Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (13): 2487-2503.doi: 10.3864/j.issn.0578-1752.2025.13.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Screening of Wheat Varieties with Low Nitrogen Tolerance and Genome-Wide Association Studies of Low Nitrogen Stress Tolerance Index

LI Ning1(), GAO LiFeng2(), HUANG Xin1, SHI HuaWei1,3, YANG JinWen1, SHI YuGang1, CHEN Ming2, JIA JiZeng2(), SUN DaiZhen1()   

  1. 1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi
    2 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081
    3 Rural Survey Institute, Shanxi Agricultural University, Taiyuan 030031
  • Received:2025-01-07 Accepted:2025-03-06 Online:2025-07-01 Published:2025-07-05

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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

Table 1

Descriptive statistical analysis of GYP and low nitrogen tolerance index of wheat under different environments"

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

Fig. 1

Analysis of the distribution and differences of various low nitrogen tolerance indices in wheat populations under different environments Different lowercase letters indicate significant differences at the 0.05 probability level"

Fig. 2

Correlation analysis of GYP and low nitrogen tolerance index of wheat under different environment A: 18SX; B: 19SX; C: 20SX; D: 19HB; E: 20HB; F: The average of the five environments. GYPhn+ln: The average value of GYP under the two nitrogen treatments. *: P<0.05, **: P<0.01, ***: P<0.001"

Fig. 3

Cluster analysis and distribution of low nitrogen tolerance of wheat natural population under different nitrogen treatments A: Cluster map of evaluation results of low nitrogen tolerance in wheat natural population; B: Distribution of grain yield per plant of different low nitrogen tolerant wheat varieties under different nitrogen treatments. HT: High tolerance; T: Tolerance; M: Moderate; S: Sensitive; HS: High sensitive. The same as below"

Table 2

Analysis of differences in GYP and yield-related traits among different low nitrogen tolerance types"

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

Table 3

Significant association SNP of low nitrogen tolerance index"

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

Table 4

Locus with significant association of STI"

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
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]
19HB 3 AX-108764077 595606825 4.43E-05 5.25
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

Fig. 4

The location of qSTI3B on the chromosome"

Table 5

Candidate genes in qSTI3B physical interval"

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

Fig. 5

Haplotype analysis of candidate genes ns: No significant difference between them"

Fig. 6

Expression analysis of candidate genes A: Expression levels of candidate genes after nitrogen starvation and nitrogen recovery; B: Expression levels of candidate genes in different tissues of wheat; C: Expression levels of candidate genes in seed embryo and endosperm"

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