Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.).

Yang Lv,Xueli Lu,Yueying Wang,Lianguang Shang,Jie Ma,Longbiao Guo,Quan Wang,Haitao Hu,Qian Qian

doi:10.3389/fpls.2021.770736

Abstract

Nitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll content, and leaf length) of the 225-rice-variety natural population from the Rice 3K Sequencing Project across normal nitrogen (NN) and low nitrogen (LN) environments. The LNGR phenotypic difference between NN and LN levels was used for gene analysis using a genome-wide association study (GWAS) combined with 111,205 single-nucleotide polymorphisms (SNPs) from the available sequenced data from the 3K project. We obtained a total of 56 significantly associated SNPs and 4 candidate genes for 4 LNGR traits. Some loci were located in the candidate regions, such as MYB61, OsOAT, and MOC2. To further study the role of candidate genes, we conducted haplotype analyses to identify the elite germplasms. Moreover, several other plausible candidate genes encoding LN-related or NUE proteins were worthy of mining. Our study provides novel insight into the genetic control of LNGR and further reveals some related novel haplotypes and potential genes with phenotypic variation in rice.

Highlights

Nitrogen (N) is an essential macronutrient element for plant growth
By evaluating the statistics data, we found a broad phenotypic variation of the nitrogen-use efficiency (NUE)-related agronomic traits of the natural rice population, indicating that the low N (LN)-induced phenotypic data were reliable for further genetic analyses
To confirm whether the phenotypic changes were related to nitrogen, we found that the mean values for the four traits under NN were higher than the mean values for the phenotypic data under LN (P SV, leaf length (LL), plant height (PH) < 0.0001, P tiller number (TN) < 0.05)

Summary

Introduction

Nitrogen (N) is an essential macronutrient element for plant growth. Plants take up N from the soil mainly in the form of nitrate (NO3−) and/or ammonium (NH4+) (Wang et al, 2012; Fan et al, 2016). Some elite rice germplasm can be harvested and produce the same biomass and grain yield under low N (LN) fertilizers, as compared with high N levels. This phenomenon is called low nitrogen-use efficiency (NUE), and it mitigates detrimental effects on ecosystems (Good et al, 2004; Zhang X. et al, 2015). It is critically important to understand the molecular mechanisms of low-N-induced growth response (LNGR) and to develop crop varieties with improved NUE (Fan et al, 2017; Du et al, 2021; Yu et al, 2021)

Methods

Results

Conclusion