Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Single-Step Genome Wide Association Study Identifies QTL Signals for Untrimmed and Trimmed Thigh Weight in Italian Crossbred Pigs for Dry-Cured Ham Production

Simple Summary

Along with the traditional traits, swine breeding programs for Italian dry-cured ham production have recently aimed to include novel phenotypes. The identification of the genomic regions underlying such new traits helps to untangle their genetic architecture and may provide useful information to be integrated in genetic selection. With this aim, we estimated genetic parameters and conducted a single step genome wide association studies (GWAS) on untrimmed and trimmed thigh weight considering two pig crossbred lines approved for Italian Protected Designation of Origin ham production. Quantitative trait loci (QTLs) were characterized based on the variance of 10-SNP sliding windows genomic estimated breeding values. In particular, we identified interesting QTL signals on several chromosomes, notably on chromosome 4, 6, 7 and 15. A high heritability and genetic correlation were observed for the two traits under investigation and although independent studies including other pig populations are required to disentangle the possible effects of specific linkage disequilibrium in our population, our findings suggest that such QTL could be investigated in future pig breeding programs to improve the reliability of genomic estimated breeding values for the dry-cured ham production.

Abstract

Protected Designation of Origin (PDO) dry-cured ham is the most important product in the Italian pig breeding industry, mainly oriented to produce heavy pig carcasses to obtain hams of the right weight and maturity. Recently, along with the traditional traits swine breeding programs have aimed to include novel carcass traits. The identification at the genome level of quantitative trait loci (QTLs) affecting such new traits helps to reveal their genetic determinism and may provide information to be integrated in prediction models in order to improve prediction accuracy as well as to identify candidate genes underlying such traits. This study aimed to estimate genetic parameters and perform a single step genome wide association studies (ssGWAS) on novel carcass traits such as untrimmed (UTW) and trimmed thigh weight (TTW) in two pig crossbred lines approved for the ham production of the Italian PDO. With this purpose, phenotypes were collected from ~1800 animals and 240 pigs were genotyped with Illumina PorcineSNP60 Beadchip. The single-step genomic BLUP procedure was used for the heritability estimation and to implement the ssGWAS. QTL were characterized based on the variance of 10-SNP sliding window genomic estimated breeding values. Moderate heritabilities were detected and QTL signals were identified on chromosome 1, 4, 6, 7, 11 and 15 for both traits. As expected, the genetic correlation among the two traits was very high (~0.99). The QTL regions encompassed a total of 249 unique candidate genes, some of which were already reported in association with growth, carcass or ham weight traits in pigs. Although independent studies are required to further verify our findings and disentangle the possible effects of specific linkage disequilibrium in our population, our results support the potential use of such new QTL information in future breeding programs to improve the reliability of genomic prediction.

A robust linkage map of the porcine autosomes based on gene-associated SNPs

BACKGROUND

Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences.

RESULTS

Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations.

CONCLUSION

The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.

Gene expression profiling, chromosome assignment and mutational analysis of the porcine Golgi-resident UDP-N-acetylglucosamine transporter SLC35A3

SLC35A3 encodes a Golgi-resident UDP-N-acetylglucosamine transporter. Here, the porcine SLC35A3 gene was assigned to Sus scrofa chromosome 4 (SSC4) by a combination of radiation hybrid and linkage analysis. Expression profiling using real time RT-PCR showed ubiquitous but variable transcription of SLC35A3 in a selection of tissues. The deduced 325 amino acid sequence revealed a hydrophobic protein with 10 predicted transmembrane helices and the N- and C-terminal tails facing the cytosolic side of the Golgi apparatus. In addition, mutated versions of the UDP-GlcNAc transporter were analyzed in a yeast complementation assay, which allowed us to identify important domains and amino acid residues. Thus, the N-terminal tail was inessential for activity, whereas removal of the first transmembrane domain inhibited yeast complementation. The hydrophilic C-terminus was dispensable while mutant proteins either fully or partially deprived of the last membrane-spanning helix were functionally impaired. The third luminal loop showed modest sequence conservation and appeared structurally flexible as certain deletions were acceptable. In contrast, the fourth luminal loop was more sensitive to changes since the competence of the mutant protein was lowered by mutations. Substitutions of glycines 190, 215 and 254, which are invariant positions in the SLC35A subfamilies affected activity negatively. Interestingly, inhibition of function by a valine to phenylalanine mutation, which has been associated with skeletal malformations, is likely caused by structural incompatibility of the bulky aromatic phenylalanine side chain with the integrity of the transmembrane helix, since substitutions with the smaller aliphatic side chains of leucine and isoleucine were acceptable changes.

SNP identification, linkage and radiation hybrid mapping of the porcine lamin A/C (LMNA) gene to chromosome 4q

The lamins are components of nuclear lamina and they have a profound influence on nuclear structure and functions. They are encoded by three genes, LMNA, LMNB1 and LMNB2. A genomic fragment of the porcine LMNA gene (822 bp; from exons 7 to 9) was amplified by polymerase chain reaction and comparatively sequenced. Four single nucleotide polymorphisms (SNPs) were identified in intronic sequences: G162A, G208A, T367G and C618T. The SNPs are within the restriction sites for enzymes Bsh1236I, HpaII, AluI and Bsh1236I respectively. Allele frequencies at SNPs G208A, T367G and C618T were determined by using eight pig breeds. Linkage analysis in the Hohenheim Meishan x Piétrain family placed the LMNA gene in the chromosome 4q linkage group, between MEF2D and GBA (MEF2D - 3.0 cM - LMNA - 0.2 cM - GBA). In radiation hybrid mapping LMNA was most significantly linked to SW270 on chromosome 4 (39 cR; LOD = 7.86). The LMNA gene is located in the quantitative trait loci region for some carcass traits on chromosome 4q.