Fine mapping and imprinting analysis for fatness trait QTLs in pigs

Quantitative trait loci (QTL) for fatness traits were reported recently in an experimental Meishan × Large White and Landrace F₂ cross. To further investigate the regions on pig Chr 2 (SSC2), SSC4, and SSC7, 25 additional markers from these regions were typed on 800 animals (619 F₂ animals, their F₁ parents, and F₀ grandfathers). Compared with the published maps, a modified order of markers was observed for SSC4 and SSC7. QTL analyses were performed both within the half-sib families as well as across families (line cross). Furthermore, a QTL model accounting for imprinting effects was tested. Information content could be increased considerably on all three chromosomes. Evidence for the backfat thickness QTL on SSC7 was increased, and the location could be reduced to a 33-cM confidence interval. The QTL for intramuscular fat on SSC4 could not be detected in this half-sib analysis, whereas under the line cross model a suggestive QTL on a different position on SSC4 was detected. For SSC2, in the half-sib analysis, a suggestive QTL for backfat thickness was detected with the best position at 26 cM. Imprinting analysis, however, revealed a genome-wise, significant, paternally expressed QTL on SSC2 with the best position at 63 cM. Our results suggest that this QTL is different from the previously reported paternally expressed QTL for muscle mass and fat deposition on the distal tip of SSC2p. Received: 15 October 1999 / Accepted: 21 February 2000     

Quantitative trait loci analysis of a Duroc commercial population highlights differences in the genetic determination of meat quality traits at two different muscles

We performed a whole‐genome scan with 110 informative microsatellites in a commercial Duroc population for which growth, fatness, carcass and meat quality phenotypes were available. Importantly, meat quality traits were recorded in two different muscles, that is, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), to find out whether these traits are determined by muscle‐specific genetic factors. At the whole‐population level, three genome‐wide QTL were identified for carcass weight (SSC7, 60 cM), meat redness (SSC13, 84 cM) and yellowness (SSC15, 108 cM). Within‐family analyses allowed us to detect genome‐wide significant QTL for muscle loin depth between the 3rd and 4th ribs (SSC15, 54 cM), backfat thickness (BFT) in vivo (SSC10, 58 cM), ham weight (SSC9, 69 cM), carcass weight (SSC7, 60 cM; SSC9, 68 cM), BFT on the last rib (SSC11, 48 cM) and GM redness (SSC8, 85 cM; SSC13, 84 cM). Interestingly, there was low positional concordance between meat quality QTL maps obtained for GM and LTL. As a matter of fact, the three genome‐wide significant QTL for colour traits (SSC8, SSC13 and SSC15) that we detected in our study were all GM specific. This result suggests that QTL effects might be modulated to a certain extent by genetic and environmental factors linked to muscle function and anatomical location.     

QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive,dominant and epistatic effects

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.     

Quantitative gene expression analysis on chromosome 6 between Korean native pigs and Yorkshire breeds for fat deposition

Pig chromosome 6 (SSC6) has been reported to have QTL affecting backfat thickness (BFT) and intramuscular fat (IMF). A human-pig comparative map covering 18 autosomes with the highest resolution has been constructed and based on this map SSC6 has conserved syntenicgroups with human chromosome (HSA) 16, 19, 1, and 18. In this study, the pig Affy elements mapped to the SSC6 were analyzed, and the differentially expressed genes in three tissues (liver, backfat and loin muscle) between Yorkshire and Korean Native Pigs (KNP) were collected, in particular those genes located in the internal between markers SW1355 and SW1823 where a quantitative trait loci (QTL) affecting the intramuscular fat content (IMF) have been detected in multiple pig populations. The genes listed here may offer information for further study the candidate genes affecting these QTL on the expression level.     

