Signatures of de‐domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Autochthonous pig breeds are usually reared in extensive or semi‐extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo‐Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south‐eastern European countries (Kr?kopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro‐geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild‐type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of ‘de‐domestication’ process, and wild resources are challenged by a ‘domestication’ drift. Both need to be further investigated and managed.     

Searching new signals for production traits through gene‐based association analysis in three Italian cattle breeds

Genome‐wide association studies (GWAS) have been widely applied to disentangle the genetic basis of complex traits. In cattle breeds, classical GWAS approaches with medium‐density marker panels are far from conclusive, especially for complex traits. This is due to the intrinsic limitations of GWAS and the assumptions that are made to step from the association signals to the functional variations. Here, we applied a gene‐based strategy to prioritize genotype–phenotype associations found for milk production and quality traits with classical approaches in three Italian dairy cattle breeds with different sample sizes (Italian Brown n = 745; Italian Holstein n = 2058; Italian Simmental n = 477). Although classical regression on single markers revealed only a single genome‐wide significant genotype–phenotype association, for Italian Holstein, the gene‐based approach identified specific genes in each breed that are associated with milk physiology and mammary gland development. As no standard method has yet been established to step from variation to functional units (i.e., genes), the strategy proposed here may contribute to revealing new genes that play significant roles in complex traits, such as those investigated here, amplifying low association signals using a gene‐centric approach.     

Nucleotide variability and haplotype heterogeneity at the porcine fat mass and obesity‐associated (FTO) gene

A large number of studies have confirmed that variants within the fat mass and obesity‐associated (FTO) gene are associated with higher obesity risk in humans. We and others have shown that FTO polymorphisms are associated with fat deposition and related traits in several pig populations, thus confirming the role of this gene in fatness across species. However, some differences observed in different pig populations may be derived, at least in part, from genetic heterogeneity at this locus. Here, we characterise the nucleotide variability and haplotype diversity of the porcine FTO gene in breeds having different predispositions to fat deposition traits. We resequenced 4749 bp of coding and non‐coding regions of the porcine FTO gene in 44 pigs of eight different breeds and identified 27 single nucleotide polymorphisms (SNPs) and four insertions/deletions. A positive Tajima's D‐value (P < 0.10) obtained in Italian Duroc pigs may be compatible with putative balancing selection. From the sequenced pig panel, 20 haplotypes were inferred, some of which clustered according to the breed of origin (Meishan and Italian Duroc). Genetic heterogeneity at this locus could complicate the dissection of the effects of this gene on fat deposition and production traits in pigs. This situation resembles, to some extent, what has been reported in humans, thus making the study of the porcine FTO gene variability especially interesting, as it could be used as a model to understand the complex and elusive role of this gene in human obesity.     

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

In this study, we investigated at the genome‐wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a P_Bonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.     

A genome‐wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry‐cured hams

Intermuscular fat content in protected designations of origin dry‐cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome‐wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance‐tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome‐wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E?04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; P_FDR < 0.05), included in the largest QTL region which spanned about 6.8 Mb on SSC1, is located within the glutamate ionotropic receptor kainate type subunit 2 (GRIK2) gene. Functional annotation of all genes included in QTL regions for VIF suggested that intermuscular fat in the Italian Large White breed is a complex trait apparently influenced by complex biological mechanisms also involving obesity‐related processes. These QTL target mainly chromosome regions different from those affecting subcutaneous and intramuscular fat deposition.     

Next generation semiconductor based sequencing of bitter taste receptor genes in different pig populations and association analysis using a selective DNA pool‐seq approach

Taste perception in animals affects feed intake and may influence production traits. In particular, bitter is sensed by receptors encoded by the family of TAS2R genes. In this research, using a DNA pool‐seq approach coupled with next generation semiconductor based target resequencing, we analysed nine porcine TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R38 and TAS2R39) to identify variability and, at the same time, estimate single nucleotide polymorphism (SNP) allele frequencies in several populations and testing differences in an association analysis. Equimolar DNA pools were prepared for five pig breeds (Italian Duroc, Italian Landrace, Pietrain, Meishan and Casertana) and wild boars (5–10 individuals each) and for two groups of Italian Large White pigs with extreme and divergent back fat thickness (50 + 50 pigs). About 1.8 million reads were obtained by sequencing amplicons generated from these pools. A total of 125 SNPs were identified, of which 37 were missense mutations. Three of them (p.Ile53Phe and p.Trp85Leu in TAS2R4; p.Leu37Ser in TAS2R39) could have important effects on the function of these bitter taste receptors, based on in silico predictions. Variability in wild boars seems lower than that in domestic breeds potentially as a result of selective pressure in the wild towards defensive bitter taste perception. Three SNPs in TAS2R38 and TAS2R39 were significantly associated with back fat thickness. These results may be important to understand the complexity of taste perception and their associated effects that could be useful to develop nutrigenetic approaches in pig breeding and nutrition.     

