An integrated fine-mapping, re-sequencing and transcriptome analysis provides further insights and candidate genes for silique number in oilseed rape (Brassica napus L.)

BACKGROUND: Silique number is an important component of yield in oilseed rape, which is largely determined by the number of flowers. Although many QTL for silique number have been identified in oilseed rape, none of these has been fine-mapped and further cloned, largely limiting their application in genetic improvement. In our previous study, a few-silique mutant (No.7931) caused by determinate inflorescence has been mapped to three close regions on C02 chromosome by bulked segregant analysis by sequencing (BSA-seq) of two pools of F2 individuals derived from this mutant and more-silique accession No.73290. RESULTS: In the current study, the hybrid F1 between No.7931 and an indeterminate inflorescence accession No.73290 showed nearly determinate inflorescence. This supported that the determinate inflorescence of No.7931 was nearly dominant to the indeterminate inflorescence of No.73290, suggesting the dosage effect of the causal gene. In the BC3F2 near-isogenic lines with No.73290 background, the numbers of plants with determinate and indeterminate inflorescence displayed a segregating ratio of 3:1, suggesting that it should be controlled by a single dominant locus (named as SNPI.C2 thereafter). The first BSA region close to the end of C02 chromosome was validated and fine-mapped to 172 Kb region containing only 23 annotated genes. The RNA-seq of shoot apical meristem (SAM) at the initial stage of floral bud differentiation identified a total of 3196 differentially expressed genes (DEGs) between No.73290 and NIL-SNPI.C2, which were significantly enriched into 22 pathways (e.g., fermentation, glycolysis, polyamine metabolism and nitrogen-metabolism) that are highly associated with floral bud differentiation and flower number regulation. The results of fine-mapping, re-sequencing and transcriptome analysis were integrated, which identified two candidate genes that are involved in regulating meristem identity and have sequence and/or expression variation. CONCLUSIONS: These results provide further insights and candidate genes for silique number in oilseed rape, which represent a significant advancement toward the cloning of causal genes and understanding of genetic mechanism for silique number in oilseed rape.