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

Abstract

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.

Genetic control of complex traits, with a focus on reproduction in pigs

“…Some of these factors have roles in sperm capacitation and fertilization (Dyck et al, ), including spermadhesins, which modulate sperm capacitation, promote sperm‐egg fusion (Caballero et al, ), and recruit immune cells (Rodríguez‐Martínez, Kvist, Ernerudh, Sanz, & Calvete, ). Functional mutations were reported for specific characteristics of semen quality (Chen, Yu, Ren, Lv, & Pan, ), and SNPs were associated with sperm motility in genome‐wide‐association studies (Diniz et al, ). The identification of markers for semen traits, such as motility, is also promising (Lin, Ponsuksili et al, ; Lin, Tholen et al, ), especially if applied to boar selection before entering the production phase.…”

A novel synonymous SNP (A47A) of the &lt;i&gt;TMEM95&lt;/i&gt; gene is significantly associated with the reproductive traits related to testis in male piglets

“…Several computational analyses have also indicated that synonymous mutations impact mRNA stability (Chamary et al, 2005;Quax et al, 2015;Lorenz et al, 2011). Synonymous mutations affected protein folding and function (Parmley et al, 2007;Gartner et al, 2013).…”

Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds

“…The sequence was contrasted and analyzed with BioEdit Software (UK) using the website (www.Msrcall.com) to calculate and analyze the genetic data for Hardy-Weinberg equilibrium (HWE), homozygosity (Ho), heterozygosity (He), effective allele numbers (Ne), and polymorphism information content (PIC; Chen et al, 2016). The chi-square test between varieties and ANOVA in varieties was conducted using SPSS software (version 18.0; International Business Machines, US) The results were subjected to statistical testing (P < 0.05; Pan et al, 2013;Zhang et al, 2016).…”