Mapping of 93 porcine ESTs preferentially expressed in liver

Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits

Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.

A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig

Muscle tenderness is an important complex trait for meat quality and thus for genetic improvement through animal breeding. However, the physiological or genetic control of tenderness development in muscle is still poorly understood. In this work, using transcriptome analysis, we found a relationship between gene expression variability and tenderness. Muscle (longissimus dorsi) samples from 30 F(2) pigs were characterized by Warner-Bratzler Shear Force (WBSF) on cooked meat as a measurement of muscle tenderness. Gene expression levels were measured using microarrays for 17 muscle samples selected to represent a range of WBSF values. Using a linear regression model, we determined that samples with WBSF values above 30 N could be effectively analysed for genes exhibiting a significant association of their expression level on shear force (false discovery rate <0.05). These genes were shown to be involved in three functional networks: cell cycle, energy metabolism and muscle development. Twenty-two genes were mapped on the pig genome and 12 were found to be located in regions previously reported to contain quantitative trait loci (QTL) affecting pig meat tenderness (chromosomes 2, 6 and 13). Some genes appear therefore as positional candidate genes for QTL.

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.

Analysis of FMO genes and off flavour in pork

Off flavours in pork sometimes produce tastes such as sourness, fishy, metallic or other non-typical flavours and are often caused by low pH. Loss of function mutations in flavin containing mono-oxygenase 3 (FMO3) are known to be associated with a fishy off flavour in both chicken eggs and cow's milk and a similar autosomal recessive disorder is present in humans resulting in a fishy odour. FMO3 is a member of a gene family that is clustered on human chromosome 1. Comparative mapping suggested that FMO3 and the remaining FMO genes (ex. FMO1 and FMO5) might map to the orthologous region on pig chromosome 9 (SSC9) where a quantitative trait locus (QTL) for off flavour was previously identified. Primers were designed to amplify FMO1, FMO3 and FMO5 gene fragments and several SNPs were discovered and genotyping tests developed. The genotypes from the Iowa State University Berkshire x Yorkshire resource population were used to linkage map FMO1 and FMO3 to SSC9 and FMO5 to pig chromosome 4 (SSC4). QTL and associations analyses were performed using the map containing FMO1 and FMO3. Results demonstrated that FMO3 and FMO1 mapped less than 1 cM away from the peak for the off flavour QTL previously detected on SSC9 and provide indications of an association between the FMO3 polymorphism and off flavour in pork.

QTL and candidate genes for fecundity in sows

Fecundity in pigs is a trait of major economic interest but low heritability. For the improvement of fecundity, genetic markers for selection are desirable and therefore, several searches for genetic variation influencing fecundity have been performed. The aim of this review is to compare and to evaluate all published QTL analyses and candidate gene approaches concerning reproductive traits in sows. For this purpose, we present a comprehensive cytogenetic map comprising 54 QTL and 11 candidate genes with influence on reproductive traits. The evaluation and comparison of the results showed similarities, but also marked differences among studies. Reasons for different results are multicausal and are due to differences between resource populations, number of evaluated animals, mating systems, measured phenotypical traits and environmental influences. We could show that chromosome 8 and to a lower extend chromosome 7 are the most important chromosomes with regard to reproductive traits in pigs. For further research, fine mapping of the identified QTL regions is necessary in order to confirm and to narrow the most likely chromosomal intervals. Although difficult to perform, an advance would be a standardization of the experimental setup in particular, in respect to the collection of phenotypic data. Furthermore, we suggest to publish the information on further identified QTL and candidate genes as comprehensive and accurate as possible in order to allow a more transparent comparison and collation of the results.

