Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize.

Xiaopeng Li,Xuecai Zhang,Jinliang Ma,Ruixia Wang,Bo Zhou,Yabin Wu,Jianyu Wu,Zongliang Xia,Jiafa Chen,Junqiang Ding,Shiwei Wang,Zijian Zhou

doi:10.3389/fpls.2016.00833

Abstract

Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.

Highlights

Maize (Zea mays L.) is one of the most cultivated crops worldwide, owing to its versatility and wide adaptability, and serves as food, animal feed, and raw material for various industrial products
There were a wide variations were observed in each population, for example, the Plant height (PH) of combined environments in recombinant inbred line (RIL) population ranged from 105 to 273 cm, whereas in the genome-wide association study (GWAS) population from 106 to 293 cm
The high repeatability and heritability indicated that much of the phenotypic variance was genetically controlled in the populations and suitable for quantitative trait loci (QTL) mapping

Summary

Introduction

Maize (Zea mays L.) is one of the most cultivated crops worldwide, owing to its versatility and wide adaptability, and serves as food, animal feed, and raw material for various industrial products. Plant density is considered an important factor to increase yield (Cardwell, 1982; Zhang et al, 2014). The mapping of quantitative trait loci (QTL) based on bi-parental populations is an effective method for detecting the genetic variation of in crops. Molecular markers have been widely used in QTL mapping for various traits in maize, including maturity (Buckler et al, 2009), disease resistance (Zwonitzer et al, 2010; Chen et al, 2012; Ding et al, 2012), abiotic stress (Agrama and Moussa, 1996), plant morphology (Xu et al, 2009; Ding et al, 2015; Chen et al, 2016), and plant

Objectives

Methods

Results

Discussion

Conclusion