Litter uniformity, which is usually represented by within-litter weight coefficient of variation at birth (CVB), could influence litter performance of sows and the profitability of pig enterprises. The objective of this study was to characterize CVB and its effect on other reproductive traits in Large White sows. Genetic parameters and genetic correlation of the reproductive traits, including CVB, within-litter weight coefficient of variation at three weeks (CVT), total number born (TNB), number born alive (NBA), number born dead (NBD), gestation length (GL), piglet mortality at birth (M₀), piglet mortality at three weeks (M₃), total litter weight at birth (TLW0), and total litter weight at three weeks (TLW₃) were estimated for 2 032 Large White litters. The effects of parity and classified litter size on CVB, CVT, TNB, NBA, NBD, GL, M₀, M₃, TLW₀, and TLW₃ were also estimated. The heritabilities of these reproductive traits ranged from 0.06 to 0.17, with the lowest heritability for CVB and the highest heritability for TLW0. Phenotypic and genetic correlations between these reproductive traits were low to highly positive and negative (ranging from −0.03 to 0.93, and −0.53 to 0.93, respectively). The genetic correlations between TNB and CVB, and between M₀ and CVB were 0.32 and 0.29, respectively. In addition, CVB was significantly influenced by parity and litter size class (P<0.05). All the results suggest that piglet uniformity should be maintained in pig production practices and pig breeding programs.

   Ear size exhibits remarkable diversity in pig breeds. LEM domain-containing 3 (LEMD3) on chromosome 5 is considered as an important candidate for porcine ear size. This is the first study on cloning and characterization of LEMD3 cDNA. The complete cDNA contains 4 843 bp, including a 2 736-bp open reading frame (ORF), a 37-bp 5´-untranslated region (UTR) and a 2 070-bp 3´-UTR. The complete LEMD3 gene is 126 241-bp and contains 13 exons and 12 introns. The ORF encodes a deduced LEMD3 protein of 911 amino acids, which shares 82–94% nucleic acid and 51–96% amino acid identity with other species. A phylogenetic tree constructed based on the amino acid sequences revealed that the porcine LEMD3 protein was closely related with cattle LEMD3. Resequencing of the ORF and promoter of LEMD3 from Minzhu pig and Large White revealed three single nucleotide polymorphisms (SNPs): L964C>A in the complete coding region, L4625A>G in the 3´ UTR, and L-394T>C in the promoter region. Genome-wide association study (GWAS) revealed that all of SNPs were shown significant association with ear size in Large White×Minzhu pig intercross population. With conditional GWAS, –log₁₀(P-value) decreased by more than 80% when each of three SNPs was included as a fixed effect. These results suggested direct involvement of LEMD3 or close linkage to the causative mutation for ear size. The findings of this study might form the basis for understanding the genetic mechanism of ear size variation in pigs and provide potential molecular markers for screening ear size diversity in pig breeds.

Rib eye muscle area (REMA) is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Illumina PorcineSNP60 BeadChip containing 62 163 single nucleotide polymorphisms (SNPs) was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA (at the 5th–6th, 10th–11th and the last ribs) was measured after slaughtered at the age of (240±7) d for each animal. Association tests between REMA trait and SNPs were performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes (NOS2, NLK) in block 1 (266 kb), one gene (TMIGD1) in block 2 (348 kb), and one gene (MAP2K4) in block 3 (453 kb). A functional analysis indicated that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.

Although quantitative trait loci (QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes (SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait (number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60K chip. Performing a genome-wide association study (GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor (NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin (VRTN), prospero homeobox 2 (PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog (FOS), and transforming growth factor beta 3 (TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.

The erythropoietin receptor (EPOR) has shown to play an important role in fetal survival by promoting the maturation of red blood cells in many studies of uterine capacity and litter size in swine. In this study, we screened the porcine EPOR gene for mutations and identified five single nucleotide polymorphisms (SNPs): g.705G>T in intron 1, g.2 373C>T in intron 4, and g.2 882C>T, g.3 035A>G, and g.3 132A>T in intron 6. We then genotyped 247 Beijing Black (BB) sows and compared the polymorphism data with the litter sizes of 1 375 parities among the sows. At first parity, there was no association of g.2 882C>T and g.3 132A>T with litter sizes. However, the CT sows in g.2 882C>T had 2.13 higher total number born (TNB) (PT had the highest litter size when compared to the two homozygotes for the later parities (PG SNP,for the later parities, the TNB of the sows with the GG genotype was 3.81 higher (PT SNP was associated with a greater litter size at both the first parity (PT SNP was significantly more common in the more prolific Chinese breeds. These results indicated that the EPOR could be an important candidate gene for litter size and g.705G>T can serve as a useful genetic marker for improving litter size in both first and later parities in swine.