Analysis of Association Between the MUC4 g.8227C>G Polymorphism and Production Traits in Italian Heavy Pigs Using a Selective Genotyping Approach

In pigs, susceptibility to enterotoxigenic Escherichia coli (ETEC) K88 strains (locus F4bcR) is determined by a dominant allele, with the recessive allele determining resistance. The susceptible allele also appeared to be associated with higher growth rate even with discordant results. A single nucleotide polymorphism (SNP) in exon 7 of the mucin 4 (MUC4) gene (DQ848681:g.8227C>G), shown to be in close linkage disequilibrium with the F4bcR locus, has been used as marker to identify susceptible pigs, substituting invasive villous adhesion tests. We herein analyzed this SNP in Italian local breeds and applied a selective genotyping approach in Italian Large White, Italian Landrace, and Italian Duroc comparing allele frequency distribution in groups of pigs with extreme estimated breeding values (EBV) for average daily gain (ADG) and backfat thickness (BFT) to evaluate if this marker is associated with these traits. Allele G (associated with susceptibility to ETEC) was associated with higher ADG and BFT in Italian Large White (P = 6.66E-04 and P = 0.012, respectively) and higher ADG in Italian Landrace (P = 7.23E-12). This polymorphism was poorly informative in Italian Duroc. Antagonistic associations of the MUC4 g.8227C>G alleles on susceptibility to ETEC and growth performances evidence the complexity of applying marker assisted selection in pig breeding.     

The porcine fat mass and obesity associated (FTO) gene is associated with fat deposition in Italian Duroc pigs

In humans, common variants in the fat mass and obesity associated ( FTO ) gene are associated with body mass index and obesity. Here we sequenced exon 4, parts of introns 3 and 4 and two portions of the 3'-untranslated region of the porcine FTO gene in a panel of nine pigs of different breeds and identified three SNPs. Allele frequencies of the g.276T>G ( AM931150 ) mutation were studied in seven pig breeds. This mutation was used to linkage-map FTO to SSC6. Association analyses between the g.276T>G polymorphism and several traits [pH of semimembranosus muscle and estimated breeding values (EBV) for average daily gain, back fat thickness, lean cuts, ham weight and feed:gain ratio] were carried out in 257 sib-tested Italian Large White pigs. Only feed:gain ratio showed P  <   0.05. A selective genotyping approach was applied, analysing two extreme and divergent groups of Italian Large White pigs selected on the basis of back fat thickness EBV (50 with most positive and 50 with most negative values). Fisher's exact test (two-tailed) was not significant when comparing the allele frequencies of these two groups. The same approach was used in the Italian Duroc breed for which two extreme and divergent groups of animals were selected according to visible intermuscular fat EBV. Differences of allele frequencies between these two groups were highly significant ( P  <   0.00001, P  <   0.001 and P  <   0.0001, considering all animals or only two- or three-generation unrelated animals respectively), indicating association between the analysed FTO marker and intermuscular fat deposition.     

Analysis of Association Between the MUC4 g.8227C>G Polymorphism and Production Traits in Italian Heavy Pigs Using a Selective Genotyping Approach

In pigs, susceptibility to enterotoxigenic Escherichia coli (ETEC) K88 strains (locus F4bcR) is determined by a dominant allele, with the recessive allele determining resistance. The susceptible allele also appeared to be associated with higher growth rate even with discordant results. A single nucleotide polymorphism (SNP) in exon 7 of the mucin 4 (MUC4) gene (DQ848681:g.8227C>G), shown to be in close linkage disequilibrium with the F4bcR locus, has been used as marker to identify susceptible pigs, substituting invasive villous adhesion tests. We herein analyzed this SNP in Italian local breeds and applied a selective genotyping approach in Italian Large White, Italian Landrace, and Italian Duroc comparing allele frequency distribution in groups of pigs with extreme estimated breeding values (EBV) for average daily gain (ADG) and backfat thickness (BFT) to evaluate if this marker is associated with these traits. Allele G (associated with susceptibility to ETEC) was associated with higher ADG and BFT in Italian Large White (P?=?6.66E-04 and P?=?0.012, respectively) and higher ADG in Italian Landrace (P?=?7.23E-12). This polymorphism was poorly informative in Italian Duroc. Antagonistic associations of the MUC4?g.8227C>G alleles on susceptibility to ETEC and growth performances evidence the complexity of applying marker assisted selection in pig breeding.     

