The effect of SCD and LEPR genetic polymorphisms on fat content and composition is maintained throughout fattening in Duroc pigs

Impact of the leptin receptor gene on pig performance and quality traits

The recessive T allele of the missense polymorphism rs709596309 C > T of the leptin receptor gene is associated with intramuscular fat. However, its overall impact on pork production is still partial. In this work, we investigated the all-round effects of the TT genotype on lean growth efficiency and carcass, meat and fat quality using data from an experiment that compared the performance of 48 TT and 48 C- (24 CT and 24 CC) Duroc barrows. The TT pigs were less efficient for lean growth than the C- pigs. Although heavier, their carcasses had less lean content, were shorter and had lighter loins. Apart from increasing marbling and saturated fatty acid content, changes caused by the TT genotype in meat and fat quality are likely not enough to be perceived by consumers. The effect on visual marbling score exceeded that on intramuscular fat content, which suggests a direct influence of the T allele on the pattern of fat distribution in muscle. With current low-protein diets, the T allele is expected to be cost-effective only in niche markets where a very high level of marbling is critical.

SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits

Retrotransposon is an important component of the mammalian genome. Previous studies have shown that the expression of protein-coding genes was affected by the insertion of retrotransposon into the proximal genes, and the phenotype variations would be related to the retrotransposon insertion polymorphisms (RIPs). In this study, leptin (LEP), leptin receptor (LEPR), and leptin receptor overlapping transcript (LEPROT), which play important roles in the regulation of fat synthesis and body weight, were screened to search for the RIPs and their effect on phenotype and gene expression, as well as to further study the function of the insertion. The results showed that three RIPs located in intron 1 of LEPROT and intron 2 and 21 of LEPR were identified, and they were all SINEA1, which was one type of retrotransposon. The SINE insertion at the LEPROT was the dominant allele in native pig breeds. The age of 100 kg body weight of SINE+/+ Large White individuals was significantly higher than those of SINE+/− and SINE−/− individuals (p < 0.05). The LEPROT gene expression in the liver and suet of 30-day-old SINE−/− Sujiang piglets were significantly higher than those of SINE+/+ and SINE+/− piglets (p < 0.01). The dual-luciferase reporter gene assay showed that SINE insertion in PK15 and 3T3-L1 cells significantly reduced the promoter activity of the LEPROT gene (p < 0.01). Therefore, SINE insertion can be a repressor to reduce the expression of LEPROT and could be a useful molecular marker for assisted selection of growth traits in pig breeding.

Age Evolution of Lipid Accretion Rate in Boars Selected for Lean Meat and Duroc Barrows

Fatty acid (FA) deposition in growing–fattening pigs is mainly based on endogenous lipid synthesis, but also direct FA incorporation from the diet. To evaluate the direct fat incorporation rates and the endogenous desaturation action of the stearoyl-CoA desaturase (SCD) enzyme, a deuterium (D)-labeled saturated FA (d35-C18:0) was added to the diet. Sixteen three-way (3W) crossbred boars, and thirty-two purebred Duroc barrows homozygous for the SCD single nucleotide polymorphism rs80912566 (16 CC/16 TT), were used. Half of the animals of each genotype belonged to the growing and fattening phases. The fractional incorporation rate (FIR) of dietary fat in growing pigs was generally higher in adipose tissues, whereas in fattening pigs it was higher in the liver. Duroc pigs exhibited lower FIRs than 3W pigs, suggesting lower rates of endogenous synthesis by 3W pigs. Real fractional unsaturation rates (FURs) increased with age by the higher FIRs in 3W pigs and the de novo synthesis pathway in Duroc genotypes. Moreover, pigs carrying the SCD_T allele showed more enhanced oleic acid biosynthesis than Duroc CC pigs. In conclusion, suitable feeding protocols should be designed for each pig type to optimize production traits, considering that the metabolic pathway of FA for its deposition may differ.

Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs

BACKGROUND

The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the stearoyl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C > T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial as it depends on the pig genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566 TT and CC pigs fed with and without a vitamin A supplement during the fattening period.

RESULTS

Vitamin A did not affect carcass traits or intramuscular fat content and fatty acid composition, but we observed an interaction between vitamin A and SCD genotype on the desaturation of fatty acids in muscle. As reported before, the SCD-TT pigs had more monounsaturated fat than the SCD-CC animals. The diet lacking the vitamin A supplement enlarged fatty acid compositional differences between SCD genotypes, partly because vitamin A had a bigger effect on fatty acid desaturation in SCD-CC pigs (positive) than in SCD-TT and SCD-TC animals (negative). The interaction between diet and genotype was also evident at the transcriptome level; the highest number of differentially expressed genes were detected between SCD-TT pigs fed with the two diets. The genes modulated by the diet with the vitamin A supplement belonged to metabolic and signalling pathways related to immunity and inflammation, transport through membrane-bounded vesicles, fat metabolism and transport, reflecting the impact of retinol on a wide range of metabolic processes.

