Selection of candidate genes affecting litter size of Congjiang Xiang pig by transcriptome sequencing

【Objective】In order to provide theoretical basis for the breeding performance studies and breeding, gene regulatory networks and the molecular mechanism of reproduction traits on Congjiang Xiang pig were screened.【Method】Three ovary tissues were selected from the high litter size family(number of average litter size ≥ 12, stable inheri-tance) and the low litter size family(number of average litter size was 8-10, stable inheritance) at puberty, and transcriptome sequenced(RNA-Seq) by Illumina HiSeq^TM 2000, and GO functional enrichment analysis and KEGG pathway enrichment analysis were performed on the differentially expressed genes(DEGs) to find the gene regulation networks related to litter size of Congjiang Xiang pigs.【Result】More than 50 million Clean reads were obtained from sequencing results of ovaries from high litter size family and low litter size family, and more than 96.00% of the Clean reads could be mapped with the reference genome of pig. With |log₂FC|≥ 1.0 and P<0.01 as the conditions, 212 DEGs in ovary between high yield family and low yield family were found, and among which 138 were up-regulated genes, 74 down-regulated genes. Ten randomly selected DEGs was verified by real-time fluorescence quantitative PCR, the expression levels of OSAP, MSMB, FGFBP1, RLN, HAS1 and PLBD1 genes in the ovary of high litter size family were significantly higher than those in the low litter size family(P<0.05, the same below). However, the expression levels of EDG7, PTX3, BSP1 and MRO genes were in the ovary of low litter size family were significantly higher than those in the high litter size family. The results showed that the sequencing results were consistent with the results of qRT-PCR. A total of 212 DEGs were enriched in 48 GO functional items, including molecular function, biological process and cellular component. Through KEGG pathway analysis, a total of 70 DEGs were annotated to specific metabolic pathways. Significant enrichment pathways included steroid biosynthesis, calcium signaling pathway, ovarian steroidogenesis, adrenergic signaling in cardiomyocytes and hypertrophic cardiomyopath(HCM). On the ovarian steroidogenesis pathway, seven genes including SCARB1, STAR, COX2, CYP11A, CYP17A, 17P17A and CYP19A1 genes were found to be closely related to reproductive performance of Congjiang Xiang pigs.【Conclusion】STAR, CYP11A, CYP17, 17βHSD and CYP19A1 genes in the ovarian steroidogenesis pathway are closely related to estrus and ovulation in pigs. These genes which are up-regulated during estrus can promote follicle development and maturation, steroid hormone expression, enhance high reproduction of Congjiang Xiang pigs by increasing the number of ovulation. Thus these genes can be used as candidate genes for breeding traits in Congjiang Xiang pigs.