A single nucleotide polymorphism in the porcine cathepsin K (<Emphasis Type="Italic">CTSK</Emphasis>) gene is associated with back fat thickness and production traits in Italian Duroc pigs

Cathepsin K (CTSK) was selected as a candidate gene for fat deposition in pigs because recently, in human and mouse, it was shown that this lysosomal proteinase is an obesity marker. A single nucleotide polymorphism (SNP) was identified in intron 4 of the porcine CTSK gene (g.15G>A; FM209043). Allele frequencies of this polymorphism were analysed in seven pig breeds. Radiation hybrid mapping confirmed the localization of CTSK to porcine chromosome 4, close to the FAT1 QTL region. Three populations of pigs (one Italian Large White and two Italian Duroc groups of pigs) were selected for association analysis. In the Italian Large White breed the g.15G>A SNP was not informative. Association analysis including all Italian Duroc pigs showed that the CTSK marker was associated with back fat thickness and lean cuts (P < 0.01), and average daily gain and feed:gain ratio (P < 0.05) estimated breeding values.     

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.     

New SNP of the porcine Perilipin 2 (<Emphasis Type="Italic">PLIN2</Emphasis>) gene,association with carcass traits and expression analysis in skeletal muscle

PLIN2 (perilipin 2) is a cytosolic protein that promotes the formation and stabilization of the intracellular lipid droplets, organelles involved in the storage of lipid depots. Porcine PLIN2 gene represents a biological and positional candidate for fat deposition, a polygenic trait that affects carcass and meat quality. The aim of the present study was to screen PLIN2 gene for polymorphisms, to evaluate the association with carcass quality traits, and to investigate the gene expression in skeletal muscle. Six new single nucleotide polymorphisms (SNP) were detected by sequencing 32 samples from five pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Belgian Landrace, Pietrain). Two SNP localized in introns, two in the 3′-untranslated region (UTR), and two missense SNP were found in exons. A 3′-UTR mutation (GU461317:g.98G>A), genotyped in 290 Italian Duroc pigs by High Resolution Melting, resulted significantly associated (P < 0.01) with average daily gain, feed conversion ratio, lean cuts and hams weight estimated breeding values. PLIN2 gene expression analysis in skeletal muscle of Italian Large White and Italian Duroc pigs divergent for backfat thickness and visible intermuscular fat showed a trend of higher expression level in pigs with higher intermuscular fat. These results suggest that PLIN2 can be a marker for carcass quality in pigs. Further investigation at both gene and protein level could elucidate its role on 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.     

The porcine <Emphasis Type="Italic">TBC1D1</Emphasis> gene: mapping,SNP identification,and association study with meat,carcass and production traits in Italian heavy pigs

TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1] is a Rab-GTPase-activating related protein implicated in regulating the trafficking of glucose transporter 4 (GLUT4 or SLC2A4) storage vesicles to the cell surface in response to insulin and AMPK-activating stimuli in skeletal muscle. Mutations in the human and mouse TBC1D1 genes confer risk of obesity or leanness. We identified five single nucleotide polymorphisms (SNPs) in the porcine TBC1D1 gene. One of them (FN677935:g.219G>A) was genotyped either by high resolution melting and PCR-RFLP analyses to study allele frequencies in a few pig breeds and evaluate association with meat production and carcass traits in five groups of sib-tested pigs of Italian Large White and Italian Duroc breeds. The g.219G>A SNP was associated (P < 0.05) with ham weight, back fat thickness and lean cuts content in Italian Large White and with visible intermuscular fat in Italian Duroc pigs.     

Exome Capture with Heterologous Enrichment in Pig (Sus scrofa)

The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY® system confirms that this “human-on-pig” approach offers new potentiality for the identification of DNA variants in protein-coding genes.     

Association between polymorphisms in cathepsin and cystatin genes with meat production and carcass traits in Italian Duroc pigs: confirmation of the effects of a cathepsin L (CTSL) gene marker

We genotyped single nucleotide polymorphisms (SNPs) in 5 cathepsin or cystatin genes (cathepsin F, CTSF; cathepsin L, CTSL; cathepsin S, CTSS; cathepsin Z, CTSZ; cystatin B, CSTB) in two groups of Italian Duroc pigs: the first group (n. 100) was chosen using a selective genotyping approach with extreme estimated breeding value (EBV) for visible intermuscular fat (VIF); the second group (n. 218) was made of performance-tested Duroc pigs not selected by any criteria. CTSL marker showed a tendency towards association (P < 0.10) with VIF (first group) and back fat thickness (BFT) and average daily gain (ADG; second group). In the second group, the CTSL polymorphism was associated with weight of lean cuts (LC; P < 0.05). Additive effects for all mentioned traits in the second group was significant (P < 0.05). The results we obtained in the Italian Duroc pigs confirmed the results and the direction of the effects already reported for the Italian Large White breed.     