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.     

Allelic heterogeneity of FGF5 mutations causes the long‐hair phenotype in dogs

Hitherto, the only known mutant gene leading to the long‐hair phenotype in mammals is the fibroblast growth factor 5 (FGF5). In many dog breeds, the previously discovered FGF5:p.Cys95Phe mutation appeared completely concordant with the long‐hair phenotype, but for some breeds, the long‐hair phenotype could not be resolved. First, we studied the role of the FGF5:p.Cys95Phe and FGF5:g.145_150dupACCAGC mutations in 268 dogs descending from 27 breeds and seven wolves. As these mutations did not explain all the long‐hair phenotypes, all exons and their neighbouring regions of FGF5 were re‐sequenced. We detected three novel mutations in the coding sequence and one novel non‐coding splice‐site mutation in FGF5 associated with the long‐hair phenotype. The FGF5:p.Ala193Val polymorphism was perfectly consistent with long hair in Akitas and probably in Siberian huskies, too. Dogs of the long‐hair breed Samoyed were either homozygous or compound heterozygous for the FGF5:p.Ala193Val or the FGF5:p.Cys95Phe polymorphisms respectively. The two newly detected polymorphisms FGF5:c.559_560dupGG and FGF5:g.8193T>A and the known mutation FGF5:p.Cys95Phe explained the long‐hair phenotype of all Afghan hounds analysed. An FGF5:c.556_571del16 mutation was found in one longhaired Eurasier. All long‐hair‐associated mutations follow a recessive mode of inheritance, and allelic heterogeneity was a common finding in breeds other than Akita.     

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene

The Mangalitza lard‐type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow‐Belly Mangalitza and Red Mangalitza. The Swallow‐Belly line has a black coat combined with yellow‐blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with Hap FLK and BayeScan , and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18–20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.     

Detecting selection signatures in three Iranian sheep breeds

The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype–phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP‐EHH (cross‐population extend haplotype homozygosity) and F_ST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori‐Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.     

Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size

Guanzhong (n = 321) and Boer (n = 191) goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the coding regions of the prolactin receptor (PRLR) gene by DNA sequencing and PCR‐RFLP. Two SNPs (c.1457G>A and c.1645G>A) were identified that caused amino acid variations p.Ser485Asn and p.Val548Met respectively. Statistical results indicated that the c.1457G>A and c.1645G>A SNPs were significantly associated with litter size in Boer and Guanzhong goat breeds. Further analysis revealed that combined genotype C4 (GGGG) and haplotype G‐G were better than the others for litter size in both goat breeds. These results might contribute to goat genetic resources and breeding.     

Genome‐wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing

The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large‐effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed‐specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.     

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances

Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome‐wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5–56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study.     

Genome-wide analyses reveal the regions involved in the phenotypic diversity in Sicilian pigs

Nero Siciliano (Sicilian Black, SB) is a local pig breed generally of uniform black color. In addition to this officially recognized breed, there are animals showing morphological characteristics resembling the SB but with gray hair (Sicilian Grey, SG). The SG, compared with the SB, also shows a more compact structure with greater transverse diameters, higher average daily gains and lower thickness of the back fat. In this study, using the Illumina PorcineSNP60 BeadChip, we run genome-wide analyses to identify regions that may explain the phenotypic differences between SB (n = 21) and SG (n = 27) individuals. Combining the results of the two case–control approaches (GWAS and F_ST), we identified two significant regions, one on SSC5 (95 401 083 bp) and one on SSC15 (55 051 435 bp), which contains several candidate genes related to growth traits in pig. The results of the Bayesian population differentiation approach identified a marker near the MGAT4C, a gene associated with average daily gain in pigs. Finally, scanning the genome for runs of homozygosity islands, we found that the two groups have different runs of homozygosity islands, with several candidate genes involved in coat color (in SG) or related to different pig performance traits (in SB). In summary, the two analyzed groups differed for several phenotypic traits, and genes involved in these traits (growth, meat traits and coat color) were detected. This study provided another contribution to the identification of genomic regions involved in phenotypic variability in local pig populations     

Distribution of the CD4 Alleles in Sus scrofa Demonstrates the Genetic Profiles of Western Breeds and Miniature Pigs

