Background The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including WNT10B and DKK2 in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of Peramivir eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- BAX and BMPR1B were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (p 0.1 or p 0.05). Conclusions Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of BAX and BMPR1B gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction. Background Reproductive traits are of primary interest in livestock because they play a major role in efficiency of production. Selection for increased number of offspring has been employed in pigs with only limited success because of its low heritability and sex-limited nature [1]. Genetic characterization of litter size and its components (e.g. ovulation rate and embryo survival) will increase our understanding of the underlying physiology and could enhance genetic improvement through use of marker-assisted selection (MAS) [2]. In the past several decades, the reproductive strategy of the Chinese Taihu pigs, a breed which farrows three to five more piglets per litter than American or European pig breeds, has come under intense scrutiny [3,4]. The greater litter size at farrowing in multiparous Chinese Taihu sows is due, in part, to a greater ovulation rate, a greater embryonic survival, a lower fertilization failure rate, and a larger uterine capability [5-7]. To be able to isolate the elements controlling the element qualities of litter size, the differentially indicated (DE) genes had been characterized during conceptus change, in Meishan-Landrace conceptuses and endometrial cells in comparison to regular Landrace sows, in the porcine endometrium between non-pregnant and pregnant DNAJC15 sows, and in the Erhualian and Huge White colored placenta [8-11]. Furthermore, DE genes had been determined in porcine ovarian follicles of multiparous sows on 12 d to 14 d from the estrous routine between a type of pigs chosen for an index of ovulation price and embryo success and its arbitrarily chosen control range [2,12]. Nevertheless, the DE genes in Chinese language Taihu and Huge White colored preovulatory follicles stay unexplored. To build up a broader look at from the gene manifestation in preovulatory ovary also to identify the main element genes involved with ovulation, we utilized Affymetrix microarrays to display the genes differentially indicated in preovulatory follicles from Chinese language Taihu and Huge White colored sows simulated by hCG at 80 h after PMSG administration. Bioinformatics evaluation has exposed these DE genes had been involved in essential biological processes such as for example duplication as well as the DE genes had been after that in silico mapped to quantitative characteristic loci (QTL) areas related to duplication qualities. Real-time RT-PCR was utilized to verify the manifestation profiles of varied genes. And association analyses of two DE genes (BAX and BMPR1B gene) with litter size had been completed to display the molecular markers for litter size. This intensive study determined applicant genes, molecular markers and pathways connected with ovulation price, and gained Peramivir a further insight into the genetic basis of the prolificacy of Chinese Taihu pigs. Results Peramivir Transcriptome analysis Expression profiling experiments of Large White and Chinese Peramivir Taihu ovary follicles were conducted by a commercial Affymetrix Porcine Genechip including 24,123 probe sets, which represent 23,999 transcripts and 124 controls. The transcriptome of ovarian follicles from Chinese Taihu sows was determined, and 23,921 Peramivir probe sets were identified to have expression in the ovary follicles..