Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of Brassica napus L.

Global climate changes on one aspect of extreme temperature records would suddenly reset environmental growth conditions for field-grown crops, which severely affects agronomic and commercial traits. Taking the cold-season preferable crop rapeseed Brassica napus L. for example, low-temperature shocks change endogenous regulatory networks and cause phenotypic damages during most lifespan. Here we screened out two genetic breeding elites with different temperature-dependent germination rates, core germplasms with good germination performance and genetic loci and candidate genes potentially involved in low-temperature tolerant functions for the pre-breeding purpose of cold-tolerant germination. By using the phenotype of the germination index of 273 core germplasms under normal temperature and 10 transcriptomic datasets of cold-tolerant Jia You (JY) 1621 and cold-sensitive JY1605 elite cultivars on three timepoints during germination process, we successfully identified clustered genes of early and late temperature response germination (ETRG and LTRG) genes and several cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators. This study performed comprehensive multi-omics research on potential cold-responsive genes for the rapeseed improvement of cold tolerance germination. Overall design: we conducted a comprehensive transcriptome sequencing using JY1621 and JY1605 materials under normal- (25 ?) and low- (8 ?) temperature conditions. Dry seeds (ZT0), germinating seeds after 8 hours (8H on ZT8) and germinating seeds after 36 hours (36H on ZT12) of JY1621 and JY1605 grown at 25 ? and 8 ? conditions were collected in three biological replications.