CONCLUSIONS

Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Vitamin A activated general pathways of retinol response in a SCD genotype-dependant manner, which affected the monounsaturated fatty acid content, particularly in SCD-CC pigs.

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program.

Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat

BACKGROUND

Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown.

RESULTS

In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E^-7), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E^-4) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis.

CONCLUSIONS

The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF.

Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 2: muscle traits and sensory quality of dry-cured ham

The quality of pork products from local breeds in extensive systems depends, among other things, on pig production. In particular, the variability in climatic conditions and feeding resources may influence the properties of tissues at slaughter and the quality of pork and processed products. The present study (part 2) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin "Noir de Bigorre", castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months and ca. 170 kg BW. Three finishing seasons were considered: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate the specific effects of season on quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. Compared to Winter pigs, Spring and Autumn pigs had higher ultimate pH in the semimembranosus and gluteus medius (GM) muscles, lower meat lightness (P < 0.05) and tended to have higher GM intramuscular fat (IMF) content (P < 0.10). They also had higher GM contents of saturated, monounsaturated and polyunsaturated fatty acids (FAs) than Winter pigs (P < 0.05). Spring pigs had the lowest n-6:n-3 polyunsaturated FA ratio and the highest GM α-tocopherol content (P < 0.001), indicating pig grazing. The finishing season did not influence the processing yield of dry-cured hams (24-month process). Within each seasonal group, ten hams selected for genetic variability and IMF content were analyzed by a trained sensory panel. The season did not modify the appearance or odor, but influenced texture and taste. Hams from Winter and Spring pigs had higher tenderness and melting fat scores than hams from Autumn pigs (P < 0.01). Hams from Spring pigs had higher taste intensity and salty taste (P < 0.01) but lower positive tastes (e.g. fruits, forest) than hams from the other groups. Overall, finishing season had moderate effects on ham sensory traits. Furthermore, our results reveal high redness, tenderness, taste and odor intensity, and low rancid flavor of hams from Gascon pigs produced in an extensive system.

Leptin receptor and fatty acid desaturase-2 gene variants affect fat, color and production profile of dry-cured hams

The effects of LEPR (rs709596309C > T) and FADS2 (rs321384923A > G) single nucleotide polymorphisms on production and quality attributes in purebred Duroc dry-cured hams were examined. As compared to LEPR-C- hams, the LEPR-TT hams had more intramuscular fat (+2.2% dry matter, P < 0.01). As a result, they showed higher saturated (+1.54%, P < 0.01) and lower polyunsaturated (-1.05%, P < 0.01) fatty acids content and were brighter (L*: +1.07, P < 0.05) and yellower (b*: +0.78, P < 0.01). The FADS2-A allele enhanced the C20:4n-6 to C18:2n-6 ratio but did not affect either fat content or color coordinates. However, hams carrying the FADS2-A allele reached the target weight loss earlier, thereby spending less time in seasoning (-8.4 d, P < 0.01). Thus, production batches could be arranged by genotype, with longer manufacturing times for fatter LEPR-TT and shorter times for FADS2-A- hams. These results confirm that genetic markers validated in raw pork are effective in dry-cured ham, but also stress that product-specific validations are still needed to unravel specific outcomes.

ssc-miR-451 Regulates Porcine Primary Adipocyte Differentiation by Targeting ACACA

miRNA is a small non-coding RNA, which plays an important role in diverse biological processes. In the present study, we explore the effect of ssc-miR-451 on porcine adipose development and meat quality. We observed that ssc-miR-451 was downregulated during porcine primary adipocyte differentiation. Overexpression of ssc-miR-451 inhibited adipogenic differentiation, while inhibition of ssc-miR-451 promoted adipogenic differentiation. The dual luciferase reporter system indicated Acetyl-CoA carboxylase alpha (ACACA) as a target gene of ssc-miR-451. Correlation analysis negatively correlated miR-451 expression with intramuscular fat content (IMF) and positively correlated ACACA expression with IMF. Further analysis of fatty acid composition revealed that pigs with high expression of ssc-miR-451 had higher monounsaturated fatty acid (MUFA) and lower polyunsaturated fatty acid (PUFA). Taken together, our study suggests that ssc-miR-451 regulates lipid deposition and fatty acid composition by targeting ACACA, and ssc-miR-451 may serve as a potential genetic marker to improve pork quality.

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Simple Summary

Simple sequence repeats (SSRs) are present at high densities in regulatory elements, suggesting that they may affect gene function and phenotypic traits. Therefore, SSRs can be exploited in marker-assisted selection. In addition, they can be widely used as molecular markers to study genetic diversity, population structure, and evolution. While SSRs have been widely studied in many mammalian species, very little research has focused on genome-wide SSRs of miniature pigs, a small but special group of pigs that express the dwarf phenotype. Based on the SSR-enriched library building and sequencing, about 30,000 novel polymorphic SSRs for four miniature pig breeds were mapped to the Duroc pig reference genome. The four miniature pig breeds had different numbers and types of SSRs and distributions of repeat units. There were 2518 polymorphic SSRs in the intron or exon regions that were common to all four breeds and functional analyses revealed 17 genes that were associated with body size and other genes that were associated with growth and development. In conclusion, the SSRs detected in the miniature pigs in this study may provide useful genetic markers for the selection of farm animals and the polymorphic SSRs provide valuable insights into the determination of mature body size, as well as the immunity, growth and development of animals.