Analysis of properdin (BF) genotypes associated with litter size in a commercial pig cross population

Properdin (BF) was investigated as a candidate gene influencing litter size in a commercial pig cross population. The BF gene was chosen because of its integral role in influencing uterine epithelium growth and because several quantitative trait loci (QTL) with impact on reproductive traits have been detected near the centromere of porcine chromosome 7. A total of 123 F2 (Large White x Landrace) x Leicoma sows were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The sows were divided into two extreme performance groups, one with a high litter size (n = 61, > or = 14.3 piglets per litter) and the other with a low litter size (n = 62, < or = 11.3 piglets per litter). Although genotype and allele frequencies were uneven with 2.4% (AA), 16.3% (AB), 81.3% (BB) and 0.11 (A): 0.89 (B), the allele A was the unfavourable one, leading to less offspring. With regard to the level of significance at p < 0.05, the total number of born (TNB) and number of born alive (NBA) piglets were associated with BF genotypes. The genotype AA led to 10.55 TNB and 10.00 NBA, whereas the genotype BB led to 13.19 TNB and 12.11 NBA. The genotype AB was intermediate. In future, a systematic mating test is necessary in order to obtain more balanced genotype frequencies. Furthermore, it should be taken into consideration that the investigated polymorphism is located in an intronic region and the causative mutation is not clear yet.

SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.

Assignment of 101 genes localized in HSA10 to a swine RH (IMpRH) map to generate a dense human-swine comparative map

Economically important traits such as growth and backfat in pigs have been shown to be influenced by genes in swine chromosome (SSC) 10q12-->qter corresponding to human chromosome (HSA) 10p. However, since gene information in the swine chromosomal region was limited, we attempted to generate a dense comparative map between SSC10 and HSA10 by mapping the 115 genes of HSA10 to a swine RH map (IMpRH map). In the mapping ten genes were assigned to SSC10, 88 to SSC14, and one to SSC3. One gene was suggested to link to SSC3, and another to SSC9. The correspondences between HSA10 and SSC10 and between HSA10 and SSC14 were essentially consistent with the observations obtained from bi/uni-directional chromosome painting or other results. This study further indicated that a large number of intrachromosomal rearrangements occurred in the synteny-conserved regions following species separation.

Isolation and enrichment of abundant microsatellites from a channel catfish (Ictalurus punctatus) brain cDNA library

Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5'-UTR, 72% contained repeats in the 3'-UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid; single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.

Identification of functional candidate genes for body composition by expression analyses and evidencing impact by association analysis and mapping

This study aims to identify hepatic genes affecting traits related to muscularity and obesity by combining expression analyses, association studies, and gene mapping. Functional candidate genes with trait-associated expression were obtained by hybridising custom made application-specific cDNA microarrays with targets of discordant sib pairs of a porcine experimental population. Out of 238 genes addressed, nine genes were regulated by the factor>or=2 between the sib pairs. Differential gene expression was independently confirmed for selected genes by real time RT-PCR. Transcript levels of four genes (APOH, PEDF, SLCO1B3, TBG) were significantly different between the phenotype groups. Screening for trait associated markers within TBG and APOH by comparative sequencing of discordant sib pairs revealed a SNP at position nt 778 (A>C) (N229H) of TBG. No polymorphism in APOH was detected. Association analysis confirmed effects of TBG on carcass traits statistically. Allocating TBG to a QTL region on chromosome X revealed genetic evidence for the effect. Moreover, our results indicate that there are probably two polymorphisms segregating-one (N229H) altering binding capability of TBG and another still to be detected altering the transcription rate of TBG.

