Genome-Wide Association Study and Transcriptome Analysis Reveal Key Genes Affecting Root Growth Dynamics In Rapeseed

Abstract

Root growth is a dynamic process mediated by interactive genetic factors and environmental cues. Seven root-related traits and two shoot-related traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. The former identified 367 differentially expressed genes (DEGs) with persistently differential expressions throughout root development that were significantly enriched in GO terms of energy metabolism and response to biotic or abiotic stress, whereas the later identified 485 stage-specific DEGs with different expressions at corresponding stage that were enriched in GO terms of nitrogen metabolism. By integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis, four and eight candidate genes less than 100 kb away from peak SNPs of QTL clusters were identified as key persistent and stage-specific genetic factors, respectively. The homologs of 3 genes ( BnaA03g52990D , BnaA06g37280D, and BnaA09g07580D ) out of 12 candidate genes have been reported to regulate root development in previous studies. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.