Detection of QTNs for kernel moisture concentration and kernel dehydration rate before physiological maturity in maize using multi-locus GWAS

Shufang Li,Xueyan Liu,Yu Wang,Deguang Yang,Xiaohui Li,Yiliang Qian,Ming Lu,Fengxue Jin,Wenguo Liu,Chunxiao Zhang

doi:10.1038/s41598-020-80391-1

Abstract

Maize is China’s largest grain crop. Mechanical grain harvesting is the key technology in maize production, and the kernel moisture concentration (KMC) is the main controlling factor in mechanical maize harvesting in China. The kernel dehydration rate (KDR) is closely related to the KMC. Thus, it is important to conduct genome-wide association studies (GWAS) of the KMC and KDR in maize, detect relevant quantitative trait nucleotides (QTNs), and mine relevant candidate genes. Here, 132 maize inbred lines were used to measure the KMC every 5 days from 10 to 40 days after pollination (DAP) in order to calculate the KDR. These lines were genotyped using a maize 55K single-nucleotide polymorphism array. QTNs for the KMC and KDR were detected based on five methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, and ISIS EM-BLASSO) in the package mrMLM. A total of 334 significant QTNs were found for both the KMC and KDR, including 175 QTNs unique to the KMC and 178 QTNs unique to the KDR; 116 and 58 QTNs were detected among the 334 QTNs by two and more than two methods, respectively; and 9 and 5 QTNs among 58 QTNs were detected in 2 and 3 years, respectively. A significant enrichment in cellular component was revealed by Gene Ontology enrichment analysis of candidate genes in the intervals adjacent to the 14 QTNs and this category contained five genes. The information provided in this study may be useful for further mining of genes associated with the KMC and KDR in maize.

Highlights

Maize (Zea mays L.) is the largest grain crop in China
The kernel moisture concentration (KMC) gradually decreased over time, while the kernel dehydration rate (KDR) gradually increased over time (Table 1)
The KMC had relatively low coefficients of variation (CV), and the lowest CVs were found at 15 days after pollination (DAP), with values of 1.34%, 1.48%, and 1.44% in 2014, 2015, and 2016, respectively

Summary

Introduction

Maize (Zea mays L.) is the largest grain crop in China. The planting area for maize and maize production were 41.3 million ha and 2.6 billion tons in 2019 in China, respectively[1]. The methods included iterative modified-sure independence screening expectation–maximization (EM)-Bayesian LASSO (ISIS EM-BLASSO), polygenic-backgroundcontrol-based least angle regression plus empirical Bayes (pLARmEB), fast multi-locus random-SNP-effect efficient mixed model association (FASTmrEMMA), and fast multi-locus random-SNP-effect mixed linear model (FASTmrMLM)[26,27,28,29,30]. These methods could effectively detect small-effect quantitative trait nucleotides (QTNs) and improve the efficiency and accuracy of GWAS

Objectives

Methods

Results

Discussion

Conclusion