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Mining of candidate genes for nitrogen use efficiency in maize based on genome-wide association study

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Abstract

Improving the nitrogen use efficiency (NUE) may considerably increase maize yield and decrease the use of nitrogen (N) fertilizer. But the genetic basis of NUE in maize is still poorly understood. In this study, an association panel of 139 maize inbred lines genotyped with 50,790 single nucleotide polymorphism (SNP) was used to dissect the genetic basis of NUE-related traits by genome-wide association study (GWAS). NUE, N uptake efficiency (NupE), N utilization efficiency (NutE), grain N concentration (GNC), stover N concentration (SNC) and N harvest index (NHI) were estimated under two N levels. GWAS was performed using a fixed and random model circulating probability unification (FarmCUP) method. In total, 27 and 23 significant SNP-traits association signals were identified under normal and low N levels. In addition, 10 significant association signals were detected based on the traits relative value (normal N supply / low N supply) of two N levels. Further, 60 candidate genes were predicted for these traits base on linkage disequilibrium (LD) and low nitrogen transcriptome analysis of significant SNP regions. Among the candidate genes identified in this study, 66.7% involved in nitrogen compound metabolic process. Zm00001d025831 and Zm00001d004633 encoded ammonium transporter1 and transmembrane amino acid transporter family protein, respectively, may be important candidate genes for NUE. The markers identified in this study maybe has important significance and could be useful in molecular marker assisted selection in breeding of high-NUE maize varieties, and the candidate genes could deepen the understanding of the genetic basis of NUE.

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Funding

This study was financially supported by the Natural Key Research and Development Program of China (No.2017YFD010120301) and National Science Foundation of China (No.31301830).

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  1. Kunhui He and Shutu Xu contributed equally to this work.

Authors and Affiliations

  1. The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Kunhui He, Shutu Xu, Xinghua Zhang, Yanan Li, Liguo Chang, Yahui Wang, Yaqin Shi, Tingting Cui, Yuan Dong, Tianru Lan, Xueyan Liu, Yutang Du, Renhe Zhang, Jianchao Liu & Jiquan Xue

  2. Maize Engineering & Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China

    Kunhui He, Shutu Xu, Xinghua Zhang, Yanan Li, Liguo Chang, Yahui Wang, Yaqin Shi, Tingting Cui, Yuan Dong, Tianru Lan, Xueyan Liu, Yutang Du, Renhe Zhang, Jianchao Liu & Jiquan Xue

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  1. Kunhui He
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Contributions

JL and JX designed the experiments. KH, XZ, YL, LC, YW, YS, TC, YD, TL, XL and YD carried out the experiments. KH, SX and RZ analyzed the data. KH and SX wrote the manuscript. JL and JX revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Jianchao Liu or Jiquan Xue.

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He, K., Xu, S., Zhang, X. et al. Mining of candidate genes for nitrogen use efficiency in maize based on genome-wide association study. Mol Breeding 40, 83 (2020). https://doi.org/10.1007/s11032-020-01163-3

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