A Missense p.Q>R234 Mutation in the Osteopontin Gene Is Associated With the Prolificacy of Iraqi Awassi Ewes

One of the most valuable traits in production and breeding is a sheep's prolificacy which is influenced by several genes, one of which is the osteopontin (OPN) gene. Thus, this study aimed to determine the effect of genetic variation within the OPN gene on Awassi ewe prolificacy. Genomic DNA was extracted from 123 single-progeny ewes and 109 twin ewes. Polymerase chain reaction (PCR) was used to amplify 4 sequence fragments (289, 275, 338, and 372 bp), representing exons 4, 5, 6, and 7 of the OPN gene. A 372 bp amplicon was identified with 3 different genotypes: TT, TC, and CC. Sequence analysis revealed a novel mutation in TC genotypes p.Q>R234. Statistical analysis revealed that the single nucleotide polymorphism (SNP) p.Q>R234 was associated with prolificacy. Ewes carrying the p.Q>R234 SNP had significantly (P ⩽ .01) lower litter sizes, twinning rates, and lambing rates, and more days to lambing than those with the TC and TT genotypes. The p.Q>R234 SNP was confirmed to be responsible for lower litter size through logistic regression analysis. From these results, we can conclude that the missense variant p.Q>R234 adversely affects the traits of interest and shows that the p.Q>R234 SNP negatively influences the prolificacy of Awassi sheep. Based on this study, it is evident that ewes in this population carrying the p.Q>R234 SNP have a lower litter size and are less prolific.

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.

Polymorphism of OPN and AREG Genes in Relation to Transcript Expression of a Panel of 12 Genes Controlling Reproduction Processes and Litter Size in Pigs

The aim of this study was to define the transcript expression of 12 genes, identify new polymorphisms in selected 2 genes and to estimate the association between the level of expression, gene polymorphism and litter size in sows. Two groups of sows were selected: 71 crossbred sows and 328 purebred sows. For transcript analysis endometrial tissue samples were collected, while blood was sampled for the purpose of DNA polymorphism analysis. For all animals data on litter size and weaned piglets were obtained. Transcript analysis of 12 genes was performed in the uterine endometrium of sows in the luteal and follicular phases. Eight out of 12 genes showed higher mRNA expression levels during the luteal phase (AREG, FABP3, IL1A, ITGAV, ITGB3, NMB, OPN, RBP4). In turn, higher expression levels in the follicular phase were observed for 4 genes (IL1B, PPARG, S100A8, SELL). Analysis of six new polymorphic sites within the OPN and AREG genes revealed the highest heterozygosity for OPNe6_Knoll, OPNp3_617 and AREGe2_317 polymorphisms and the lowest heterozygosity in the AREGe3_561 locus. Association analyses concerning transcript expression levels of the 12 genes and the OPN and AREG genotypes in the two groups of sows showed a significant relationship between the IL1A, ITGB3 transcript expression and the OPNe7_603 genotype also between OPNp3_617 genotype and ITGB3 transcript expression. With regard to the litter size and the number of weaned piglets a significant relation with the OPNp3_617, OPNe6_462 and AREGe2_317 genotypes was observed only in the purebred sows. Transcript expression of the genes encoding osteopontin and amphiregulin in the uterus of the sows affect reproductive traits by preparing the uterus for embryo reception.

Association of IL-4 and IL-4R Polymorphisms with Litter Size Traits in Pigs

Simple Summary

The IL-4 and IL-4R cytokine genes are responsible for immune response in the reproductive system and are related to embryonic implantation and fetal survival during pregnancy in females. However, to date, their effects on litter size traits in pigs have been not elucidated. Therefore, the present study was conducted to verify the porcine IL-4 and IL-4R polymorphisms and assess how they affect litter size traits in commercial pigs. The findings suggested that the porcine IL-4 g.134993898T > C and IL-4R c.1577A > T polymorphisms were associated with the litter size traits. Therefore, the porcine IL-4 and IL-4R genes may be potentially effective genetic markers to improve the litter size traits in pigs.

Abstract

The interleukin-4 (IL-4) and interleukin-4 receptor (IL-4R) are cytokines that are involved in the immune and reproductive systems. This study aimed to verify the polymorphisms in the porcine IL-4 and IL-4R genes and to assess their effects on litter size traits in commercial pigs. Single nucleotide polymorphisms (SNPs) in the porcine IL-4 and IL-4R genes were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. A non-coding SNP of IL-4 g.134993898T > C and a non-synonymous SNP of IL-4R c.1577A > T (amino acid change at position 526, Q526L) were found to be segregating in Landrace sows. The IL-4 g.134993898T > C polymorphism was significantly associated with the number of piglets weaned alive (NWA) trait. The IL-4R c.1577A > T polymorphism was significantly associated with the number born alive (NBA) and NWA traits. Moreover, the accumulation of favorable alleles of these two SNP markers revealed significant associations with the NBA, NWA, and mean weight of piglets at weaning (MWW) traits. These findings indicate that the porcine IL-4 and IL-4R genes may contribute to the reproductive traits of pigs and could be used as candidate genes to improve litter size traits in the pig breeding industry.

