功能注释，筛选与小麦耐低氮性相关的候选基因。【结果】共筛选出12份具有强耐低氮性的小麦品种，分别为中洛08-1、冀麦15、京花2号、科红1号、绵阳19、济麦22、镇麦4号、豫麦35、丰抗7号、绵阳11、晋麦31和鲁麦5号。共检测到14个与STI显著关联的位点，其中4个位点（qSTI1A.1、qSTI3B、qSTI6A和qSTI7A.2）的物理区间与前人已报道的小麦耐低氮性或产量相关遗传位点存在重叠，且qSTI3B在3个环境中被重复检测到，是一个调控小麦耐低氮性的重要遗传位点，进而对其候选基因进行了筛选。结果显示，候选基因TraesCS3B02G042400的功能注释为AP2/EREBP（APETALA2/乙烯响应元件结合蛋白）转录因子。携带该基因不同单倍型的小麦品种间STI值呈现显著差异，且其表达水平会随着氮素供应而持续上升。结果表明，TraesCS3B02G042400是一个与小麦耐低氮性相关的关键候选基因。【结论】筛选出12份强耐低氮性的小麦品种。鉴定到一个与小麦耐低氮性稳定关联的重要遗传位点qSTI3B。挖掘到一个小麦耐低氮候选基因TraesCS3B02G042400。

关键词: 小麦, 耐低氮性, 耐低氮指数, 全基因组关联分析, 候选基因

Abstract:

【Objective】 The excessive application of nitrogen fertilizers has led to ecological pollution and waste of agricultural resources. Developing nitrogen-efficient wheat varieties and improving nitrogen use efficiency are effective approaches for achieving sustainable agricultural development and environmental protection. Screening low-nitrogen-tolerant germplasm resources and identifying genetic loci and candidate genes associated with low-nitrogen tolerance can provide materials and theoretical foundations for breeding nitrogen-efficient wheat varieties. 【Method】 A natural population consisting of 389 wheat varieties was cultivated under high-nitrogen (HN) and low-nitrogen (LN) treatments in 10 field environments. Grain yield per plant (GYP) was measured to calculate the stress tolerance index (STI), thereby enabling the classification of varieties with differential low-nitrogen tolerance. Genome-wide association studies (GWAS) were conducted using 660K SNP array genotyping data to identify stable genetic loci associated with low-nitrogen tolerance. Candidate genes were prioritized through haplotype analysis, expression profiling, and functional annotation. 【Result】 Twelve wheat varieties with strong low-nitrogen tolerance were identified, including Zhongluo 08-1, Jimai 15, Jinghua 2, Kehong 1, Mianyang 19, Jimai 22, Zhenmai 4, Yumai 35, Fengkang 7, Mianyang 11, Jinmai 31, and Lumai 5. Fourteen loci significantly associated with STI were detected, among which four (qSTI1A.1, qSTI3B, qSTI6A, and qSTI7A.2) overlapped with previously reported low-nitrogen tolerance or yield-related QTLs. Notably, qSTI3B-replicated across three environments-was identified as a key locus governing low-nitrogen tolerance. Functional annotation revealed that its candidate gene, TraesCS3B02G042400, encodes an AP2/EREBP (APETALA2/ethylene-responsive element-binding protein) transcription factor. Haplotype analysis showed significant STI divergence among varieties carrying distinct haplotypes, while expression levels of TraesCS3B02G042400 exhibited nitrogen dose-responsive upregulation. 【Conclusion】 Twelve wheat varieties with strong low-nitrogen tolerance were screened. A stable genetic locus, qSTI3B, and a candidate gene, TraesCS3B02G042400, associated with low-nitrogen tolerance were identified.

Key words: wheat, low nitrogen tolerance, stress tolerance index, genome-wide association study, candidate gene

李宁, 高丽锋, 黄鑫, 史华伟, 杨进文, 史雨刚, 陈明, 贾继增, 孙黛珍. 耐低氮小麦品种的筛选及耐低氮指数的全基因组关联分析[J]. 中国农业科学, 2025, 58(13): 2487-2503.

