Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Abstract

Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

Comparative analysis of ovarian transcriptomes between prolific and non‐prolific goat breeds via high‐throughput sequencing

“…Among them, cell parts and cells, binding and catalytic activity, metabolic processes, and cellular processes were predominant in each of the three main categories, respectively. These observations are consistent with previous studies regarding ovarian transcriptomes of goats (Ling et al., ; Miao et al., ; Wang et al., ; Zhao et al., ) and pigs (Zhang et al., ). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway significant enrichment analysis revealed that the DEGs participated in 331 pathways, of which 22 significantly enriched pathways were identified in the current study.…”

“…were also significantly upregulated in prolific JTGs compared to non-prolific TBGs (Table 1). These genes were also significantly upregulated in other prolific breeds of goats and pigs (Miao et al, 2016;Zhang et al, 2015). HSD3B and STAR regulate hormone metabolism pathways and follicle development (Khan, Guillemette, Sirard, & Richard, 2015;Loureiro, Ereno, Favoreto, & Barros, 2016).…”

“…The most significantly enriched pathways included the metabolic pathways, ECM–receptor interaction, phagosomes, the PPAR signalling pathway and amoebiasis. In pigs, the 10 most significant DEGs between large and small litter size samples were mainly in the metabolic pathways, ovarian steroidogenesis, citrate cycle, pyruvate metabolism and the PPAR signalling pathway (Zhang et al., ). In goats, the most significant DEGs of high‐ and low‐fecundity samples were mainly in the metabolic pathways, ECM–receptor interaction, focal adhesion and amoebiasis (Miao et al., ; Wang et al., ; Zhao et al., ).…”

“…The RNA‐Seq approach produces millions of short cDNA reads that are mapped to a reference genome to obtain a genome‐scale transcriptional map, which consists of the transcriptional structure and the expression level for each gene (Mortazavi, Williams, McCue, Schaeffer, & Wold, ). Transcriptomes of ovaries have been initially compared in some goats (Ling, Xiang, Li, Liu, & Zhang, ; Miao, Luo, & Qin, ; Wang et al., ; Zhao et al., ) and pigs (Zhang et al., ) with different prolificacy using RNA‐Seq technology, and a large number of differentially expressed genes (DEGs) have been identified, although the results are not consistent. The Jintang black goat (JTG) is an excellent local Chinese breed that has a high kidding rate (248% on average) and superior meat performance.…”

Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

“…To find the quantitative trait loci (QTL) and causal genes for these traits, several studies for linkages [11-13] and candidate genes ([14-17] have been conducted by using modern molecular information. Many of the major genes involved in the prolificacy of pig, such as ESR , FSHB , RBP4 , PRLR , MTNR1A , OPN , BMP families, and GDF9 genes have been characterized [18, 19]. Genetic studies have revealed an increasing number of associated QTLs and candidate genes involved in pig litter size [20-22].…”