Association of Porcine IGF Binding Protein-5 Gene with Meat Quality

IGFBP-5 is a member of the IGF families. Using PCR-SSCP, genotypic and allelic frequencies were analyzed in 18 pig breeds (n = 600). The association between haplotypes and production performance was analyzed in a Jinhua × Pietrain population family (n = 212, total 24 traits). Two SNPs (T199C and G485A) within the gene were analyzed. The breeds had different genotypic and allelic frequencies. Typically, the Chinese native pig breeds carried a higher allele C and G frequency (over 50%) than those of the European pigs, and only Guangdong Large White and wild boar were at Hardy–Weinberg equilibrium. The pigs carrying the CG haplotype had higher hue, loin, and thigh pH1 values than pigs with the TA haplotype, and pigs with the TA haplotype had the lowest loin pH2 value and highest color-a value among the haplotypes. It is proposed that the IGFBP-5 gene is associated with the variation in meat quality, especially in pH value together with other QTLs on chromosome 15.     

A SNP in the miR-27a gene is associated with litter size in pigs

MicroRNAs (miRNAs) are 20–25 nt, endogenous non-coding RNA molecules that act by binding to the complementary sequence of target messenger RNAs. Many evidences showed that miRNAs were involved in the process of germ proliferation and differentiation. In the present study, miR-27a gene was selected as a candidate gene for litter size due to its biological function, its location near a mummified pigs QTL, and its differentially expressed profile in Large White and Chinese Erhualian PMSG-hCG stimulated preovulatory ovaries. By comparative sequencing of miR-27a gene in Large White and Chinese Meishan pigs, one SNP (T/C) which created an additional HpaII site was detected. Then associations of this SNP with litter size traits were assessed in Large White (n = 142) and DIV (n = 140) pig populations. The statistical analysis demonstrated that AA differed from AB (P < 0.01) and BB (P < 0.05) for total number of piglets born in the first parities, and also differed from AB (P < 0.01) for the number of piglets born alive in all parities (P < 0.05) in DIV pigs. No significant difference was observed between different genotypes in Large White pigs.     

SLCO2B1 genetic polymorphisms in a Korean population: pyrosequencing analyses and comprehensive comparison with other populations

SLCO2B1, also known as OATP2B1 (Organic Anion Transporter) or OATP-B or SLC21A9, is an organic anion uptake transporter that is encoded by the SLCO2B1 gene. In this study we assessed the frequencies of SLCO2B1 polymorphisms in a Korean population using newly developed pyrosequencing methods and compared their frequencies with those in other ethnic groups. We developed pyrosequencing methods to identify the following six SLCO2B1 non-synonymous polymorphisms: c.1175C > T (rs1621378), c.1457C > T (rs2306168), c.43C > T (rs56837383), c.935G > A (rs12422149), c.601G > A (rs35199625) and c.644A > T (rs72559740). The allele frequencies of these polymorphisms were analyzed in 227 Korean subjects. The allele frequencies of SLCO2B1 polymorphisms in the population tested were as follows: 0.0 for c.1175C > T, c.43C > T and c.644A > T; 0.2687 for c.1457C > T; 0.4273 for c.935G > A; and 0.0727 for c. 601G > A. Even though the allele frequencies of the c.1175C > T and c.1457C > T polymorphisms were comparable to those in Japanese subjects, the frequencies in this Korean population differed from those in other ethnic groups. The developed pyrosequencing methods are rapid and reliable for detecting non-synonymous SLCO2B1 polymorphisms. Large ethnic differences in the frequency of SLCO2B1 genetic polymorphisms were noted among ethnic groups. The SLCO2B1 polymorphisms at c.1175C > T, c.43C > T and c.644A > T were not found in the Korean population while c.1457C > T, c.935G > A and c.601G > A exhibited mostly higher frequencies in Koreans compared with Finnish, Caucasian and African-American populations.     

五指山猪IGF2基因5′调控区单核苷酸多态性分析

利用PCR产物直接测序法, 对五指山猪、滇南小耳猪、香猪、梅山猪和大白猪共60个样本的IGF2基因5＇调控区部分片段的单核苷酸多态性进行了研究。找到13个SNP, 分别是: C5872T、C5888T、A5976G、C6010T、T6029A、C6037T、C6043T、C6063T、C6112T、C6164T、G13520A、G13563A和G13669A。T6029A为T←→A碱基颠换, A5976G、G13520A、G13563A和G13669A为A←→G转换, 其他均为C←→T转换。针对13个SNP位点得到23种组合基因型。统计各位点等位基因和基因型以及各组合基因型在总群体与各品种内的分布频率, 发现3个小型猪在A5976G、C6164T和G13669A位点上的优势等位基因均分别为G、T和A, 而梅山猪和大白猪的优势等位基因均分别为A、C和G; H19型为3个小型猪的特征组合基因型, 而另两个猪品种为H15型。同时对123头五指山猪IGF2基因C5888T位点进行了PCR-RFLP分析, 研究表明该位点C为优势等位基因(0.8536), CC为优势基因型(0.7235)。卡方检验表明该位点处于Hardy-Weinberg平衡状态。这些结果可为五指山猪等小型猪的生长发育规律、矮小机制等方面的研究提供遗传学依据。     

