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Kernel size‐related genes revealed by an integrated eQTL analysis during early maize kernel development
Author(s) -
Pang Junling,
Fu Junjie,
Zong Na,
Wang Jing,
Song Dandan,
Zhang Xia,
He Cheng,
Fang Ting,
Zhang Hongwei,
Fan Yunliu,
Wang Guoying,
Zhao Jun
Publication year - 2019
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.14193
Subject(s) - expression quantitative trait loci , biology , quantitative trait locus , genetics , endosperm , computational biology , gene , locus (genetics) , transcriptome , genome , genotype , gene expression , single nucleotide polymorphism
Summary In maize, kernel traits strongly impact overall grain yields, and it is known that sophisticated spatiotemporal programs of gene expression coordinate kernel development, so advancing our knowledge of kernel development can help efforts to improve grain yields. Here, using phenotype, genotype and transcriptomics data of maize kernels at 5 and 15 days after pollination ( DAP ) for a large association mapping panel, we employed multiple quantitative genetics approaches—genome‐wide association studies ( GWAS ) as well as expression quantitative trait loci ( eQTL ) and quantitative trait transcript ( QTT ) analyses—to gain insights about molecular genetic basis of kernel development in maize. This resulted in the identification of 137 putative kernel length‐related genes at 5 DAP , of which 43 are located in previously reported QTL regions. Strikingly, we identified an eQTL that overlaps the locus encoding a maize homolog of the recently described m 6 A methylation reader protein ECT 2 from Arabidopsis; this putative epi e QTL is associated with 53 genes and may represent a master epi‐transcriptomic regulator of kernel development. Notably, among the genes associated with this epi e QTL , 10 are for the main storage proteins in the maize endosperm (zeins) and two are known regulators of zein expression or endosperm development ( Opaque2 and Zm ICE 1 ). Collectively, beyond cataloging and characterizing genomic attributes of a large number of eQTL associated with kernel development in maize, our study highlights how an eQTL approach can bolster the impact of both GWAS and QTT studies and can drive insights about the basic biology of plants.