Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar x Large White intercross

An assessment of genomic connectedness measures in Nellore cattle

An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness: the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile data set from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 to 1.707, and CD from 0.146 to 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds.

Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig

Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.

Mapping and Validating QTL for Fatty Acid Compositions and Growth Traits in Asian Seabass

Asian seabass is an important food fish species. While improving growth, increasing the nutritional value is important, omega-3 fatty acids are indispensable to human health. Identifying and validating DNA markers associated with traits is the first step towards marker-assisted selection (MAS). We quantified 13 different fatty acids and three growth traits in 213 F₂ Asian seabass from a family at the age 270 days post hatch, and screened QTL for these traits. The content of total fatty acids in 100 g flesh was 2.57 ± 0.80 g, while the proportions of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 16.96 ± 2.20% and 5.42 ± 0.90%, respectively. A linkage map with 2424 SNPs was constructed and used for QTL mapping. For fatty acid compositions, 14 significant QTL were identified on three linkage groups (LG5, LG11 and LG14), with phenotypic variance explained (PVE) from 12.8 to 24.6%. Thirty-nine suggestive QTL were detected on 16 LGs. Two significant QTL for EPA were identified on LG5 and LG14, with PVE of 15.2% and 15.1%, respectively. No significant QTL was identified for DHA. For growth traits, six significant and 13 suggestive QTL were identified on two and seven LGs, respectively. Only a few significant QTL for fatty acids overlapped with previously mapped QTL for these traits, suggesting that most QTL detected in a family are family-specific and could only be used in MAS in the family per se. To facilitate population-wide molecular breeding, more powerful methods (e.g. GWAS) should be used to identify SNPs for genomic selection.

Relationship among ovarian follicular status, developmental competence of oocytes, and anti-Müllerian hormone levels: A comparative study in Japanese wild boar crossbred gilts and Large White gilts

The aim of this study was to investigate the ovarian follicular development, developmental competence of oocytes, and plasma anti-Müllerian hormone (AMH) levels of Japanese wild boar crossbred (wild hybrid) gilts, whose litter size is inferior to that of European breeds. Ovary and plasma samples were collected from two different breeds of gilts (wild hybrid and Large White breeds). The ovaries from the wild hybrid gilts had a lower average numbers of secondary follicles and vesicular follicles in ovarian cross-sections and of good quality oocytes collected from ovarian follicles as compared with those from Large White gilts (p < 0.05). The development rate to the blastocyst stage of good quality oocytes after in vitro maturation, fertilization and culture was also lower (p < 0.05) in wild hybrid gilts than in Large White gilts. Plasma AMH levels with >0.16 ng/ml were detected in 8.3% of the examined wild hybrid gilts and 33% of the Large White gilts. These results indicate that the low reproductive performance of wild hybrid breed may result in part from low numbers of vesicular follicles and good quality oocytes, and low developmental competence of oocytes. Moreover, plasma AMH levels may support low number of vesicular follicles in ovaries of wild hybrid gilts.

Comparison of fatty acid profile of three adipose tissues in Ningxiang pigs

The present study is conducted to determinate fatty acids (FA) composition in 3 adipose tissues. Subcutaneous and perirenal adipose tissues were prepared from 24 Ningxiang castrated boars and 24 castrated gilts fattened by a traditional diet for 56 d, respectively. The results showed that the FA profile in the 3 adipose tissues (dorsal subcutaneous adipose [DSA], abdominal subcutaneous adipose [ASA], and perirenal adipose [PA]) differed greatly. In boars, the proportions of oleic acid (c18:1n9c) (P < 0.05), cis-11-20c acid (c20:1) (P < 0.05), and α-linolenic acid (c18:3n3) (P < 0.05) in DSA were the highest among 3 adipose tissues, whereas palmitic acid (c16:0) (P < 0.05) and stearic acid (c18:0) (P < 0.05) in DSA had the lowest proportion. In gilts, cis-11-20c acid (c20:1) (P < 0.05) in DSA was the highest, while stearic acid (c18:0) (P < 0.05) in subcutaneous adipose was the lowest among these deposits. Overall, the results indicate that from external to inner carcass of boars, the sum of saturated fatty acids (SFA) increase, but the sum of monounsaturated fatty acids (MUFA) decrease, while ASA of gilts have the greatest proportion of MUFA and the lowest SFA. Sex and adipose locations as significant effects on the FA profile are interaction.

Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs

Background

Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace.

Results

Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7.

Conclusions

This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3752-0) contains supplementary material, which is available to authorized users.

Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs

OBJECTIVE

This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F₂ intercross between Landrace and Korean native pigs.

METHODS

Eighteen FA composition traits were measured in more than 960 F₂ progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes.

RESULTS

We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10^-39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance.

CONCLUSION

Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD) gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.

Mapping quantitative trait loci for omega-3 fatty acids in Asian seabass

Omega-3 fatty acids are essential fatty acids for human health. Therefore, increasing both percentage of omega-3 and a better fatty acid profile in fish fillets is one of the breeding goals in aquaculture. However, it is difficult to increase the omega-3 content in fish fillets, as the phenotypic selection of these traits is not easily feasible. To facilitate the genetic improvement of the Asian seabass for optimal fatty acid profiles, a genome-wide scan for quantitative trait loci (QTL) affecting fatty acid level in the flesh of the Asian seabass was performed on an F2 family containing 314 offspring. All family members were genotyped using 123 informative microsatellites and 22 SNPs. High percentages of n-3 polyunsaturated fatty acids (PUFA), especially C22:6 (DHA 16.48 ± 3.09 %) and C20:5 (EPA 7.19 ± 0.86 %) were detected in the flesh. One significant and 54 suggestive QTL for different fatty acids and a water content trait were detected on the whole genome. QTL for C18:0b was located on linkage groups (LG) 5. QTL for total n-3 PUFA content in flesh were mapped onto LG6 and LG23 with the phenotypic variance explained ranging from 3.8 to 6.3 %. Four QTL for C22:6 were detected on LG6, LG23, and LG24, explaining 3.9 to 4.9 % of the phenotypic variance, respectively. Mapping of QTL for contents of different fatty acids is the first step towards improving the omega-3 content in the fillets of fish by using marker-assisted selection and is important for understanding the biology of fatty acid deposition.

Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data

Background

Porcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to point out different genetic control of fatty acid composition conditional on the fat deposits. Those studies have been conducted using simple approaches and most of them focused on one single tissue. The first objective of the present study was to identify tissue-specific and tissue-consistent QTLs for fatty acid composition in backfat and intramuscular fat, combining linkage mapping and GWAS approaches and conducted under single and multitrait models. A second aim was to identify powerful candidate genes for these tissue-consistent QTLs, using microarray gene expression data and following a targeted genetical genomics approach.

Results

The single model analyses, linkage and GWAS, revealed over 30 and 20 chromosomal regions, 24 of them identified here for the first time, specifically associated to the content of diverse fatty acids in BF and IMF, respectively. The analyses with multitrait models allowed identifying for the first time with a formal statistical approach seven different regions with pleiotropic effects on particular fatty acids in both fat deposits. The most relevant were found on SSC8 for C16:0 and C16:1(n-7) fatty acids, detected by both linkage and GWAS approaches. Other detected pleiotropic regions included one on SSC1 for C16:0, two on SSC4 for C16:0 and C18:2, one on SSC11 for C20:3 and the last one on SSC17 for C16:0. Finally, a targeted eQTL scan focused on regions showing tissue-consistent effects was conducted with Longissimus and fat gene expression data. Some powerful candidate genes and regions were identified such as the PBX1, RGS4, TRIB3 and a transcription regulatory element close to ELOVL6 gene to be further studied.

Conclusions

Complementary genome scans have confirmed several chromosome regions previously associated to fatty acid composition in backfat and intramuscular fat, but even more, to identify new ones. Although most of the detected regions were tissue-specific, supporting the hypothesis that the major part of genes affecting fatty acid composition differs among tissues, seven chromosomal regions showed tissue-consistent effects. Additional gene expression analyses have revealed powerful target regions to carry the mutation responsible for the pleiotropic effects.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-845) contains supplementary material, which is available to authorized users.