LI Ning, GAO LiFeng, HUANG Xin, SHI HuaWei, YANG JinWen, SHI YuGang, CHEN Ming, JIA JiZeng, SUN DaiZhen. Screening of Wheat Varieties with Low Nitrogen Tolerance and Genome-Wide Association Studies of Low Nitrogen Stress Tolerance Index[J]. Scientia Agricultura Sinica, 2025, 58(13): 2487-2503.

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性状 Trait	环境 Environment	平均值 Average	最小值 Min	最大值 Max	标准差 SD	变异系数 CV (%)
高氮下单株籽粒产量 GYP under HN treatment (g)	20HB	18.92	9.29	29.71	3.53	18.66
	19HB	19.98	9.43	36.78	4.20	21.02
	20SX	7.05	2.17	17.39	2.18	30.95
	19SX	10.77	2.42	21.93	3.75	34.79
	18SX	7.18	3.13	14.43	1.91	26.22
低氮下单株籽粒产量 GYP under LN treatment (g)	20HB	16.11^***	8.00	25.71	3.10	19.27
	19HB	16.00^***	8.74	23.41	3.01	18.77
	20SX	5.51^***	1.63	11.68	1.66	30.22
	19SX	8.16^***	1.45	15.94	2.70	33.16
	18SX	5.51^***	2.34	13.55	1.53	27.58
产量稳定指数 YSI	20HB	0.86	0.54	1.28	0.11	12.79
	19HB	0.82	0.48	1.10	0.14	17.07
	20SX	0.80	0.41	1.17	0.15	18.75
	19SX	0.77	0.49	1.14	0.14	18.18
	18SX	0.78	0.43	1.06	0.15	19.23
胁迫敏感指数 SSI	20HB	0.95	-1.86	3.11	0.65	68.42
	19HB	0.91	-0.50	2.61	0.62	68.13
	20SX	0.92	-0.75	2.69	0.58	63.04
	19SX	0.93	-0.59	2.12	0.57	61.29
	18SX	0.94	-0.26	2.45	0.64	68.09
耐低氮指数 STI	20HB	0.87	0.25	2.13	0.30	34.48
	19HB	0.82	0.21	1.67	0.28	34.15
	20SX	0.83	0.07	2.22	0.44	53.01
	19SX	0.83	0.03	2.73	0.52	62.65
	18SX	0.80	0.16	2.66	0.39	48.75
氮响应值 NRV	20HB	0.19	-0.22	0.86	0.12	63.16
	19HB	0.27	-0.09	1.09	0.18	66.66
	20SX	0.30	-0.14	1.44	0.21	70.00
	19SX	0.33	-0.13	1.06	0.24	72.72
	18SX	0.33	-0.06	1.33	0.21	63.63

性状 Traits	耐低氮类型 Low nitrogen tolerant type	HN环境平均值±标准差 Average value in HN environment± Standard deviation	LN环境平均值±标准差 Average value in LN environment± Standard deviation
单株籽粒产量 GYP (g)	HT	18.42±1.28a	14.63±0.94a
	T	15.79±0.99b	12.53±0.83b
	M	13.64±0.89c	10.98±0.67c
	S	11.20±1.00d	9.15±0.81d
	HS	7.69±1.22e	5.84±1.11e
千粒重 TKW (g)	HT	45.35±2.96a	42.36±2.76ab
	T	45.19±3.92a	43.17±3.77a
	M	43.83±4.12ab	41.70±4.00bc
	S	43.31±4.19b	41.03±4.41c
	HS	40.69±5.39c	38.02±5.55d
每穗粒数 GNS	HT	57.93±5.32a	52.66±5.02a
	T	57.19±6.62a	51.57±5.16a
	M	56.78±7.52a	51.36±6.23a
	S	55.82±7.25a	50.05±6.02a
	HS	56.00±12.18a	50.11±8.04a
分蘖数TN	HT	8.34±1.04ab	6.88±0.98ab
	T	8.43±1.00a	7.07±0.84a
	M	8.38±1.11a	6.98±0.93a
	S	7.97±1.08bc	6.65±0.85b
	HS	7.56±1.08c	5.90±1.05c

