Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Brassica napus L.)

Abstract

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes’ homologs—BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS—have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

Morpho-physiological, Genomic, and Transcriptional Diversities in Response to Potassium Deficiency in Rapeseed (Brassica napus L.) Genotypes

“…Genetic variations in the sensitivity to K deficiency found in rapeseed genotypes highlight the complex regulatory mechanisms . However, previous studies have mainly focused on the morpho-physiological and transcriptomic responses of single rapeseed genotype to K deficiency, ,, or rough mapping of some QTLs for rapeseed low K resistance . Few of the previous studies have integrated morpho-physiological responses, genomic variations, and transcriptional profiling into the dissection of differential low K resistance among rapeseed genotypes.…”

“…Weighted gene coexpression network analysis (WGCNA) was used to identify hub genes that have significant impacts and modules of highly connected genes in the regulation of low K resistance. 36 WGCNA was used to identify the core members among all the genome-wide DEGs in the shoots and roots of the low-K resistant and low-K sensitive rapeseed genotypes under high K and low K conditions. The comparisons were paired, and the P value was less than 0.05.…”

Genome-Wide and Transcriptome-Wide Association Analysis Identifies qRS-6D and Its Candidate Genes Regulating Root Development of Wheat Seedlings

“…The root system is vital for absorbing water and soil nutrients and also plays a key role in sensing and responding to environmental stresses [4], such as low temperatures [5], drought [6], and salinity [7]. A well-developed root structure has the potential to enhance plant resilience [8], such as by improving soil nutrient utilization efficiency and reducing water usage [9], thereby increasing the final crop yield under climate change conditions. However, the past genetic improvement efforts in wheat mainly targeted the aboveground traits, including plant height [10], yield components [11], and disease resistance [12], due to the difficulties in observing the root-related traits.…”