Haplotype sharing refines the location of an imprinted quantitative trait locus with major effect on muscle mass to a 250-kb chromosome segment containing the porcine IGF2 gene

We herein describe the fine mapping of an imprinted QTL with major effect on muscle mass that was previously assigned to distal SSC2p in the pig. The proposed approach exploits linkage disequilibrium in combination with QTL genotyping by marker-assisted segregation analysis. By identifying a haplotype shared by all "Q" chromosomes, we map the QTL to an approximately 250-kb chromosome segment containing INS and IGF2 as the only known paternally expressed genes. This considerably reinforces the candidacy of these genes, justifying their detailed analysis.     

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

Porcine MYOD1 gene has been mapped to swine chromosome (SSC) 2p14-p17, which is involved in the regulation of the proliferation and differentiation of skeletal muscle cells. The LDHA (lactate dehydrogenase A) and COPB1 (coatomer protein complex, subunit beta 1) genes, which map close to MYOD1, are involved in energy metabolism and protein transport processes. Both genes might play important roles in muscle development. However, little is known about the porcine LDHA and COPB1 genes. In the present study, the full-length cDNA of these two genes were cloned. The mapping results demonstrated that porcine LDHA and COPB1 were all mapped to SSC 2p14-p17. In this region, there are several QTL for growth and carcass traits, including average backfat thickness, lean and fat percentage. The RT-PCR results revealed that both LDHA and COPB1 were highly expressed in porcine skeletal muscle tissues, implying their potential regulatory function of muscle development. LDHA and COPB1 were then mapped to the region and multipoint analyses generated a best sex-averaged map order of each gene between linked markers: MYOD1_75.2 cM _LDHA_79 cM _CSRP3_83.8 cM _TEF-1_86.5 cM _COPB1_90 cM. Association analyses revealed that the substitution of c.423A>G had a significant effect on average daily gain on test, average backfat thickness (BFT), loin muscle area, lumbar BFT, marbling score, tenth rib BFT, average drip loss and fiber type II ratio. The substitution of c.3096C>T had a significant effect on average BFT, lumbar BFT, tenth rib BFT, carcass weight and last rib BFT. Interestingly, both SNPs were all associated with average BFT, lumbar BFT and tenth rib BFT.     

Number and mode of inheritance of QTL influencing backfat thickness on SSC2p in Sino-European pig pedigrees

Background

In the pig, multiple QTL associated with growth and fatness traits have been mapped to chromosome 2 (SSC2) and among these, at least one shows paternal expression due to the IGF2-intron3-G3072A substitution. Previously published results on the position and imprinting status of this QTL disagree between analyses from French and Dutch F2 crossbred pig populations obtained with the same breeds (Meishan crossed with Large White or Landrace).

Methods

To study the role of paternal and maternal alleles at the IGF2 locus and to test the hypothesis of a second QTL affecting backfat thickness on the short arm of SSC2 (SSC2p), a QTL mapping analysis was carried out on a combined pedigree including both the French and Dutch F2 populations, on the progeny of F1 males that were heterozygous (A/G) and homozygous (G/G) at the IGF2 locus. Simulations were performed to clarify the relations between the two QTL and to understand to what extent they can explain the discrepancies previously reported.

Results

The QTL analyses showed the segregation of at least two QTL on chromosome 2 in both pedigrees, i.e. the IGF2 locus and a second QTL segregating at least in the G/G F1 males and located between positions 30 and 51 cM. Statistical analyses highlighted that the maternally inherited allele at the IGF2 locus had a significant effect but simulation studies showed that this is probably a spurious effect due to the segregation of the second QTL.

Conclusions

Our results show that two QTL on SSC2p affect backfat thickness. Differences in the pedigree structures and in the number of heterozygous females at the IGF2 locus result in different imprinting statuses in the two pedigrees studied. The spurious effect observed when a maternally allele is present at the IGF2 locus, is in fact due to the presence of a second closely located QTL. This work confirms that pig chromosome 2 is a major region associated with fattening traits.     

Interval mapping of carcass and meat quality traits in a divergent swine cross.

