title: Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize.
abstract: A detailed understanding of genetic architecture of mRNA expression by millions of genetic variants is important for studying quantitative trait variation. In this study, we identified 1.25M SNPs with a minor allele frequency greater than 0.05 by combining reduced genome sequencing (GBS), high-density array technologies (600K), and previous deep RNA-sequencing data from 368 diverse inbred lines of maize. The balanced allelic frequencies and distributions in a relatively large and diverse natural panel helped to identify expression quantitative trait loci (eQTLs) associated with more than 18 000 genes (63.4% of tested genes). We found that distant eQTLs were more frequent (∼75% of all eQTLs) across the whole genome. Thirteen novel associated loci affecting maize kernel oil concentration were identified using the new dataset, among which one intergenic locus affected the kernel oil variation by controlling expression of three other known oil-related genes. Altogether, this study provides resources for expanding our understanding of cellular regulatory mechanisms of transcriptome variation and the landscape of functional variants within the maize genome, thereby enhancing the understanding of quantitative variations.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Haijun
authors.initials: H
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Luyao
authors.initials: L
authors.lastname: Niu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yingjie
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiaqing
authors.initials: X
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Minliang
authors.initials: M
authors.lastname: Jin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wenqiang
authors.initials: W
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: yjianbing@mail.hzau.edu.cn.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
mesh_terms: D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D040641:Quantitative Trait Loci / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
keywords: GBS; GWAS; RNA-seq; Zea mays; eQTL; non-coding regulation