Polymorphism of candidate genes associated with reproductive performance in crossbred pigs

This investigation was done to analyze the polymorphism of 5 SNPs in candidate genes associated with reproductive performance in crossbred pig population by PCR-RFLP. The results revealed that out of 5 SNPs genotyped, 2 were polymorphic and 3 were monomorphic. Genotypic frequency of crossbred pigs were CC (100%) for ESR1; GG (21%), GT 65%) and TT (14%) for Prei3; CC (100%) for FSHβ; AA (100%) for OPN and CC (21%), CT (63%) and TT (16%) for CDK20 SNPs, respectively. Allelic frequencies for these SNPs {ESR1 (c.1227C>T), Prei3 (T802G), FSHβ (c.930A>G), OPN (c.425G>A) and CDK20 (T96C)} were 1.00 (C), 0.53 and 0.47 (G/T), 1.00 (C), 1.00 (A) and 0.52 and 0.48 (C/T), respectively. The least squares analysis revealed that both polymorphic SNPs had non-significant effect on litter traits. The values of PIC, heterozygosity and allelic diversity indicated that crossbred population under investigation was of intermediate diversity for both polymorphic SNP loci.

The Use of Vagina⁻Cervix Length Measurement in Evaluation of Future Reproductive Performance of Sows: A Preliminary Study under Commercial Conditions

The length of the distal part of the internal reproductive tract seems to be related to the length and capacity of uterine horns, which is the most important anatomical property influencing litter size in sows. The aim of this study was to evaluate variation in vagina-cervix length (VCL) in gilts and differences in reproductive performance of sows according to VCL. The study was performed in a commercial farm using 221 gilts introduced into the breeding herd. Females were divided into three groups: (S) short (26.0 ± 2.0 cm, n = 36), (M) medium (31.3 ± 1.46 cm; n = 121), and (L) long VCL (36.0 ± 1.4 cm; n = 42) (p < 0.01). Mean live weight of gilts did not differ significantly among groups. Mean first litter size significantly varied between groups S (10.47 ± 3.01) and L (11.98 ± 2.32) (p = 0.0075) and M (10.67 ± 2.98) and L (p = 0.0054), while there was no significant difference between group S and M. Significant advantage (p = 0.023) was noted in the number of litters obtained from sows in groups L (4.69 ± 3.14), M (3.67 ± 2.71), and S (3.36 ± 2.40), and thus in total life production of sows (p = 0.0054), i.e., the number of piglets born alive. To conclude, the differences in vagina-cervix length in gilts during the first service was associated with significant variability in litter size during the first reproductive cycle, giving an advantage to females with longer VCL. Gilts with longer VCL were culled later and gave significantly more litters. Consequently, their lifetime piglet production was greater than gilts with shorter VCL.

Association of single-nucleotide polymorphisms in NAT9 and MAP3K3 genes with litter size traits in Berkshire pigs

Litter size is an economically important trait in the pig industry. We aimed to identify genetic markers associated with litter size, which can be used in breeding programs for improving reproductive traits. Single-nucleotide polymorphisms (SNPs) of Berkshire pigs in the N-acetyltransferase 9 (NAT9) and Mitogen-activated protein kinase kinase kinase 3 (MAP3K3) genes were from RNA sequencing results, and already exist in the databank (NCBI), and were confirmed by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). A total of 272 Berkshire sows were used to examine the genotype, and their association with litter size traits was analyzed. The NAT9 SNP was located in chromosome 12 exon 640 mRNA (A > G) and the MAP3K3 SNP was located in chromosome 12 intron 11 (80, C > T). Association analysis indicated that the GG genotype of NAT9 and the CT genotype of MAP3K3 had the highest values for litter size traits. The GG genotype expressed higher levels of NAT9 mRNA in the endometrium than the other genotypes did, and a positive correlation was found between litter size traits and NAT9, but not MAP3K3 expression level. These results indicate that the NAT9 and MAP3K3 can be used as candidate genes applicable in breeding program for the improvement of litter size traits in Berkshire pigs.

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. 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.