Meta-analysis of QTLs controlling seed quality traits based on QTL alignment in Brassica napus

A growing demand in oilseed use for food, feed and fuel has caused added pressure on rapeseed breeders to improve higher-quality cultivars. To gain a better understanding of the genetics of oil, fatty acids, sterols, protein and amino acids contents in Brassica napus, 2138 QTLs in 16 populations were collected from 22 studies published since 2000. The physical position of 1567 initial QTLs could be found in the physical map of Darmor-bzh that finally revealed 294 QTL overlapping regions from different populations potentially associated with seed quality traits, distributed unequally in most of the chromosomes. We detected enrichment regions with more than 10 initial QTLs in some traits, which could provide clues in discovering varied or protected areas. Additionally, 111 overlapping QTLs regions were found, controlling at least two traits. These regions with broad pleiotropic effects or tight linkages might have merit in improving B. napus in targeting more than one desirable trait simultaneously. Furthermore, to validate our findings, candidate genes were subjected to three types of gene set analyses: KEGG pathway and interaction networks for Arabidopsis thaliana genes, and expression enrichment analysis for candidate genes of B. napus. The results indicated key known genes, novel genes, and genes with unknown functions in the overlapping regions that were involved in different biological processes of quality traits, such as highly expressed genes in seed, including BnaA08g13680D, BnaA08g13750D, BnaA08g13730D, BnaA08g14030D, BnaA08g14060D, BnaA08g12340D and BnaC05g42910D, which were observed in overlapping QTLs of multiple traits. Further validation also depicted that 107 overlapping QTLs were co-located with 366 SNP peak positions reported based on the genome-wide association studies (GWAS) for quality traits in rapeseed. Our results will serve as a resource for future researches in functional gene analysis, genetic engineering and breeding programs.