Genetic Dissection of Mature Root Characteristics by Genome-Wide Association Studies in Rapeseed (Brassica napus L.)

Abstract

Roots are complicated quantitative characteristics that play an essential role in absorbing water and nutrients. To uncover the genetic variations for root-related traits in rapeseed, twelve mature root traits of a Brassica napus association panel were investigated in the field within three environments. All traits showed significant phenotypic variation among genotypes, with heritabilities ranging from 55.18% to 79.68%. Genome-wide association studies (GWAS) using 20,131 SNPs discovered 172 marker-trait associations, including 103 significant SNPs (−log10 (p) > 4.30) that explained 5.24–20.31% of the phenotypic variance. With the linkage disequilibrium r2 > 0.2, these significant associations were binned into 40 quantitative trait loci (QTL) clusters. Among them, 14 important QTL clusters were discovered in two environments and/or with phenotypic contributions greater than 10%. By analyzing the genomic regions within 100 kb upstream and downstream of the peak SNPs within the 14 loci, 334 annotated genes were found. Among these, 32 genes were potentially associated with root development according to their expression analysis. Furthermore, the protein interaction network using the 334 annotated genes gave nine genes involved in a substantial number of interactions, including a key gene associated with root development, BnaC09g36350D. This research provides the groundwork for deciphering B. napus’ genetic variations and improving its root system architecture.

Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions

“…Favorable and unfavorable alleles can be found in certain species with simple genetic backgrounds without taking heterozygous SNPs into account [ 64 ]. Our result is consistent with the findings of a similar study in B. napus [ 37 ], which found that the proportion of TRL, TSA, and TRV of germplasm with favorable alleles was higher than the proportion of TRL, TSA, and TRV of germplasm with unfavorable alleles. These results revealed that the genetic modulation of root development in B. napus has a largely multiplicative effect.…”

“…Six of the B. napus genes were detected in each of group I and II, but only one gene was found in Group III ( Figure 3 A). Li et al [ 38 ] and Ibrahim et al [ 37 ] classified genes from rapeseed and three other plant species, including Brassica rapa , Brassica oleracea , and Arabidopsis thaliana , into four main groups. To learn more about gene-structure evolution and structural features, the putative genes’ coding sequences were aligned to the genomic sequences.…”

“…The 327 B . napus germplasms were genotyped by a B. napus 50 K Illumina Infinium [ 37 ]. The 21,242 SNP markers developed for the 327 B .…”

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

“…Genome-wide association study (GWAS) is an effective method for identifying loci/genes associated with complex traits in a genetically diverse crop population, including root architectural traits in rice, wheat, soybean, maize, rapeseed, etc. [ 20 , 21 , 22 , 23 , 24 , 25 , 26 ]. Transcriptome analysis has proven to be valuable for identifying candidate genes, especially differentially expressed genes (DEGs), between samples with contrasting traits.…”

“…Different artificial systems have been used to evaluate root traits, including sand, germination paper, and hydroponic-based cultures [ 31 ]. Hydroponic culture with digital imaging could quickly and precisely detect a variety of root traits in large populations and has been used to examine variations in root architecture among different crops, including rice, wheat, maize, soybean, and rapeseed [ 25 , 30 , 32 , 33 , 34 , 35 ]. In the present study, 13 RSA traits were investigated in hydroponic culture under control and low nitrogen (LN) treatments in an association panel of 327 B. napus cultivars, which was genotyped by the 50 K Brassica Infinium SNP array [ 25 ].…”