Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs

Huibin Song; Lihua Zhu; Yan Li; Changping Ma; Kaifeng Guan; Xuanyan Xia; Fenge Li

doi:10.1016/j.gene.2015.07.057

Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs

Gene. 2015 Dec 1;573(2):303-9. doi: 10.1016/j.gene.2015.07.057. Epub 2015 Jul 17.

Authors

Huibin Song¹, Lihua Zhu¹, Yan Li¹, Changping Ma¹, Kaifeng Guan¹, Xuanyan Xia², Fenge Li³

Affiliations

¹ Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.
² College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
³ Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: lifener@mail.hzau.edu.cn.

PMID: 26192463
DOI: 10.1016/j.gene.2015.07.057

Abstract

Mammalian testis development and spermatogenesis play critical roles in male fertility. However, little genomic information is available for porcine sexually mature and immature testis. Presently, we detected approximately 76% of previously annotated genes that were expressed in the porcine testes by RNA sequencing. Taking an FDR of 0.001 and a |log2Ratio| of 1 as cutoffs, 10,095 genes were significantly differentially expressed between two stages, including 242 spermatogenesis-associated genes. These genes were significantly enriched to GO BP terms concerning spermatogenesis, male gamete generation, developmental process and sexual reproduction; to the KEEG pathways, including focal adhesion, ECM-receptor interaction, and phagosome. 186 extended transcripts, 1273 alternative splicing events and 2846 SNPs were detected in spermatogenesis-associated DEGs. Two PIWIL4 SNPs were successfully validated and suggested to be the potential molecular markers for semen quality. This study will help identify the specific genes and isoforms that are active in porcine spermatogenesis and sexual maturity.

Keywords: Pig; RNA-sequencing; Spermatogenesis; Testis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing
Animals
Base Sequence
Gene Expression
Genetic Association Studies
Male
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Sequence Analysis, RNA
Sperm Motility / genetics
Spermatogenesis / genetics*
Sus scrofa / genetics*
Testis / physiology*
Transcriptome