Open AccessGenome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize
Author(s) -
Yinchao Zhang,
Peng Liu,
Chen Wang,
Na Zhang,
Yuxiao Zhu,
Chaoying Zou,
Guangsheng Yuan,
Cong Yang,
Shibin Gao,
Guangtang Pan,
Langlang Ma,
Yaou Shen
Publication year - 2021
Publication title -
peerj
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.927
H-Index - 70
ISSN - 2167-8359
DOI - 10.7717/peerj.11707
Subject(s) - germination , candidate gene , biology , abiotic stress , single nucleotide polymorphism , gene , genome wide association study , abiotic component , inbred strain , genetic association , genetics , quantitative trait locus , botany , genotype , paleontology
As one of the major crops, maize ( Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant ( P < 2.03 × 10 -6 ) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454 , Zm00001d010458 , Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.