An autosomal scan of the swine genome with 119 polymorphic microsatellite (ms) markers and data from 116 F2 barrows of the University of Illinois Meishan x Yorkshire Swine Resource Families identified genomic regions with effects on variance in carcass composition and meat quality at nominal significance (p-value <0.05). Marker intervals on chromosomes 1, 6, 7, 8 and 12 (SSC1, SSC6, SSC7, SSC8, SSC12) with phenotypic effects on carcass length, 10th rib backfat thickness, average backfat thickness, leaf fat, loin eye area and intramuscular fat content confirm QTL effects identified previously based on genome wide significance (p-value <0.05). Several marker intervals included nominally significant (p-value <0.05) dominance effects on leaf fat, 10th rib backfat thickness, loin eye area, muscle pH and intramuscular fat content.     

A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population

We performed a genome-wide QTL scan for production traits in a line cross between Duroc and Pietrain breeds of pigs, which included 585 F(2) progeny produced from 31 full-sib families genotyped with 106 informative microsatellites. A linkage map covering all 18 autosomes and spanning 1987 Kosambi cM was constructed. Thirty-five phenotypic traits including body weight, growth, carcass composition and meat quality traits were analysed using least square regression interval mapping. Twenty-four QTL exceeded the genome-wide significance threshold, while 47 QTL reached the suggestive threshold. These QTL were located at 28 genomic regions on 16 autosomal chromosomes and QTL in 11 regions were significant at the genome-wide level. A QTL affecting pH value in loin was detected on SSC1 between marker-interval S0312-S0113 with strong statistical support (P < 3.0 x 10(-14)); this QTL was also associated with meat colour and conductivity. QTL for carcass composition and average daily gain was also found on SSC1, suggesting multiple QTL. Seventeen genomic segments had only a single QTL that reached at least suggestive significance. Forty QTL exhibited additive inheritance whereas 31 QTL showed (over-) dominance effects. Two QTL for trait backfat thickness were detected on SSC2; a significant paternal effect was found for a QTL in the IGF2 region while another QTL in the middle of SSC2 showed Mendelian expression.     

Linked and pleiotropic QTLs influencing carcass composition traits detected on porcine chromosome 7

A multivariate QTL detection was carried out on fatness and carcass composition traits on porcine chromosome 7 (SSC7). Single-trait QTLs have already been detected in the SLA region, and multivariate approaches have been used to exploit the correlations between the traits to obtain more information on their pattern: almost 500 measurements were recorded for backfat thickness (BFT1, BFT2), backfat weight (BFW) and leaf fat weight (LFW) but only about half that number for intramuscular fat content (IMF), affecting the detection. First, groups of traits were selected using a backward selection procedure: traits were selected based on their contribution to the linear combination of traits discriminating the putative QTL haplotypes. Three groups of traits could be distinguished based on successive discriminant analyses: external fat (BFT1, BFT2), internal fat (LFW, IMF) and BFW. At least four regions were distinguished, preferentially affecting one or the other group, with the SLA region always influencing all the traits. Meishan alleles decreased all trait values except IMF, confirming an opportunity for marker-assisted selection to improve meat quality with maintenance of carcass composition based on Meishan alleles.     

Detection of quantitative trait loci for carcass composition traits in pigs

A quantitative trait locus (QTL) analysis of carcass composition data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained.     

Quantitative trait loci mapping for fatty acid contents in the backfat on porcine chromosomes 1, 13, and 18

A partial genome scan using microsatellite markers was conducted in order to detect quantitative trait loci (QTLs) for 10 fatty acid contents of the backfat in a pig reference population. Two QTLs were found by studying SSC1, SSC13, and SSC18, where QTLs had already been identified for backfat thickness. A QTL was located between marker loci S0113 and SW974 on chromosome 1; this QTL was only significantly detected (P < 0.05) for linoleic acid. The other QTL was discovered between markers S0062 and S0120 on chromosome 18, and its significance only showed (P < 0.05) for myristic acid. The two QTLs mapped to the same location as the backfat thickness QTL. A third of the phenotypic variation was explained for linoleic acid by the QTL on chromosome 1, and a quarter for myristic acid by the QTL on chromosome 18. Further studies on fine mapping and positional comparative candidate gene analyses will be the next step toward a better understanding of the genetic architecture of fatty acid contents.     

