Genetic effect and combined genotype effect of ESR, FSHβ, CTNNAL1 and miR-27a loci on litter size in a Large White population

Effect of SNPs on Litter Size in Swine

Although sows do not directly enter the market, they play an important role in piglet breeding on farms. They consume large amounts of feed, resulting in a significant environmental burden. Pig farms can increase their income and reduce environmental pollution by increasing the litter size (LS) of swine. PCR-RFLP/SSCP and GWAS are common methods to evaluate single-nucleotide polymorphisms (SNPs) in candidate genes. We conducted a systematic meta-analysis of the effect of SNPs on pig LS. We collected and analysed data published over the past 30 years using traditional and network meta-analyses. Trial sequential analysis (TSA) was used to analyse population data. Gene set enrichment analysis and protein-protein interaction network analysis were used to analyse the GWAS dataset. The results showed that the candidate genes were positively correlated with LS, and defects in PCR-RFLP/SSCP affected the reliability of candidate gene results. However, the genotypes with high and low LSs did not have a significant advantage. Current breeding and management practices for sows should consider increasing the LS while reducing lactation length and minimizing the sows' non-pregnancy period as much as possible.

Genetic polymorphisms in ESR and FSHβ genes and their association with litter traits in Large White pigs

The estrogen receptor (ESR) gene and follicle-stimulating hormone β (FSHβ) gene are responsible for litter traits. The present study aimed to verify the polymorphisms of ESR and FSHβ and assess their effects on the litter traits in 201 Large White pigs. Four SNPs (g.C669T, g.A1296G, g.C1665T and g.A1755G) were found in ESR. The TT genotype at g.C1665T locus and AA genotype at g.A1755G locus could significantly increase the total litter size of the first litter of American Large White pigs (p < 0.05). Eight SNPs were found in exon 3 of FSHβ. The AA genotype at g.A511G locus, AA and AG genotypes at g.A617G locus, CC and CT genotypes at g.C630T locus, CT and TT genotypes at g.C652T locus, CT and TT genotypes at g.C735T locus, AA and AG genotypes at g.A746G, AA and AG genotypes at g.A921G and CT genotype at g.C678T could significantly increase the litter size of different strains of Large White pigs (p < 0.05). Our study revealed that the genetic variations of ESR and FSHβ were closely related to the litter trait of Large White pigs. Therefore, ESR and FSHβ genes could be used as molecular markers for the genetic selection of Large White pigs.

Effect of NLR family pyrin domain containing 9 gene polymorphism on litter size in large white pigs

NLR family pyrin domain containing 9 (NLRP9) is a mammalian reproduction-related gene. In this study, we researched the associations between polymorphisms located in the coding sequence (CDS) of the NLRP9 gene, and both the total number of piglets born per litter (TNB) and the number of piglets born alive per litter (NBA) in Canada Large White pigs (CLW). We detected a single nucleotide polymorphism (SNP) within exon 3 (g.10910C > T). The allele frequencies at the NLRP9 locus were 0.474 for the C allele and 0.526 for the T allele. Three genotypes, CC, CT, and TT, occurred with frequencies of 0.216, 0.515, and 0.269, respectively. Sows with the CC genotype had the largest TNB and NBA, sows with TT had the smallest, and those with CT were in-between. This difference was statistically significant (p < 0.05). Furthermore, CC females grew faster than CT or TT females, and there was a significant relationship between NLRP9 polymorphism and the average daily gain (p < 0.05). Here, we provide the first evidence for a novel SNP in NLRP9 associated with litter size in CLW sows, which could be used as a genetic marker to improve litter size in pig breeding and production.

Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits

Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

miR-27a-3p targets NR5A2 to regulate CYP19A1 expression and 17-β estradiol synthesis in ovine granulosa cells

Although 17-β estradiol (E2) synthesis is important in regulating female fertility, we know little regarding the molecular mechanism of miRNA-regulated ovine E2 synthesis. Here, our experiments with granulosa cells (GCs) from Hu sheep revealed miR-27a-3p involvement in E2 synthesis and its association with ovine litter size. First, we showed that miR-27a-3p of sheep and other mammals share a high nucleotide identity. Next, gain- and loss-of-function assays indicated that miR-27a-3p inhibits CYP19A1 expression and E2 synthesis in GCs. Moreover, we demonstrated that NR5A2 is a direct target of miR-27a-3p. Ovine miR-27a-3p suppresses E2 synthesis via the NR5A2 and CYP19A1 axes. We also identified four single nucleotide polymorphisms in the ovine miR-27a gene, and g.-13 G>A and g 0.24 T > G were significantly associated with the first and the second parity litter size, respectively (P < 0.05). In summary, our findings reveal that miR-27a-3p is a novel regulator of E2 synthesis and may predict litter size of Hu sheep, providing insight into mechanisms underlying granulosa cell function and female fertility.

Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts

BACKGROUND

Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits.

RESULTS

Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0.08 ± 0.06, respectively. Genetic correlations within VS traits were very high for both breeds, with the lowest of 0.67 ± 0.29 for VH and VW for Landrace. Genome-wide association studies (GWAS) for Landrace, reveled genomic region associated with VS traits on Sus scrofa chromosome (SSC) 2 (154-157 Mb), 7 (107-110 Mb), 8 (4-6 Mb), and 10 (8-19 Mb). For Yorkshire, genomic regions on SSC 1 (87-91 and 282-287 Mb) and 5 (67 Mb) were identified. All regions explained at least 3.4% of the genetic variance. Accuracies of genomic prediction were moderate in Landrace, ranging from 0.30 (VH) to 0.61 (VA), and lower for Yorkshire, with 0.07 (VW) to 0.11 (VH). Between-breed and multi-breed genomic prediction accuracies were low.

CONCLUSIONS

Our findings suggest that VS traits are heritable in Landrace and Yorkshire gilts. Genomic analyses show that major QTL control these traits, and they differ between breed. Genomic information can be used to increase genetic gains for these traits in gilts. Additional research must be done to validate the GWAS and genomic prediction results reported in our study.

Variants in BMP7 and BMP15 3'-UTRs Associated with Reproductive Traits in a Large White Pig Population

Bone morphogenetic protein 7 (BMP7) and BMP15, which encode members of the BMP family, have been identified by whole-genome resequencing as breeding-related genes that overlap with a known quantitative trait locus for reproductive traits. In this study, we investigated the effects of variants at the BMP7 and BMP15 gene loci on sow reproductive traits. We isolated 669 and 1213 bp sequences of the 3’-untranslated region (3’-UTR) of the porcine BMP7 and BMP15 genes, respectively, and detected several RNA regulatory elements, such as miRNA response elements and AU-rich elements. Pooled DNA sequencing identified two novel point mutations (viz., BMP7 c.1569A>G and BMP15 c.2366G>A) in the 3’-UTR. Association analysis showed that the c.1569A>G polymorphism was associated with the litter weight trait in a Large White pig population. Furthermore, analysis of the combined genetic effects revealed that AA/GA and AG/GG were the favorable combined genotypes for the total number of piglets born (TNB) and the total number of piglets born alive (NBA), whereas. Together, our findings confirm that BMP7 and BMP15 are candidate genes for porcine reproductive performance.