A combined association mapping and t-test analysis of SNP loci and candidate genes involving in resistance to low nitrogen traits by a wheat mutant population.

Hongchun Xiong,Shirong Zhao,Yuping Ding,Huijun Guo,Jiayu Gu,Chunyun Zhou,Linshu Zhao,Luxiang Liu,Yongdun Xie,Xiaotong Guo,Wujun Ma

doi:10.1371/journal.pone.0211492

Abstract

Crop productivity is highly dependent on the application of N fertilizers, but ever-increasing N application is causing serious environmental impacts. To facilitate the development of new wheat cultivars that can thrive in low N growth conditions, key loci and genes associated with wheat responses to low N must be identified. In this GWAS and t-test study of 190 M6 mutant wheat lines (Jing 411-derived) based on genotype data from the wheat 660k SNP array, we identified a total of 221 significant SNPs associated four seedling phenotypic traits that have been implicated in resistance to low N: relative root length, relative shoot length, relative root weight, and relative shoot weight. Notably, we detected large numbers of significantly associated SNP in what appear to be genomic ‘hotspots’ for resistance to low N on chromosomes 2A and 6B, strongly suggesting that these regions are functionally related to the resistance phenotypes that we observed in some of the mutant lines. Moreover, the candidate genes, including genes encoding high-affinity nitrate transporter 2.1, gibberellin responsive protein, were identified for resistance to low N. This study raises plausible mechanistic hypotheses that can be evaluated in future applied or basic efforts by breeders or plant biologists seeking to develop new high-NUE wheat cultivars.

Highlights

Nitrogen (N) is one of the essential elements for plant growth, and the application of N fertilizer to crops results in a dramatically increased yield [1]
Based on the measured data, the relative root length (RRL), relative shoot length (RSL), relative root weight (RRW), and relative shoot weight (RSW) values were calculated according to the following formulas, respectively: RRL = Root length in low N / Root length in normal N; RSL = Shoot length in low N / Shoot length in normal N; RRW = Root weight in low N / Root weight in normal N; RSW = Shoot weight in low N / Shoot weight in normal N
The best linear unbiased estimates (BLUE) values for RRL, RSL, RRW, and RSW from 8 replicates and 2 independent experiments were used for marker-trait association

Summary

Introduction

Nitrogen (N) is one of the essential elements for plant growth, and the application of N fertilizer to crops results in a dramatically increased yield [1]. 50% to 70% of the N fertilizer applied to production fields is not utilized by crops; this results in negative impacts to the environment such as the eutrophication of water supplies [2]. The improvement of nitrogen use efficiency (NUE) in crops is of enormous importance [3]. Viewed in this context, the identification of any genetic loci or significant molecular markers associated with resistance to low N will be useful for the improvement of NUE in crops [4].

Methods

Results

Discussion

Conclusion