Genomic regions affecting backfat thickness and cannon bone circumference identified by genome‐wide association study in a Duroc pig population

We performed a genome‐wide association study using the porcine 60K SNP array to detect QTL regions for nine traits in a three‐generational Duroc samples (n = 651), viz. generations 1, 2 and 3 from a population selected over five generations using a closed nucleus breeding scheme. We applied a linear mixed model for association mapping to detect SNP effects, adjusting for fixed effects (sex and season) and random polygenic effects (reflecting genetic relatedness), and derived a likelihood ratio statistic for each SNP using the efficient mixed‐model association method. We detected a region on SSC6 for backfat thickness (BFT) and on SSC7 for cannon bone circumference (CANNON), with a genome‐wide significance of P < 0.01 after Bonferroni correction. These regions had been detected previously in other pig populations. Six genes are located in the BFT‐associated region, while the CANNON‐associated region includes 66 genes. In the future, significantly associated SNPs, derived by sequencing the coding regions of the six genes in the BFT region, can be used in marker‐assisted selection of BFT, whereas haplotypes constructed from the SSC7 region with strong LD can be used to select for the CANNON trait in our resource family.     

Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2 population

A whole-genome scan was performed on 660 F₂ animals including 250 barrows and 410 gilts in a White Duroc × Erhualian intercross population to detect quantitative trait loci (QTL) for fatty acid composition in the longissimus dorsi muscle and abdominal fat. A total of 153 QTL including 63 genome-wide significant QTL and 90 suggestive effects were identified for the traits measured. Significant effects were mainly evident on pig chromosomes (SSC) 4, 7, 8 and X. No association was detected on SSC3 and 11. In general, the QTL detected in this study showed distinct effects on fatty acid composition in the longissimus muscle and abdominal fat. The QTL for fatty acid composition in abdominal fat did not correspond to those identified previously in backfat and the majority of QTL for the muscle fatty acid composition were mapped to chromosomal regions different from previous studies. Two regions on SSC4 and SSC7 showed significant pleiotropic effects on monounsaturated (MUFA) and polyunsaturated fatty acid (PUFA) in both longissimus muscle and abdominal fat. Another two QTL with significant multi-faceted effects on MUFA and PUFA in the longissimus muscle were found each on SSC8 and SSCX. Chinese Erhualian alleles were associated with increased ratios of MUFA to saturated fatty acid at most of the QTL detected, showing beneficial effect in terms of human health.     

A high-resolution comparative RH map of porcine Chromosome (SSC) 2

A high-resolution comparative map was constructed for porcine Chromosome (SSC) 2, where a QTL for back fat thickness (BFT) is located. A radiation hybrid (RH) map containing 33 genes and 25 microsatellite markers was constructed for this chromosome with a 3000-rad porcine RH panel. In total, 16 genes from human Chromosome (HSA) 11p, HSA19p, and HSA5q were newly assigned to SSC2. One linkage group was observed at LOD 3.0, and five linkage groups at LOD 4.0. Comparison of the porcine RH map with homologous human gene orders identified four conserved segments between SSC2 and HSA11, HSA19, and HSA5. Concerning HSA11, a rearrangement of gene order is observed. The segment HSA11p15.4-q13 is inverted on SSC2 when compared with the distal tip of SSC2p, which is homologous to HSA11p15.5. The boundaries of the conserved segments between human and pig were defined more precisely. This high-resolution comparative map will be a valuable tool for further fine mapping of the QTL area. Received: 10 November 2000 / Accepted: 23 January 2001     

