Title : An integrated omics analysis reveals candidate genes underlying grain filling period in Brassica napus L. under drought stress
Grain filling is an important developmental process associated with the yield and quality of rapeseed (Brassica napus L.). However, the molecular mechanisms of grain filling are rarely reported in rapeseed. Drought impedes rapeseed performance at all growth stages which is more critical during the grain-filling phases. This study aims to dissect the genetic architecture of grain filling period in rapeseed varieties in different irrigation regimes. To understand the underlying mechanism of grain filling period and identify candidate genes (CGs) for breeding drought tolerance varieties, a combined genome-wide association studies (GWAS) and RNA-seq analysis was performed using a total of 119 rapeseed accessions tested under two irrigation treatments, one a well-watered condition and the other a drought stress treatment across three years. Genotyping was performed using a total of 29,311 high-quality SNPs obtained by 60K single nucleotide polymorphisms (SNP) array. Analysis of linkage disequilibrium (LD) and population structure in the 119 accessions was carried out based on the 29K high-quality SNPs. Extensive and highly heritable variation in grain filling period was observed. A total of 80 SNPs on chromosomes A01, A03, A07, A10, C01, C02, C03, and C06 showed significant associations with the grain filling period (p < 3.06 × 10−4). Analysis of relation of the SNP positions and CGs showed that 118 CGs were found for the characters. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed in two contrasting high and low-grain yielding varieties. A total of 2,757 significantly differentially expressed genes (DEGs) were detected, of which 771 were upregulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the up-regulated genes were mainly enriched in the “response to water” (GO: 0009415), “cell wall macromolecule catabolic process” (GO: 0016998), cell wall modification” (GO: 0042545), and “peptidoglycan biosynthetic process” (GO: 0009252). Through the integration of the GWAS and the RNA-sequencing, 14 CGs were identified. Four of the identified genes; XXT2 (LOC106381598), LRX5 (LOC106379540), QUA2 (LOC106418313), and SYP52 (LOC106381501) were xylosyltransferases, extensin-like proteins, methyltransferases, and transporters. These genes may play an important role in grain filing under drought stress and can be used for further analysis of grain filling in rapeseed. Our findings provide new insights into the response mechanisms of rapeseed against drought stress and contribute to further genetic breeding programs for drought tolerance.
What will audience learn from your presentation?
- The genetic architecture information of the grain filing period revealed in this study, and the genomic regions identified for the trait-environment combination are useful in accelerating the efforts on rapid development of the stress-tolerant rapeseed germplasm through marker-assisted selection (MAS) and/or genomic selection (GS).
- Our study provides a novel genetic resource for the breeding of high-yield rapeseed cultivars resistant to drought stress.
- The marker traits associations (MTAs) reported in this population could be useful to targeted grain yield introgression of rapeseed under drought-stressed and non-stressed conditions, and for fine mapping and cloning of the underlying genes
- Our investigations are profitable for the improvement of crop varieties through transgenic engineering.