Molecular advances in QTL discovery and application in pig breeding

Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

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Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size.

The relationship between estrogen receptor (ESR) genotype and reproductive traits in a population of Yorkshire, Large White, and crossbred animals was studied. Reproductive tract and litter data were analyzed for associations with ESR genotype, parity, and breed. Forty-six Yorkshire, 31 Large White, and 70 crossbred females from the above population were mated to Hampshire boars and slaughtered at 75 d of gestation. Data collected included ovulation rate, uterine horn length, number of fetuses, fetal weight, uterine weight, number of mummies, fetal sex, fetal placement, fetal survival, and fetal space. Data were analyzed using a model that included the fixed effects of ESR genotype, breed, parity, and all significant two-way interactions. Litter data representing 212 litter records were analyzed in a model that included the fixed effects of ESR genotype of dam, parity, farrowing month, dam breed, sire breed, and all significant two-way interactions. The ESR genotype was significantly associated with the total litter weight of piglets born and total litter weight of piglets born alive. Dams with the AA genotype had significantly (P = 0.04) heavier litters at birth (14.44 +/- 0.36 kg) than dams with the BB genotype (13.43 +/- 0.47 kg). Ovulation rate was significantly (P or = 3 (19.92 +/- 0.85). Significant breed effects were observed for fetal weight, with purebred Large White animals having a greater fetal weight per horn (3,909 +/- 114 g) than purebred Yorkshire animals (3,553 +/- 92 g). Notable, but nonsignificant, trends with respect to ESR genotype were also observed for number of piglets alive at weaning and total litter weight at weaning. The ESR gene is positively associated with several previously uninvestigated reproductive traits.

Examination of the relationship between the estrogen receptor gene and reproductive traits in swine.

Previous results from a genome scan in an F2 Iberian × Meishan pig intercross showed several chromosome regions associated with litter size traits in this species. In order to identify candidate genes underlying these quantitative trait loci (QTL), we performed an ovary gene expression analysis during the sow's pregnancy. F2 sows were ranked by their estimated breeding values for prolificacy: six sows with the highest estimated breeding value (EBV) (i.e., high prolificacy) and six sows with the lowest EBV (low prolificacy) were selected. Samples were hybridized using an Affymetrix GeneChip porcine genome array. Statistical analysis with a mixed model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify genetic pathways overrepresented in this list. Among the functional groups most represented was, in first position, immune system response activation against external stimulus. The second group consisted of integrated g...

https://bioone.org/journals/Biology-of-Reproduction/volume-84/issue-2/biolreprod.110.085589/Differential-Gene-Expression-in-Ovaries-of-Pregnant-Pigs-with-High/10.1095/biolreprod.110.085589.pdf

Differential gene expression in ovaries of pregnant pigs with high and low prolificacy levels and identification of candidate genes for litter size.

Embryonic mortality during the implantation period strongly affects litter size in pigs. To analyze the differentially expressed genes (DEGs) in the endometrium during implantation and further to identify candidate genes for litter size, tissues of endometrial attachment sites and intersites were collected from nine pregnant sows on Days 13, 18, and 24 of pregnancy. Endometrium tissue was also collected from another three nonpregnant sows. Samples were hybridized to the porcine Agilent GeneChip microarray. The analysis of gene expression patterns over the implantation period revealed 858 DEGs at endometrial attachment sites. Comparisons of the gene files of attachment sites and intersites revealed 12, 51, and 89 DEGs on Days 13, 18, and 24 of pregnancy, respectively. Annotated function was used to identify overrepresented genetic processes, and several biological processes were considered as the most enriched. Genes related to vascular development, proteolysis, RNA metabolism and translation, protein modification, immune response, and hormone-related are discussed in detail. Then we combined microarray technology and linkage analysis to select powerful candidate genes for quantitative trait loci affecting pig litter size. Eighty-seven DEGs were located in quantitative trait loci related to litter size, that is, total number born and number born alive. Those candidate genes were thought to affect litter size by influencing embryonic implantation. Furthermore, single nucleotide polymorphism of VEGFA was shown to be associated with litter size in pigs. This study identified candidate genes for litter size that were related to embryonic implantation and could be a resource for target studies of genetic markers for litter size in pigs.

https://bioone.org/journals/Biology-of-Reproduction/volume-92/issue-2/biolreprod.114.123075/Differential-Gene-Expression-in-Uterine-Endometrium-During-Implantation-in-Pigs1/10.1095/biolreprod.114.123075.pdf

Differential Gene Expression in Uterine Endometrium During Implantation in Pigs

An insertion fragment in porcine FSHbeta subunit gene was cloned by PCR. Sequencing data show that the insertion is a retroposon of 292 bp sitting in intron I at the site between + 809 and +810 base. Based on these results, a PCR programme was created to genotype animal individuals in different pig breeds at FSW locus and polymorphism of FSHbeta gene was analyzed. With the combination of genotype and litter size of sows, it was demonstrated that FSHbeta locus is closely associated with major gene controlling litter size in commercial pig breeds, such as Yorkshire, Landrace, Durco. Averagely the AA sows give more 1.5 piglets than BB sows do per litter.

G Cao

Papers

FSHB subunit gene is associated with major gene controlling litter size in commercial pig breeds.