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. 2016 Jun 15:7:833.
doi: 10.3389/fpls.2016.00833. eCollection 2016.

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

Xiaopeng Li  1 , Zijian Zhou  1 , Junqiang Ding  1 , Yabin Wu  1 , Bo Zhou  1 , Ruixia Wang  1 , Jinliang Ma  1 , Shiwei Wang  1 , Xuecai Zhang  1 , Zongliang Xia  1 , Jiafa Chen  1 , Jianyu Wu  1
Affiliations

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

Xiaopeng Li et al. Front Plant Sci. .

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.

Keywords: association mapping; candidate gene; ear height; maize; plant height; quantitative trait locus.

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Figures

Figure 1
Figure 1
Population structure of the genome-wide association study (GWAS) panel. (A) Plot of LnP(D) and an ad-hoc statistic ΔP calculated for K = 1–12. LnP(D) is the output of STRUCTURE obtained by first computing the natural logarithm of the probability at each step of Markov chain Monte Carlo, ΔP is the difference of LnP(D) between adjacent K. (B) Population structure of the GWAS panel at K = 3.
Figure 2
Figure 2
Manhattan plots for combined genome-wide association study (GWAS) using the mixed linear model (MLM) for plant height (upper plot) and ear height (lower plot). Chromosomes and physical positions of single nucleotide polymorphisms (SNPs) on the X-axis and −log10 p-value of each SNP derived from the association study on the Y-axis.
Figure 3
Figure 3
Meta- quantitative trait locus (QTL) analysis for QTL detected by two bi-parental populations and significant SNPs detected by genome-wide association study (GWAS) in this study. Colored lines represent different QTL or SNPs detected in this study.
Figure 4
Figure 4
Quantitative trait locus (QTL) in bin 1.05 was validated using two opposite BC4F3 near isogenic line (NIL) populations and the genome-wide association study (GWAS) result in the QTL region. (A,B) Compare the two BC4F3 NIL populations for plant height (A) and ear height (B) under different environments. Blue bar indicates the target region of a homozygous allele from the recurrent parent. Red bar indicate the target region of a homozygous allele from the donor parent. (C) Manhattan plot for the GWAS result in the QTL region.
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