Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel

Enhancement of selectivity, 25-hydroxyvitamin D3 level, alkaline phosphatase activity and reproductive performance in gilts and primiparous sows using 14-epimer of 25-hydroxyvitamin D3

Selecting breed-worthy gilts as sow replacements is essential for continuity of pig production cycle. Though vitamin D3 (VD3) is known to enhance reproductive performance of multiparous sows, there is still a knowledge gap on its impact in developing gilts and primiparous sows. This study was aimed to quantify plasma 25-hydroxyvitamin D3 (25(OH)D3), serum alkaline phosphatase (ALP), and examine the reproductive performance of primiparous sows fed diets supplemented with regular VD3, and its 25(OH)D3 epimers. The study sample comprised 10-week-old replacement gilts (50 % Landrace x 50 % Yorkshire, N = 180) assigned in a randomized complete block design to three treatments [2,000 IU/kg of VD3 (T1), 25 µg/kg of 14‑epi-25(OH)D3, half dose (T2), and 50 µg/kg of 25(OH)D3 (T3)] equilibrated to 2,000 IU/kg in base diets. Selections occurred at 22, 27 and 35 weeks of age, respectively. Plasma 25(OH)D3, serum alkaline phosphatase (ALP), bone structure and reproductive performance were analyzed. Dietary treatments influenced carpus (P = 0.023), fore view stance (P = 0.017), infantile vulva (P = 0.014), inverted (P = 0.048), and prominent teat (P < 0.001). Post-partum 25(OH)D3 concentration and ALP activity were elevated by day 25 (P < 0.001). Treatment diets also influenced total born (P < 0.001), born alive (P = 0.048), and still born (P = 0.049). Two factors affect circulating 25(OH)D3 and ALP activity: physiological changes in sows during lactation, and dietary 25(OH)D3 intake. 14‑epi-25(OH)D3 is a potent metabolite for improving maturation of reproductive organs in developing gilts. It also reduces still birth in primiparous sows.

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs

The teat number is a pivotal reproductive trait that significantly influences the survival rate of piglets. A meta-analysis is a robust instrument, enhancing the universality of research findings and improving statistical power by increasing the sample size. This study aimed to identify universal candidate genes associated with teat number traits using a genome-wide association study (GWAS) meta-analysis with three breeds. We identified 21 chromosome threshold significant single-nucleotide polymorphisms (SNPs) associated with five teat number traits in single-breed and cross-breed meta-GWAS analyses. Using a co-localization analysis of expression quantitative trait loci and GWAS loci, we detected four unique genes that were co-localized with cross-breed GWAS loci associated with teat number traits. Through a meta-analysis and integrative analysis, we identified more reliable candidate genes associated with multiple-breed teat number traits. Our research provides new information for exploring the genetic mechanism affecting pig teat number for breeding selection and improvement.

Lost pigs of Angola: Whole genome sequencing reveals unique regions of selection with emphasis on metabolism and feed efficiency

Angola, in the western coast of Africa, has been through dramatic social events that have led to the near-disappearance of native swine populations, and the recent introduction of European exotic breeds has also contributed to the erosion of this native swine repertoire. In an effort to investigate the genetic basis of native pigs in Angola (ANG) we have generated whole genomes from animals of a remote local pig population in Huambo province, which we have compared with 78 genomes of European and Asian pig breeds as well as European and Asian wild boars that are currently in public domain. Analyses of population structure showed that ANG pigs grouped within the European cluster and were clearly separated from Asian pig breeds. Pairwise F_ST ranged from 0.14 to 0.26, ANG pigs display lower levels of genetic differentiation towards European breeds. Finally, we have identified candidate regions for selection using a complementary approach based on various methods. All results suggest that selection towards feed efficiency and metabolism has occurred. Moreover, all analysis identified CDKAL1 gene, which is related with insulin and cholesterol metabolism, as a candidate gene overlapping signatures of selection unique to ANG pigs. This study presents the first assessment of the genetic relationship between ANG pigs and other world breeds and uncovers selection signatures that may indicate adaptation features unique to this important genetic resource.

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (FROH) and the Spearman coefficient between FROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to FROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.