title: Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs.
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.
authors.affiliation: 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.
authors.forename: Huibin
authors.initials: H
authors.lastname: Song
authors.affiliation: 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.
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhu
authors.affiliation: 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.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Changping
authors.initials: C
authors.lastname: Ma
authors.affiliation: 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.
authors.forename: Kaifeng
authors.initials: K
authors.lastname: Guan
authors.affiliation: College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
authors.forename: Xuanyan
authors.initials: X
authors.lastname: Xia
authors.affiliation: 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.
authors.forename: Fenge
authors.initials: F
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D015870:Gene Expression; D056726:Genetic Association Studies; D008297:Male; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D013081:Sperm Motility / Q000235:genetics; D013091:Spermatogenesis / Q000235:genetics*; D034421:Sus scrofa / Q000235:genetics*; D013737:Testis / Q000502:physiology*; D059467:Transcriptome
keywords: Pig; RNA-sequencing; Spermatogenesis; Testis