Genome-wide association studies for the number of teats and teat asymmetry patterns in Large White pigs

The number of teats is a morphological trait that influences the mothering ability of the sows and thus their reproduction performances. In this study, we carried out GWASs for the total number of teats and other 12 related parameters in 821 Italian Large White heavy pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip array. For four investigated parameters (total number of teats, the number of teats of the left line, the number of teats of the right line and the maximum number of teats comparing the two sides), significant markers were identified on SSC7, in the region of the vertnin (VRTN) gene. Significant markers for the numbers of posterior teats and the absolute difference between anterior and posterior teat numbers were consistently identified on SSC6. The most significant SNP for these parameters was an intron variant in the TOX high mobility group box family member 3 (TOX3) gene. For the other four parameters (absolute difference between the two sides; anterior teats; the ratio between the posterior and the anterior number of teats; and the absence or the presence of extra teats) only suggestively significant markers were identified on several other chromosomes. This study further supported the role of the VRTN gene region in affecting the recorded variability of the number of teats in the Italian Large White pig population and identified a genomic region potentially affecting the biological mechanisms controlling the developmental programme of morphological features in pigs.     

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.     

SNPs of MYPN and TTN genes are associated to meat and carcass traits in Italian Large White and Italian Duroc pigs

Myopalladin (MYPN) and titin (TTN) play key roles in skeletal muscle structural organisation and for this reason they may be functional candidates for meat production traits in pigs. We analysed by PCR–RFLP two polymorphisms previously identified and described in the 3′UTR of MYPN and TTN genes in a group of Italian Large White (ILW) and Italian Duroc (ID) pigs with extreme divergent estimated breeding values for some production traits. Significant allele frequency differences were observed for lean cuts (LC) at the MYPN locus in ILW breed and for visible intermuscular fat (VIF) at MYPN and TTN loci in ID breed. Moreover, association analysis between the two genes and some production traits (average daily gain, LC, backfat thickness, ham weight, feed conversion ratio and VIF) was performed in a sample of 409 ILW and 381 ID pigs. On the whole, the results showed significant effects of both genes on some of the considered traits in ID breed, and for TTN gene in ILW animals. These results indicate that both genes can be considered as candidates for meat and carcass traits in ID 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.     

Evaluation of the causality of the low‐density lipoprotein receptor gene (LDLR) for serum lipids in pigs

A significant quantitative trait locus (QTL) for low‐density lipoprotein cholesterol (LDL‐C) and total cholesterol (TC) was identified around the LDLR gene on chromosome 2 (SSC2) in a White Duroc × Erhualian F₂ resource population and Sutai pigs in our previous study. However, in previous reports, the causality of LDLR with serum lipids is controversial in pigs. To systematically assess the causality of LDLR with serum lipids, association analyses were successively performed in three populations: Sutai pigs, a White Duroc × Erhualian F₂ resource population and a Duroc × (Landrace × Large White) population. We first performed a haplotype‐based association study with 60K SNP genotyping data and evidenced the significant association with LDL‐C and TC around the LDLR gene region. We also found that there is more than one QTL for LDL‐C and TC on SSC2. Then, we evaluated the causalities of two missense mutations, c.1812C>T and c.1520A>G, with LDL‐C and TC. We revealed that the c.1812C>T SNP showed the strongest association with LDL‐C (P = 5.40 × 10^?11) and TC (P = 3.64 × 10^?8) and explained all the QTL effect in Sutai pigs. Haplotype analysis found that two missense SNPs locate within a 1.93‐Mb haplotype block. One major haplotype showed the strongest significant association with LDL‐C (P = 4.62 × 10^?18) and TC (P = 1.06 × 10^?9). However, the c.1812C>T SNP was not identified in the White Duroc × Erhualian intercross, and the association of c.1520A>G with both LDL‐C and TC did not achieve significance in this F₂ population, suggesting population heterogeneity. Both missense mutations were identified in the Duroc × (Landrace × Large White) population and showed significant associations with LDL‐C and TC. Our data give evidence that the LDLR gene should be a candidate causative gene for LDL‐C and TC in pigs, but heterogeneity exists in different populations.