Widely used antipig CD4 monoclonal antibodies (mAbs) fail to recognize CD4 alleles characteristic of miniature pig lines such as the National Institutes of Health (NIH) miniature pigs and microminipigs. We surveyed polymorphisms in the coding sequence of the porcine CD4 gene among Western and Oriental pig breeds and Japanese wild boars and investigated their distribution. Of the 13 alleles that we identified among the 47 animals, 2 in group I and 3 in group II were found exclusively in Western breed pigs. Group IV alleles, which included mAb-nonbinding alleles, were found frequently in Oriental breed pigs, suggesting that the mAb-nonbinding allele arose from the gene pool of Oriental pigs. Group IV alleles were also found in Duroc and Large White pigs, suggesting genetic inflow from Oriental pig breeds into Western breeds. Comparison of the CD4 sequences of species in Cetartiodactyla suggested that the group IV alleles in Sus scrofa occurred before the divergence of this species from the other artiodactyls. The different antibody specificities of the various CD4 alleles may facilitate the discrimination of T-cell populations in transplantation studies using miniature pigs. The significance of the preservation of CD4 polymorphisms to immune function in pigs warrants further investigation.     

A machine learning approach for the identification of population-informative markers from high-throughput genotyping data: application to several pig breeds

Single nucleotide polymorphisms (SNPs) able to describe population differences can be used for important applications in livestock, including breed assignment of individual animals, authentication of mono-breed products and parentage verification among several other applications. To identify the most discriminating SNPs among thousands of markers in the available commercial SNP chip tools, several methods have been used. Random forest (RF) is a machine learning technique that has been proposed for this purpose. In this study, we used RF to analyse PorcineSNP60 BeadChip array genotyping data obtained from a total of 2737 pigs of 7 Italian pig breeds (3 cosmopolitan-derived breeds: Italian Large White, Italian Duroc and Italian Landrace, and 4 autochthonous breeds: Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano) to identify breed informative and reduced SNP panels using the mean decrease in the Gini Index and the Mean Decrease in Accuracy parameters with stability evaluation. Other reduced informative SNP panels were obtained using Delta, Fixation index and principal component analysis statistics, and their performances were compared with those obtained using the RF-defined panels using the RF classification method and its derived Out Of Bag rates and correct prediction proportions. Therefore, the performances of a total of six reduced panels were evaluated. The correct assignment of the animals to its breed was close to 100% for all tested approaches. Porcine chromosome 8 harboured the largest number of selected SNPs across all panels. Many SNPs were included in genomic regions in which previous studies identified signatures of selection or genes (e.g. ESR1, KITL and LCORL) that could contribute to explain, at least in part, phenotypically or economically relevant traits that might differentiate cosmopolitan and autochthonous pig breeds. Random forest used as preselection statistics highlighted informative SNPs that were not the same as those identified by other methods. This might be due to specific features of this machine learning methodology. It will be interesting to explore if the adaptation of RF methods for the identification of selection signature regions could be able to describe population-specific features that are not captured by other approaches.     

Copy number variants in Italian Large White pigs detected using high‐density single nucleotide polymorphisms and their association with back fat thickness

The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P < 0.10, and seven were significant at P < 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.     

Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds

The competitive equilibrium of fatty acid biosynthesis and oxidation in vivo determines porcine subcutaneous fat thickness (SFT) and intramuscular fat (IMF) content. Obese and lean-type pig breeds show obvious differences in adipose deposition; however, the molecular mechanism underlying this phenotypic variation remains unclear. We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with meat quality and carcass traits in backfat at five growth stages (1–5 months) of Landrace (a leaner, Western breed) and Taihu pigs (a fatty, indigenous, Chinese breed). Variance analysis (ANOVA) revealed that differences in the expression of 25 genes in Landrace pigs were significant (FDR adjusted permutation, P<0.05) among 5 growth stages. Gene class test (GCT) indicated that a gene-group was very significant between 2 pig breeds across 5 growth stages (P _ErmineJ<0.01), which consisted of 23 genes encoding enzymes and regulatory proteins associated with lipid and steroid metabolism. These findings suggest that the distinct differences in fat deposition ability between Landrace and Taihu pigs may closely correlate with the expression changes of these genes. Clustering analysis revealed a very high level of significance (FDR adjusted, P<0.01) for 2 gene expression patterns in Landrace pigs and a high level of significance (FDR adjusted, P<0.05) for 2 gene expression patterns in Taihu pigs. Also, expression patterns of genes were more diversified in Taihu pigs than those in Landrace pigs, which suggests that the regulatory mechanism of micro-effect polygenes in adipocytes may be more complex in Taihu pigs than in Landrace pigs. Based on a dynamic Bayesian network (DBN) model, gene regulatory networks (GRNs) were reconstructed from time-series data for each pig breed. These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of adipose metabolism between the two pig breeds; from these results, some potential key genes could be identified. Quantitative, real-time RT-PCR (QRT-PCR) was used to verify the microarray data for five modulated genes, and a good correlation between the two measures of expression was observed for both 2 pig breeds at different growth stages (R=0.874±0.071). These results highlight some possible candidate genes for porcine fat characteristics and provide some data on which to base further study of the molecular basis of adipose metabolism.