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

Xiaodong Zhang,Yueyun Ding,Tao Wu,Pengfei Ye,Yifang Feng,Long Huang,Zongjun Yin,Ramona Natacha Pena I Subirà

doi:10.1371/journal.pone.0139514

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.

Highlights

Litter size is one of the most important economic factors in pig production and is affected by interactions between multiple genes and the environment [1, 2]
The results showed that 11 genes appeared in the two or more sets, including the CO1, glutathione peroxidase 3 (GPX3), beta-microseminoprotein (MSMB), COX3, tissue inhibitor of metalloproteinase 1 (TIMP1), cytochrome b (CYTB), steroidogenic acute regulatory protein (STAR), 3-beta hydroxysteroid dehydrogenase (HSD3B), CYP11A1, scavenger receptor class B member 1 (SCARB1), and hydroxysteroid (17-beta) dehydrogenase 2 (HSD17B2) (Fig 3)
From our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we found that the functions of the 10 most differential expression of genes (DEGs) between high and low litter size samples were mainly in the metabolic pathways, ovarian steroidogenesis, citrate cycle (TCA cycle), pyruvate metabolism, and the PPAR signaling pathway

Summary

Introduction

Litter size is one of the most important economic factors in pig production and is affected by interactions between multiple genes and the environment [1, 2]. The size of litters varies between pigs in different breeding farms. Altering litter size by conventional breeding methods can be slow, and has shown low heritability. Using marker assisted selection (MAS) can speed up genetic improvements in litter size traits [3]. As the ovary directly mediates ovulation, it has a significant impact on the fecundity of mammals, and genetic differences in the ovaries may contribute to the observed differences in litter size [4, 5].

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Results

Discussion

Conclusion