A QTL affecting daily feed intake maps to Chromosome 2 in pigs

Our understanding of the molecular genetic basis of several key performance traits in pigs has been significantly advanced through the quantitative trait loci (QTL) mapping approach. However, in contrast to growth and fatness traits, the genetic basis of feed intake traits has rarely been investigated through QTL mapping. Since feed intake is an important component of efficient pig production, the identification of QTL affecting feed intake may lead to the identification of genetic markers that can be used in selection programs. In this study a QTL analysis for feed intake, feeding behavior, and growth traits was performed in an F₂ population derived from a cross between Chinese Meishan and European Large White pigs. A QTL with a significant effect on daily feed intake (DFI) was identified on Sus scrofa Chromosome 2 (SSC2). A number of suggestive QTL with effects on daily gain, feed conversion, and feeding behavior traits were also located. The significant QTL lies close to a previously identified mutation in the insulin-like growth factor 2 gene (IGF2) that affects carcass composition traits, although the IGF2 mutation is not segregating in the populations analyzed in the current study. Therefore, a distinct causal variant may exist on the P arm of SSC2 with an effect on feed intake.     

Detection of quantitative trait loci for growth- and fatness-related traits in a large-scale White Duroc × Erhualian intercross pig population

Growth and fatness are economically important traits in pigs. In this study, a genome scan was performed to detect quantitative trait loci (QTL) for 14 growth and fatness traits related to body weight, backfat thickness and fat weight in a large-scale White Duroc × Erhualian F(2) intercross. A total of 76 genome-wide significant QTL were mapped to 16 chromosomes. The most significant QTL was found on pig chromosome (SSC) 7 for fatness with unexpectedly small confidence intervals of ～2 cM, providing an excellent starting point to identify causal variants. Common QTL for both fatness and growth traits were found on SSC4, 5, 7 and 8, and shared QTL for fat deposition were detected on SSC1, 2 and X. Time-series analysis of QTL for body weight at six growth stages revealed the continuously significant effects of the QTL on SSC4 at the fattening period and the temporal-specific expression of the QTL on SSC7 at the foetus and fattening stages. For fatness traits, Chinese Erhualian alleles were associated with increased fat deposition except that at the major QTL on SSC7. For growth traits, most of White Duroc alleles enhanced growth rates except for those at three significant QTL on SSC6, 7 and 9. The results confirmed many previously reported QTL and also detected novel QTL, revealing the complexity of the genetic basis of growth and fatness in pigs.     

Indirect effect of IGF2 intron3 g.3072G>A mutation on prolificacy in sows

A QTL located in the paternally expressed insulin-like growth factor 2 (IGF2) gene is known to increase muscle growth and reduce fat deposition in pigs. This makes the QTL in IGF2 a good marker for use in pig breeding programmes. However, care has to be taken as it is postulated that increased leanness and lowered fat deposition may have a negative effect on the prolificacy and longevity of sows. Selection of sire and dam lines for different alleles of the mutation in the paternally imprinted IGF2 gene could actually provide a solution to this problem. Therefore, in this study, the effect of the IGF2 QTL on prolificacy-related traits in sows was investigated. It was found that the paternal IGF2 wild-type allele was associated with higher reproduction performance in the sow. Moreover, it was also examined whether the difference in prolificacy in sows could be a consequence of differential IGF2 expression in the ovarian follicles of the sow or whether it is mainly a secondary effect caused by differences in fatness traits. Therefore, IGF2 expression was measured in follicles of different sizes from sows with different genotypes for the paternal IGF2 allele. It was observed that, however, while the size of the follicles was associated with follicular IGF2 expression level, the IGF2 genotype was not. It could be concluded that the difference in prolificacy of sows with a different paternal IGF2 genotype could be a secondary effect, resulting from differences in fat deposition.