Genome-wide copy number variations inferred from SNP genotyping arrays using a Large White and Minzhu intercross population

Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained 249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.

Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues

Fatty acid composition is an important phenotypic trait in pigs as it affects nutritional, technical and sensory quality of pork. Here, we reported a genome-wide association study (GWAS) for fatty acid composition in the longissimus muscle and abdominal fat tissues of 591 White Duroc×Erhualian F2 animals and in muscle samples of 282 Chinese Sutai pigs. A total of 46 loci surpassing the suggestive significance level were identified on 15 pig chromosomes (SSC) for 12 fatty acids, revealing the complex genetic architecture of fatty acid composition in pigs. Of the 46 loci, 15 on SSC5, 7, 14 and 16 reached the genome-wide significance level. The two most significant SNPs were ss131535508 (P = 2.48×10(-25)) at 41.39 Mb on SSC16 for C20∶0 in abdominal fat and ss478935891 (P = 3.29×10(-13)) at 121.31 Mb on SSC14 for muscle C18∶0. A meta-analysis of GWAS identified 4 novel loci and enhanced the association strength at 6 loci compared to those evidenced in a single population, suggesting the presence of common underlying variants. The longissimus muscle and abdominal fat showed consistent association profiles at most of the identified loci and distinct association signals at several loci. All loci have specific effects on fatty acid composition, except for two loci on SSC4 and SSC7 affecting multiple fatness traits. Several promising candidate genes were found in the neighboring regions of the lead SNPs at the genome-wide significant loci, such as SCD for C18∶0 and C16∶1 on SSC14 and ELOVL7 for C20∶0 on SSC16. The findings provide insights into the molecular basis of fatty acid composition in pigs, and would benefit the final identification of the underlying mutations.

Association analysis with lipid traits of 2 candidate genes (LRP12 and TRIB1) mapping to a SSC4 QTL for serum triglyceride concentration in pigs

The performance of a genome scan for serum lipid traits at 45 and 190 d in 5 half-sib families of Duroc pigs allowed us to detect several pig chromosomal regions with significant effects on these phenotypes. In the current work, we aimed to refine the position of 1 chromosome 4 (SSC4) genome-wide significant QTL for serum triglyceride concentration at 190 d. Genotyping of 4 additional microsatellites allowed reduction of the 90% confidence interval of this QTL to the genomic interval between markers SW2409 and SW839. Sequencing experiments were performed to characterize the variability of 2 lipid-related genes, the lipoprotein receptor-related protein 12 (LRP12) and tribbles homolog 1 (TRIB1) loci, that map to this region. In this way, 2 (c.771A > G and c.1101A > G) and 1 (c.*156_157del) polymorphisms were identified at the LRP12 coding region and TRIB1 3' untranslated region, respectively. Association analyses between LRP12 and TRIB1 genotypes did not reveal any significant effect on serum lipid concentrations, suggesting that variation of these two loci does not explain the segregation of the SSC4 QTL. However, highly significant associations were observed for gluteus medius saturated fatty acid content (LRP12 c.1101A > G, P = 0.0006; TRIB1 c.*156_157del, P = 0.0003). In the light of these and other findings, the potential involvement of LRP12 and TRIB1 in muscle lipid metabolism deserves to be further explored.

Meat from wild boar (Sus scrofa L.): a review

Wild boar is a species that is utilised for food and sport hunting throughout the world. Recent increases in natural populations and the potential of farming wild boars have stimulated interest in this species as a meat producer. Compared to domestic pigs, wild boars present a higher degree of carcass fatness and larger loin areas, more slow-twitch oxidative (I) and fast-twitch oxidative glycolytic (IIA) and less fast-twitch glycolytic (IIB) muscle fibres, and darker, less tender and leaner meat. Differences in diets might contribute to differences in cooked meat flavour and fatty acid composition between wild boars and domestic pigs. Higher α-tocopherol concentrations in wild boar might extend its meat shelf-life. Mechanical massaging of muscles, vacuum package ageing and addition of marinates have been attempted to tenderise wild boar meat. Further research on hunting protocols for wild boar, and value-added products from its meat, are needed.

Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs

Genetic parameters such as heritability and correlations of fat traits in a Duroc population were dissected using molecular markers. The heritabilities of intramuscular fat in 2 muscles, the gluteus medius and LM, and back fat were 0.54, 0.48, and 0.23, respectively. The genetic correlations were well estimated with standardized SNP effects, being 0.65 between intramuscular fat traits and ∼0.37 between any intramuscular fat trait and back fat. Genetic correlations were overestimated when ignoring molecular information. Twelve chromosomes showed additive genetic variance for intramuscular fat compared with 8 for back fat. Population structure was accommodated using 4 different models. The number of significant, P < 5 × 10(-5) (suggestive, P < 2 × 10(-3)), SNP varied across models and ranged from 0 to 4 (2 to 261) for intramuscular fat in the gluteus medius, from 0 to 57 (9 to 564) for intramuscular fat in the LM, and from 3 to 4 (22 to 168) for back fat. Several SNP showed significant deviations from an additive mode of action. Only 2 SNP significantly affected 2 traits simultaneously.

Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data

Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content.

Mapping quantitative trait loci for metabolic and cytological fatness traits of connected F2 crosses in pigs

In the present study 3 connected F(2) crosses were used to map QTL for classical fat traits as well as fat-related metabolic and cytological traits in pigs. The founder breeds were Chinese Meishan, European Wild Boar, and Pietrain with to some extent the same founder animals in the different crosses. The different selection history of the breeds for fatness traits as well as the connectedness of the crosses led to a high statistical power. The total number of F(2) animals varied between 694 and 966, depending on the trait. The animals were genotyped for around 250 genetic markers, mostly microsatellites. The statistical model was a multi-allele, multi-QTL model that accounted for imprinting. The model was previously introduced from plant breeding experiments. The traits investigated were backfat depth and fat area as well as relative number of fat cells with different sizes and 2 metabolic traits (i.e., soluble protein content as an indicator for the level of metabolic turnover and NADP-malate dehydrogenase as an indicator for enzyme activity). The results revealed in total 37 significant QTL on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 14, 17, and 18, with often an overlap of confidence intervals of several traits. These confidence intervals were in some cases remarkably small, which is due to the high statistical power of the design. In total, 18 QTL showed significant imprinting effects. The small and overlapping confidence intervals for the classical fatness traits as well as for the cytological and metabolic traits enabled positional and functional candidate gene identification for several mapped QTL.

Molecular characterization and expression patterns of Lbx1 in porcine skeletal muscle

Ladybird-like genes were recently identified in mammals. The first member characterized, Lbx1, is expressed in developing skeletal muscle and the nervous system. However, little is known about the porcine Lbx1 gene. In the present study, we cloned and characterized Lbx1 from porcine muscle. RT-PCR analyses showed that Lbx1 was highly expressed in porcine skeletal muscle tissues. And we provide the first evidence that Lbx1 has a certain regulated expression pattern during the postnatal period of the porcine skeletal muscle development. Lbx1 gene expressed at higher levels in biceps femoris muscles compared with masseter, semitendinosus and longissimus dorsi muscles in Meishan pigs. Phylogenetic tree was constructed by aligning the amino acid sequences of different species. Moreover, single nucleotide polymorphism (SNP) scanning in the Lbx1 genomic fragment identified two mutations, g.752A>G and g.-1559C>G. Association analysis in our experimental pig populations showed that the mutation of g.752A>G was significantly associated with loin muscle area (P<0.05) and internal fat rate (P<0.05). Our results suggest that the Lbx1 gene might be a candidate gene of carcass traits and provide useful information for further studies on its roles in porcine skeletal muscle.

