Articles | Volume 59, issue 2
Arch. Anim. Breed., 59, 275–283, 2016
https://doi.org/10.5194/aab-59-275-2016
Arch. Anim. Breed., 59, 275–283, 2016
https://doi.org/10.5194/aab-59-275-2016

Original study 15 Jun 2016

Original study | 15 Jun 2016

Detection of one large insertion/deletion (indel) and two novel SNPs within the SPEF2 gene and their associations with male piglet reproduction traits

Rui Chen1,2, Shuai Yu2, Fa Ren2, Xiao Yan Lv3, and Chuan Ying Pan2 Rui Chen et al.
  • 1Innovation Experimental College, Northwest A&F University, Yangling 712100, China
  • 2College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
  • 3National Swine Foundation Seed Farm of Ankang Yangchen Modern Agriculture Group Co. Ltd, Ankang 725000, China

Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.

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Short summary
Allele "D" (deletion) within the insertion/deletion of SPEF2 gene was dominant in male Large White and Landrace pigs from China. In addition, two novel single-nucleotide polymorphisms of this gene were first identified in pigs. NC_010458:g.19886C > G was significantly associated with testis long circumference (P < 0.05). These findings could not only extend the spectrum of genetic variations of pig SPEF2 gene but also contribute to implementing MAS in pigs.