Genome-wide detection of genotype environment interactions for flowering time in Brassica napus

Abstract

Flowering time is strongly related to the environment, while the genotype-by-environment interaction study for flowering time is lacking in <i>Brassica napus</i>. Here, a total of 11,700,689 single nucleotide polymorphisms in 490 <i>B. napus</i> accessions were used to associate with the flowering time and related climatic index in eight environments using a compressed variance-component mixed model, 3VmrMLM. As a result, 19 stable main-effect quantitative trait nucleotides (QTNs) and 32 QTN-by-environment interactions (QEIs) for flowering time were detected. Four windows of daily average temperature and precipitation were found to be climatic factors highly correlated with flowering time. Ten main-effect QTNs were found to be associated with these flowering-time-related climatic indexes. Using differentially expressed gene (DEG) analysis in semi-winter and spring oilseed rapes, 5,850 and 5,511 DEGs were found to be significantly expressed before and after vernalization. Twelve and 14 DEGs, including 7 and 9 known homologs in <i>Arabidopsis</i>, were found to be candidate genes for stable QTNs and QEIs for flowering time, respectively. Five DEGs were found to be candidate genes for main-effect QTNs for flowering-time-related climatic index. These candidate genes, such as <i>BnaFLC</i>s, <i>BnaFT</i>s, <i>BnaA02.VIN3</i>, and <i>BnaC09.PRR7</i>, were further validated by the haplotype, selective sweep, and co-expression networks analysis. The candidate genes identified in this study will be helpful to breed <i>B. napus</i> varieties adapted to particular environments with optimized flowering time.