Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat
Zaicheng Zhang,
Chaojun Peng,
Weigang Xu,
Yan Li,
Xueli Qi,
Mingzhong Zhao
Affiliations
Zaicheng Zhang
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
Chaojun Peng
Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences
Weigang Xu
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
Yan Li
Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences
Xueli Qi
Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences
Mingzhong Zhao
Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences
Abstract Background Nitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study. Results In this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r 2 > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses. Conclusions This study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.
