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Combining QTL and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed.

Quantitative trait loci (QTL) have been discovered in crops, where some of causal quantitative trait genes (QTGs) may not be functionally characterized even in model plant Arabidopsis. We propose an approach to delineate QTGs by coordinating expression of genes located within QTL in crops and known orthologs related with trait from Arabidopsis. Using this method, we established an acyl-lipid metabolism co-expression network in developing siliques 15 days after pollination in 71 lines of rapeseed with 21 modules, which are composed of 270 known acyl-lipid genes and 3,503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein process, seed maturation and phytohormone metabolism. Moreover, the core module closely associates with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analyzed using Arabidopsis knockout and over-expression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 over-expression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping provides new insights into the detection of QTGs.