环境 Environments	SNP数量 No. of SNPs	染色体 Chromosomes	P值 P value	R² (%)
18SX	58	1A, 1B, 2A, 3A, 3B, 4D, 5B, 6B, 7D	2.04E-06—9.70E-05	4.87—7.44
19SX	27	1B, 2A, 4A, 5B, 5D, 7D	6.27E-06—9.86E-05	5.33—7.41
20SX	22	1A, 1B, 3A, 3B, 5B, 5D, 6A, 7A, 7B, 7D	1.69E-05—9.88E-05	4.88—7.58
19HB	8	1A, 1B, 2B, 4A, 5A, 6A, 7B	4.43E-05—9.94E-05	4.69—5.67
20HB	15	3A, 3B, 5B, 5D, 6A, 6B	3.54E-05—9.42E-05	4.85—6.69

关联位点 Associated locus	染色体 Chromosomes	置信区间 Confidence interval (bp)	环境 Environments	显著SNP数量 No. of significant SNPs	峰值SNP Peak SNP	物理位置 Physical location (bp)	P值 P value	R² (%)	已报道位点 Reported locus
qSTI1A.1	1A	573330409—575076937	18SX	2	AX-108813611	573502309	6.57E-06	6.92	qTNR1A.2^[18]
qSTI1A.2	1A	590711547—590986034	20SX	2	AX-109863561	590977148	7.49E-05	5.25
qSTI2A.1	2A	155876092—156876092	18SX	2	AX-110423504	156376092	3.91E-05	5.74
qSTI2A.2	2A	157543327—158435888	18SX	4	AX-109846450	158045085	6.47E-06	5.22
qSTI2A.3	2A	158455885—159864551	18SX	2	AX-108746106	159092995	7.68E-05	5.51
qSTI3A.1	3A	36089540—36658499	18SX	3	AX-110714576	36647841	2.82E-05	5.69
qSTI3A.2	3A	36667916—37820677	18SX	29	AX-111680971	36892106	2.19E-06	7.44
qSTI3A.2	3A	36667916—37820677	20SX	2	AX-111680971	36892106	3.57E-05	6.34
qSTI3B	3B	21002550—22060773	20HB	3	AX-111217726	21005270	4.82E-05	5.48	MQTL-3B-2^[31]
			20SX	4	AX-109372197	21958702	1.69E-05	5.96
			19SX	3	AX-109483119	21146511	6.30E-05	5.33
qSTI4A.1	4A	742336253—742890671	19SX	16	AX-111002722	742825633	1.04E-05	7.41
qSTI4A.2	4A	744154769—744311695	19SX	3	AX-111184770	744276864	2.81E-05	6.26
qSTI6A	6A	595581230—596160987	20HB	6	AX-110988432	595581230	3.77E-05	5.37	MQTL-6A-7^[31]
qSTI6A	6A	595581230—596160987	19HB	3	AX-108764077	595606825	4.43E-05	5.25	MQTL-6A-7^[31]
qSTI7A.1	7A	54704803—55369001	20SX	3	AX-109038648	55349021	3.86E-05	5.73
qSTI7A.2	7A	67737933—68737933	20SX	2	AX-110092291	68237933	9.10E-05	5.11	MQTL-7A-1^[31]
qSTI7D	7D	1196736—1241409	19SX	2	AX-109901882	1196736	7.38E-05	5.43

基因ID Gene ID	物理位置 Physical location (bp)	注释功能 Annotation function
TraesCS3B02G042000	Chr.3B: 21002815—21003875	染色质重塑子8 Chromatin remodeling 8
TraesCS3B02G042100	Chr.3B: 21346119—21347117	F-box结构域蛋白F-box domain containing protein
TraesCS3B02G042200	Chr.3B: 21384803—21387745	F-box结构域蛋白F-box domain containing protein
TraesCS3B02G042300	Chr.3B: 21402835—21405805	单磷酸鸟苷合酶GMP synthase
TraesCS3B02G042400	Chr.3B: 21770070—21771613	AP2/EREBP转录因子AP2/EREBP transcription factor
TraesCS3B02G042500	Chr.3B: 21880115—21880378	含P环的核苷三磷酸水解酶超家族蛋白 P-loop containing nucleoside triphosphate hydrolases superfamily protein
TraesCS3B02G042600	Chr.3B: 22053762—22056996	信号肽酶亚家族蛋白Signal peptidase subunit family protein