Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed

Abstract

Background In terms of global demand, rapeseed is the third-largest oilseed crop after soybeans and palm, which produces vegetable oil for human consumption and biofuel for industrial production. Roots are vital organs for plant to absorb water and attain mineral nutrients, thus they are of great importance to plant productivity. However, the genetic mechanisms regulating root development in rapeseed remain unclear. In the present study, seven root-related traits and shoot biomass traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. Results 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 the investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. A total of 367 differentially expressed genes (DEGs) with persistent differential expressions throughout root development were identified, and these DEGs were significantly enriched in GO terms, such as energy metabolism and response to biotic or abiotic stress. Totally, 485 stage-specific DEGs with different expressions at specific stage were identified, and these DEGs were enriched in GO terms, such as nitrogen metabolism. Four candidate genes were identified as key persistent genetic factors and eight as stage-specific ones by integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. These candidate genes were speculated to regulate root system development, and they were less than 100 kb away from peak SNPs of QTL clusters. The homologs of three genes (BnaA03g52990D, BnaA06g37280D, and BnaA09g07580D) out of 12 candidate genes have been reported to regulate root development in previous studies. Conclusions Sixteen QTL clusters and four candidate genes controlling persistently root development, and 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed were detected in this study. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.

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

“…Moreover, many of these QTLs have been linked to traits such as yield, water/nutrient absorption, and abiotic stress tolerance [ 57 , 59 , 60 , 61 , 62 ]. In this work, the peak SNPs of 15 QTN clusters were found in the same haplotype blocks as the 27 previously reported important SNPs associated with B. napus root-development dynamics ( Table S8 ; [ 38 ]). Nonetheless, previously identified QTL ( qcA02-1 , qcA02-2 , and qcA02-3 ) associated with total root number, shoot dry weight, and root–shoot ratio in dry weight discovered under low-nitrogen conditions were likewise colocalized with our cluster qRT.A02-4 [ 15 , 41 ].…”

“…Furthermore, if the peak SNPs with near vicinity (within 1 Mb) and have an LD r 2 > 0.2, they are categorized as the same QTL [ 38 ]; therefore, the 453 significant MTAs were integrated into 206 QTL clusters ( Table S3 ). These QTL clusters were distributed on all the 19 B. napus chromosomes with the highest number on C04 and C06.…”

“…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.…”

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

“…In response to cadmium stress, three hub-genes ( OsHSP , OsHSFC2A , and OsDJA5 ) were identified through RNA sequencing and WGCNA in rice [ 29 ]. Through the integration of GWAS, WGCNA, and differential expression analysis, four and eight important candidate genes related to root growth in B. napus were identified during the persistent and specific stages, respectively [ 30 ].…”

“…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 ].…”