The leptin receptor gene (LEPR) maps to porcine chromosome 6

Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits

Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL, protein content (PRO) and CY ( < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO ( < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.

Identification of Carcass and Meat Quality QTL in an F(2) Duroc × Pietrain Pig Resource Population Using Different Least-Squares Analysis Models

A three-generation resource population was constructed by crossing pigs from the Duroc and Pietrain breeds. In this study, 954 F₂ animals were used to identify quantitative trait loci (QTL) affecting carcass and meat quality traits. Based on results of the first scan analyzed with a line-cross (LC) model using 124 microsatellite markers and 510 F₂ animals, 9 chromosomes were selected for genotyping of additional markers. Twenty additional markers were genotyped for 954 F₂ animals and 20 markers used in the first scan were genotyped for 444 additional F₂ animals. Three different Mendelian models using least-squares for QTL analysis were applied for the second scan: a LC model, a half-sib (HS) model, and a combined LC and HS model. Significance thresholds were determined by false discovery rate (FDR). In total, 50 QTL using the LC model, 38 QTL using the HS model, and 3 additional QTL using the combined LC and HS model were identified (q < 0.05). The LC and HS models revealed strong evidence for QTL regions on SSC6 for carcass traits (e.g., 10th-rib backfat; q < 0.0001) and on SSC15 for meat quality traits (e.g., tenderness, color, pH; q < 0.01), respectively. QTL for pH (SSC3), dressing percent (SSC7), marbling score and moisture percent (SSC12), CIE a* (SSC16), and carcass length and spareribs weight (SSC18) were also significant (q < 0.01). Additional marker and animal genotypes increased the statistical power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL.

Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population

Background

A variety of analysis approaches have been applied to detect quantitative trait loci (QTL) in experimental populations. The initial genome scan of our Duroc x Pietrain F₂ resource population included 510 F₂ animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F₂ animals and 20 markers used in the first scan were genotyped for 444 additional F₂ animals. Three least-squares Mendelian models for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model.

Results

In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR) significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15.

Conclusions

Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.

Characterization of Porcine Leptin Receptor Polymorphisms and Their Association with Reproduction and Production Traits

Fatness in pigs is of prime economic importance due to market incentives for production of lean pork and elevated fatness increasing the feed costs. Leptin (LEP) action, mediated through its specific receptors (LEPR), was reported to be involved in the regulation of fatness via feed intake, energy expenditure, and whole-body energy balance in pigs. In this study, we have designed 17 primer sets based on the human and mouse LEPR sequences and successfully amplified coding regions of 15 porcine LEPR exon fragments by polymerase chain reactions (PCR). Four single nucleotide polymorphisms (SNP) of Intron 2, Exons 2, 6, and 18 were found in Landrace, Yorkshire, and Duroc by mutagenetically separated-PCR (MS-PCR) and PCR-restriction fragment length polymorphisms (PCR-RFLP). Chi-square statistics was used to calculate homogeneity of genotypic frequencies of 4 gene polymorphisms for three breeds of animals. Effects of Intron 2, Exon 2, and Exon 18 polymorphisms on the reproduction trait such as litter sizes of sows were evident (p < 0.05) in Duroc and Yorkshire. There was no (p > 0.05) significant influence on the production trait of average daily gain due to four candidate gene polymorphisms in three porcine breeds. However, effects of Exon 6 and 18 polymorphisms on the production trait of backfat thickness were significant (p < 0.05) in Landrace and Yorkshire, respectively. Effects of Exon 18 polymorphisms on feed efficiency were also evident (p < 0.05) in Duroc.

Porcine leptin receptor: molecular structure and expression in the ovary

The porcine leptin receptor complementary DNA was cloned and sequenced and the leptin receptor gene expression evaluated in the porcine ovary. An open reading frame of 3498 nt cDNA was amplified from pig liver mRNA by RT-PCR. Sequence homology with the extracellular, transmembrane, and cytoplasmic domains of human, mouse, rat, sheep, and cow leptin receptors varied between 45% and 90%. Leptin receptor mRNA was present in porcine kidney, liver, spleen, lung, brain, testis, uterus, ovary, corpus luteum (CL), theca, and granulosa cells. The abundance of leptin receptor transcripts and protein varied during luteinization of granulosa cells in vitro and in the CL during the pig luteal phase. In the postovulatory CL, both mRNA and protein were low but detectable, maximal expression was observed in the midcycle CL, and lowest abundance occurred in regressed CL. Leptin receptor mRNA was present in granulosa cells at isolation and increased in abundance as the cells luteinized over 96 hr in culture. Leptin receptor protein was detectable after 12 hr of in vitro luteinization. We conclude that leptin receptor is expressed in granulosa and luteal cells, and varies during pig ovarian cell differentiation.