Analysis of the mouse high-growth region in pigs

In the mouse, homozygous animals for the high growth mutation show a 30-50% increase in growth without becoming obese. This region is homologous to the distal part of pig chromosome 5 (SSC5). A previous genome scan detected several quantitative trait loci (QTL) in this region for body composition and meat quality using a three generation Berkshire x Yorkshire resource family. In this study, the effects on swine growth, fat and meat quality traits of three genes previously identified within the mouse high growth region were analysed. The genes studied were CASP2 and RIPKI domain containing adaptor with death domain (CRADD), suppressor of cytokine signalling 2 (SOCS2) and plexinC1 (PLXNC1). In addition, the influence of two other genes located very close to this region, namely the plasma membrane calcium-transporting ATPase 1 (ATP2B1) and dual specificity phosphatase 6 (DUSP6) genes, was also investigated. Single nucleotide polymorphisms were identified and used to map these genes to the QTL region on SSC5. Results indicate significant associations between these genes and several phenotypic traits, including fat deposition and growth in pigs. The present study suggests associations of these genes with swine fat and growth related traits, but further studies are needed in order to clearly identify the genes involved in the regulation of the QTL located on SSC5.

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

BACKGROUND

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH).

RESULTS

Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming.

CONCLUSION

This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

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

A whole-genome scan was performed on 660 F(2) animals including 250 barrows and 410 gilts in a White Duroc x 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.

Characterization of the porcine differentially expressed PDK4 gene and association with meat quality

To investigate the differential expression of genes in the skeletal muscle between Yorkshire and Chinese indigenous breed Meishan pigs, suppression subtractive hybridization was carried out and many genes were proved to be expressed significantly different in the two breeds. One gene highly expressed in Meishan but lowly expressed in Yorkshire specific library, shared strong homology with human pyruvate dehydrogenase kinase 4 (PDK4). Using semi-quantity and quantity PCR, We confirmed its differential expression between the two breeds. Temporal and spatial expression analysis indicated that porcine PDK4 gene is highly expressed in skeletal muscle and the highest in neonatal pigs. Complete cDNA cloning and sequence analysis revealed that porcine PDK4 gene contains an open reading frame of 1,221 bp. The deduced amino acid sequence showed conservation in evolution. A G/A mutation in intron 9 was identified and association analysis showed that it was significantly associated with intramuscular fat, muscle water content.

Pork Fat Composition of Male Hybrids from Lithuanian Indigenous Wattle Pigs and Wild Boar Intercross

The aim of this study was to compare the fatty acid composition of lipids from hybrids of Lithuanian indigenous wattle pigs × wild boar (WB) intercross. A total of 39 entire and castrated males from 1/4 and 1/2 WB genotype were included into the study. The fatness of carcasses from ½ WB genotype ( p<0.01) and castrated males ( p<0.01) was higher than that from 1/4 WB genotype and entire boars. 1/2 WB hybrids had higher content of C17 : 0 ( p<0.01), C17 : 1 and C18 : 3n - 3 fatty acids ( p<0.05) and higher PUFA:SFA ratio ( p<0.05) but lower content of C16:0 fatty acid of intramuscular fat than 1/4 WB hybrids. In subcutaneous tissue 1/2 WB hybrids had higher proportion of C17:0 ( p<0.001), C17:1 ( p<0.05), C18 : 3n - 3 ( p<0.05) but lower proportion of C16 : 1 ( p<0.05). Entire boars had lower content of C16:0 ( p<0.01), C18:1 ( p<0.05), C20 :1 ( p<0.05), and the total MUFA ( p<0.05) but higher content of C18 : 2n - 6 ( p<0.05) and the total PUFA ( p<0.01), PUFA:SFA ratio ( p<0.01) than castrates. Significant Pearson's correlations of the intramuscular fat content from both genotypes with MUFA were positive, but those with PUFA and PUFA : SFA ratio were negative. High positive correlation of IMF with SFA was found only in 1/4 WB genotype. PUFA and PUFA: SFA ratio also showed negative correlation with backfat thickness in both genotypes. The correlation coefficients within entire boar and castrate groups were lower than within genetic groups.

