Population structure analysis and identification of genomic regions under selection associated with low-nitrogen tolerance in tropical maize lines.

Gustavo César Sant’Ana,Fernando Garcia Espolador,Aluízio Borém,Roberto Fritsche-Neto,Ítalo Stefanine Correia Granato,Leandro Freitas Mendonça,Chengdao Li

doi:10.1371/journal.pone.0239900

Gustavo César Sant’Ana, Fernando Garcia Espolador + Show 5 more

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https://doi.org/10.1371/journal.pone.0239900

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Abstract

Increasing low nitrogen (N) tolerance in maize is an important goal for food security and agricultural sustainability. In order to analyze the population structure of tropical maize lines and identify genomic regions associated with low-N tolerance, a set of 64 inbred lines were evaluated under low-N and optimal-N conditions. The low-N Agronomic Efficiency index (LNAE) of each line was calculated. The maize lines were genotyped using 417,112 SNPs markers. The grouping based on the LNAE values classified the lines into two phenotypic groups, the first comprised by genotypes with high LNAE (named H_LNAE group), while the second one comprised genotypes with low LNAE (named L_LNAE group). The H_LNAE and L_LNAE groups had LNAE mean values of 3,304 and 1,644, respectively. The population structure analysis revealed a weak relationship between genetic and phenotypic diversity. Pairs of lines were identified, having at the same time high LNAE and high genetic distance from each other. A set of 29 SNPs markers exhibited a significant difference in allelic frequencies (Fst > 0.2) between H_LNAE and L_LNAE groups. The Pearson’s correlation between LNAE and the favorable alleles in this set of SNPs was 0.69. These SNPs could be useful for marker-assisted selection for low-N tolerance in maize breeding programs. The results of this study could help maize breeders identify accessions to be used in the development of low-N tolerant cultivars.

Highlights

High levels of nitrogen (N) fertilization is required to achieve high maize (Zea mays L.) grain yield
Based on the Scott-Knott test, the maize lines were classified into two phenotypic groups, one formed from 29 lines with high Low-N Agronomic Efficiency (LNAE) values and another comprising 35 lines with low LNAE
Population structure and genomic regions associated with maize low-nitrogen tolerance deviation of 1,644 and 521, respectively

Summary

Introduction

High levels of nitrogen (N) fertilization is required to achieve high maize (Zea mays L.) grain yield. The maize crop utilizes only about 30–40% of the N available in the soil while the remaining is lost through surface runoff, denitrification, volatilization and microbial consumption [1]. N fertilization is expensive and harmful to the environment because of the negative effect on water quality. In this context, the development of nutritionally efficient maize cultivars, which yield more with low fertilization, is a way to reduce fertilizer usage [2, 3].

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