Molecular cloning and sequencing of porcine C5 gene and its association with immunological traits

The complement system helps in the lysis of invading pathogens and modulates the inflammatory as well as the humoral and cellular immune responses. C5 mediates many potent inflammatory and cytolytic events after proteolytic activation by complement convertase enzymes. Hence, to investigate the role of pig C5 ( pC5) as a candidate gene for disease resistance in pigs, the complete cDNA of pC5 was sequenced, screened for single nucleotide polymorphisms (SNPs), and an association analysis with various immunological parameters measured in F2 animals of a pig resource population based on a cross of Duroc and Berlin miniature pigs (DUMI) was carried out. In total, 5,422 bp of pC5 cDNA was sequenced, which codes for the 1,677-amino-acid precursor of C5. Four polymorphic sites were detected, one of which was segregating in the DUMI population in three genotypic patterns: AA, AC and CC. Classical (CH50) and alternative (AH50) complement activities, C3c levels, haptoglobin (HP) acute phase protein levels, and antibody titers against Mycoplasma (Mk) and Aujesky (ADV) vaccines were measured in the resource population. Association analysis between C5 and the immunological parameters was carried out using repeated measures mixed and general linear model analysis. The homozygote AA was found to be significantly different from the other two genotypes with respect to AH50 and CH50, whereas genotype CC was found to be significantly different from the other genotypes for C3c and HP levels. No significant difference could be seen between genotypes for antibody titers against vaccinations. Association of C5 with complement activity traits and acute phase proteins promotes pC5 as a candidate gene for innate disease resistance.

Comparative mapping in the pig: localization of 214 expressed sequence tags

In total, 214 ESTs (Expressed Sequence Tags) were assigned to the porcine gene map by using somatic cell hybrid mapping, radiation hybrid mapping, and FISH. The ESTs were isolated from a porcine small intestine cDNA library on the basis of significant sequence identity with human annotated genes. In total, 390 primer pairs were designed primarily in the 3' UTR of the sequences. Overall, 58.6% of the ESTs were successfully mapped by this approach. In total, 191 of the localizations are in agreement with the human comparative map, strongly indicating that these represent true orthologous genes. The remaining 23 ESTs provide new comparative mapping data, which should be considered as preliminary until confirmed by other studies. Our mapping efforts provide a significant contribution to the porcine map as well as to the comparative map for human and pig.

Comparative mapping of a region on chromosome 10 containing QTL for reproduction in swine

Several quantitative trait loci (QTL) for important reproductive traits (age of puberty, ovulation rate, nipple number and plasma FSH) have been identified on the long arm of porcine chromosome 10. Bi-directional chromosome painting has shown that this region is homologous to human chromosome 10p. Because few microsatellite or type I markers have been placed on SSC10, we wanted to increase the density of known ESTs mapped in this region of the porcine genome. Genes were chosen for their position on human chromosome 10, sequence availability from the TIGR pig gene indices, and their potential as a candidate gene. The PCR primers were designed to amplify across introns or 3'-UTR to maximize single nucleotide polymorphism (SNP) discovery. Parents of the mapping population (one sire and seven dams) were amplified and sequenced to find informative markers. The SNPs were genotyped using primer extension and mass spectrometry. These amplification products were also used to probe a BAC library (RPCI-44, Roswell Park Cancer Institute) for positive clones and screened for microsatellites. Six genes from human chromosome 10p (AKR1C2, PRKCQ, ITIH2, ATP5C1, PIP5K2A and GAD2) were mapped in the MARC swine mapping population. Gene order was conserved within these markers from centromere to telomere of porcine chromosome 10q, as compared with human chromosome 10p. Four of these genes (PIP5K2A, ITIH2, GAD2 and AKR1C2), which map under QTL, are potential candidate genes. Identification of porcine homologues near important QTL and development of a comparative map for this chromosome will allow further fine- mapping and positional cloning of candidate genes affecting reproductive traits.

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)

The GENETPIG database has been established for storing and disseminating the results of the European project: 'GENETPIG: identification of genes controlling economic traits in pig'. The partners of this project have mapped about 630 porcine and human ESTs onto the pig genome. The database collects the mapping results and links them to other sources of mapping data; this includes pig maps as well as available comparative mapping information. Functional annotation of the mapped ESTs is also given when a significant similarity to cognate genes was established. The database is accessible for consultation via the Internet at http://www.infobiogen.fr/services/Genetpig/.