Molecular cloning and properties of the chicken leptin-receptor (CLEPR) gene

The mammalian leptin receptor (LEPR) (formerly OB-R) mediates the weight regulatory effects of the circulating hormone leptin. The extreme obese phenotype of recessive mutations in the mouse leptin or LEPR genes (ob/ob and db/db mice, respectively) indicate the high potential of these genes for medical and agricultural research. In this paper, we report on the cloning of the full-length chicken leptin receptor (CLEPR) cDNA, which is the first non-mammalian cloning of a LEPR gene. The CLEPR gene shares a relatively low sequence similarity with its mammalian counterparts, with an average of 60% identical nucleotides. However, comparison between the predicted protein sequences has shown a tight conservation of most previously characterized LEPR motifs and essential tyrosine residues. Similarities between the chicken and the mammalian LEPR genes were also observed in the pattern of mRNA expression. The identification of the CLEPR gene should facilitate the study of the molecular mechanism involved in the regulation of body growth and composition in avian.

Confirmed quantitative trait loci for fatness and growth on pig chromosome 4

Quantitative trait loci (QTLs) with large effects on fatness and growth have been identified previously on pig chromosome 4 in an intercross between the European wild pig and Large White domestic pigs. Two F2 sows, heterozygous for the actual chromosome region, were backcrossed to a Large White boar, and two backcross (BC1) boars were in turn backcrossed to Large White/Landrace sows. One of the boars was heterozygous for an intact wild pig-derived QTL region, whereas the other carried a recombinant haplotype. A total of 85 BC2 animals were produced. Phenotypical measurements included daily weight gain, ultrasonic measurements of fat depth at 70 and 90 kg and several carcass traits. QTL segregation was deduced using 15 markers previously assigned to chromosome 4. Highly significant QTL effects were observed on all fatness traits and on the length of the carcass. A small but significant effect on growth was also observed. The results confirm the presence of one or more QTLs on chromosome 4 affecting fatness and growth. There was a good agreement between the estimates of QTL effects in the F2 and BC2 generations. The results from the recombinant sire family allowed us to map the major QTL effect distal to the recombination breakpoint. We propose that this confirmed QTL with a major effect on fatness is designated FAT1.

Identification of sequence tagged sites in the Asian and African elephant

To date, gene identification in elephants has essentially related to evolutionary studies. Further identification of genes in elephants could provide additional information for evolutionary studies and for evaluating genetic diversity in existing elephant populations. The objective of this project was to identify sequence tagged sites (STSs) in the Asian and the African elephant for the following genes: melatonin receptor 1a (MTNR1A), retinoic acid receptor beta (RARB), and leptin receptor (LEPR). These genes are highly conserved among mammals, and all may play a role in reproduction. Heterologous primers for PCR were designed from sequences available in other species. Fragments of size 141 base pairs (bp) for RARB and 327 bp for LEPR were obtained by amplifying genomic Asian and African elephant DNA. The LEPR fragment included an intron of 164 bp. Also, a 417 bp fragment for MTNR1A was obtained in the Asian elephant only. All PCR products were sequenced and comparison computations were made at the nucleotide and amino acid levels to sequence available in the GenBank database. Nucleotide sequence for RARB was identical for both Asian and African elephants and differed by only 3 bp for LEPR. Deduced amino acid sequence was identical for both STSs in both species. Elephants were relatively similar in comparison to other mammals and less similar to chickens.

Xenoduplex analysis--a method for comparative gene mapping using hybrid panels

Somatic cell hybrid (SCH) panels and radiation hybrid (RH) panels are powerful resources for comparative gene mapping because gene assignments are made without the detection of genetic polymorphism as needed for linkage mapping. A frequently encountered problem, however, is that the gene specific primers may amplify homologous PCR products of equal length from the donor and recipient species of the panel. Here, we describe a simple solution to this problem in which we utilize the formation of interspecies heteroduplexes that can be easily distinguished from the corresponding homoduplexes by native polyacrylamide gel electrophoresis. We denote these DNA-DNA interspecies hybrids, xenoduplexes (xeno = Gr. Xenos, foreigner). A merit of the method is that the formation of xenoduplexes strongly suggests that the PCR products from the two species represent homologous sequences. The method is thus particularly useful for comparative gene mapping when the PCR primers have been designed by use of sequence information from other species. In this study we have successfully used xenoduplex analysis and a pig-rodent SCH panel to map seven porcine genes (ACADM, AT3, HOXD, IL8RB, LEPR, PAX8, PKLR) for which no previous sequence information was available. The assignment of the leptin receptor gene (LEPR) to pig chromosome 6q32-35 excluded LEPR as a candidate gene for a QTL on pig chromosome 4 with a major effect on fatness.