Familial aggregation of red blood cell membrane fatty acid composition: the Kibbutzim Family Study

The fatty acid composition of membranes plays an important role in health and diseases. Whether genetic factors play a role in interindividual variability in membrane fatty acid levels has received limited attention. Using variance decomposition methods, we estimated the heritability of red blood cell (RBC) membrane fatty acids in an unselected population sample of 80 families (205 male and 212 female subjects) living in kibbutz settlements in Israel. Fatty acid levels were measured by gas chromatography. We estimated that polygenes explained 40% to 70% of the sex- and age-adjusted interindividual variability in all RBC fatty acids: saturated, monounsaturated, and polyunsaturated. The heritability estimates remained very similar after further adjustment for smoking, alcohol consumption, physical activity, lipoproteins, body mass index, waist to hip ratio, education, and religiosity. In bivariate genetic analyses, we observed positive genetic correlations for the fatty acid pairs 20:4n6-22:6n3 and 20:5n3-22:6n3, and negative genetic correlations for the pairs 16:0-20:4n6, 16:0-22:6n3, 18:1n9-20:3n6, 18:2n6-20:4n6, 18:2n6-24:0, and 20:3n6-20:4n6, suggesting that shared effects of the same sets of loci account for 12% to 30% of the additive genetic variance in these pairs of fatty acids. This study suggests a considerable polygenic component for all RBC membrane fatty acids and provides evidence that shared genetic effects account for the additive genetic variance in various fatty acid pairs. Future studies are needed to map the genes underlying the interindividual variation in these inherited phenotypes.

QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes

Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian x Landrace cross. The concentrations of ten fatty acids were assayed in backfat tissue from which four metabolic ratios were calculated for 403 F2 animals. Linkage analysis identified two significant QTL. The first QTL was associated with the average chain length ratio and the percentages of myristic, palmitic and gadoleic acids. The second QTL was associated with percentages of palmitoleic, stearic and vaccenic acids. Based upon its position on SSC12, fatty acid synthase was tested as a candidate gene for the first QTL and no significant effects were found. Similarly, gastric inhibitory polypeptide (GIP) and acetyl-coenzyme A carboxylase alpha (ACACA) were tested as candidate genes for the second QTL using three SNPs in GIP and 15 synonymous SNPs in ACACA cDNA sequences. Two missense SNPs in GIP showed significant effects with palmitoleic and stearic fatty-acid concentration. Highly significant associations were found for two SNPs in ACACA with stearic, palmitoleic and vaccenic fatty-acid concentrations. These associations could be due to linkage disequilibrium with the causal mutations.

Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc x Large White cross

Background

Improving pork quality can be done by increasing intramuscular fat (IMF) content. This trait is influenced by quantitative trait loci (QTL) sought out in different pig populations. Considering the high IMF content observed in the Duroc pig, it was appealing to determine whether favourable alleles at a major gene or QTL could be found. The detection was performed in an experimental F2 Duroc × Large White population first by segregation analysis, then by QTL mapping using additional molecular information.

Results

Segregation analysis provided evidence for a major gene, with a recessive Duroc allele increasing IMF by 1.8% in Duroc homozygous pigs. However, results depended on whether data were normalised or not. After Box-Cox transformation, likelihood ratio was indeed 12 times lower and no longer significant. The QTL detection results were partly consistent with the segregation analysis. Three QTL significant at the chromosome wide level were evidenced. Two QTL, located on chromosomes 13 and 15, showed a high IMF Duroc recessive allele with an overall effect slightly lower than that expected from segregation analysis (+0.4 g/100 g muscle). The third QTL was located on chromosome 1, with a dominant Large White allele inducing high IMF content (+0.5 g/100 g muscle). Additional QTL were detected for muscular fatty acid composition.

Conclusion

The study presented results from two complementary approaches, a segregation analysis and a QTL detection, to seek out genes involved in the higher IMF content observed in the Duroc population. Discrepancies between both methods might be partially explained by the existence of at least two QTL with similar characteristics located on two different chromosomes for which different boars were heterozygous. The favourable and dominant allele detected in the Large White population was unexpected. Obviously, in both populations, the favourable alleles inducing high IMF content were not fixed and improving IMF by fixing favourable alleles using markers can then be applied both in Duroc and LW populations. With QTL affecting fatty acid composition, combining an increase of IMF content enhancing monounsaturated fatty acid percentage would be of great interest.