Abstract

Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.

Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results

Simple Summary

This study aimed to evaluate mutations within three candidate genes (SCD, ACACA, FASN) for their effects on fattening and slaughter characteristics, as well as meat quality traits, including intramuscular fat (IMF) level in pork. They were selected within differentially expressed genes activated in response to variable backfat content obtained using the RNA sequencing method. The RNA-seq analysis identifies mutations/SNPs located in the mRNA and could be a useful tool for prediction of genetic markers in farm animals. The results showed that selection for FASN A allele in Polish Large White pigs could lead to improved meat quality traits such as water exudation and meat colour. However, analysed polymorphisms showed only slight effects on fat metabolism and IMF content.

Abstract

In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.

Relationship among porcine lncRNA TCONS_00010987, miR-323, and leptin receptor based on dual luciferase reporter gene assays and expression patterns

Objective

Considering the physiological and clinical importance of leptin receptor (LEPR) in regulating obesity and the fact that porcine LEPR expression is not known to be controlled by lncRNAs and miRNAs, we aim to characterize this gene as a potential target of SSC-miR-323 and the lncRNA TCONS_00010987.

Methods

Bioinformatics analyses revealed that lncRNA TCONS_00010987 and LEPR have SSC-miR-323-binding sites and that LEPR might be a target of lncRNA TCONS_00010987 based on cis prediction. Wild-type and mutant TCONS_00010987-target sequence fragments and wild-type and mutant LEPR 3′-UTR fragments were generated and cloned into pmiR-RB-REPORT^TM-Control vectors to construct respective recombinant plasmids. HEK293T cells were co-transfected with the SSC-miR-323 mimics or a negative control with constructs harboring the corresponding binding sites and relative luciferase activities were determined. Tissue expression patterns of lncRNA TCONS_00010987, SSC-miR-323, and LEPR in Anqing six-end-white (AQ, the obese breed) and Large White (LW, the lean breed) pigs were detected by real-time quantitative polymerase chain reaction; backfat expression of LEPR protein was detected by western blotting.

Results

Target gene fragments were successfully cloned, and the four recombinant vectors were constructed. Compared to the negative control, SSC-miR-323 mimics significantly inhibited luciferase activity from the wild-type TCONS_00010987-target sequence and wild-type LEPR-3′-UTR (p<0.01 for both) but not from the mutant TCONS_00010987-target sequence and mutant LEPR-3′-UTR (p>0.05 for both). Backfat expression levels of TCONS_ 00010987 and LEPR in AQ pigs were significantly higher than those in LW pigs (p<0.01), whereas levels of SSC-miR-323 in AQ pigs were significantly lower than those in LW pigs (p<0.05). LEPR protein levels in the backfat tissues of AQ pigs were markedly higher than those in LW pigs (p<0.01).

Conclusion

LEPR is a potential target of SSC-miR-323, and TCONS_00010987 might act as a sponge for SSC-miR-323 to regulate LEPR expression.

TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Genetics and breeding for intramuscular fat and oleic acid content in pigs

The intramuscular fat (IMF) and oleic acid (OL) content have been favorably related to pork quality and human health. This influences the purchasing behavior of consumers and, therefore, also shifts the attention of breeding companies toward whether these traits are included into the breeding goal of the lines producing for high-valued markets. Because IMF and OL are unfavorably associated with lean content, a key economic trait, the real challenge for the industry is not simply to increase IMF and OL, but rather to come up with the right trade-off between them and lean content. In this paper we review the efforts performed to genetically improve IMF and OL, with particular reference to the research we conducted in a Duroc line aimed at producing high quality fresh and dry-cured pork products. Based on this research, we conclude that there are selection strategies that lead to response scenarios where IMF, OL, and lean content can be simultaneously improved. Such scenarios involve regular recording of IMF and OL, so that developing a cost-efficient phenotyping system for these traits is paramount. With the economic benefits of genomic selection needing further assessment in pigs, selection on a combination of pedigree-connected phenotypes and genotypes from a panel of selected genetic markers is presented as a suitable alternative. Evidence is provided supporting that at least a polymorphism in the leptin receptor and another in the stearoyl-CoA desaturase genes should be in that panel. Selection for IMF and OL results in an opportunity cost on lean growth. The extent to which it is affordable relies on the consumers' willingness to pay for premium products and on the cost to benefit ratio of alternative management strategies, such as specific dietary manipulations. How the genotype can influence the effect of the diet on IMF and OL remains a topic for further research.

Carotenoid intake and SCD genotype exert complementary effects over fat content and fatty acid composition in Duroc pigs

Nutritional and genetic strategies are needed to enhance intramuscular fat (IMF) and MUFA content without altering carcass leanness. Dietary vitamin A restriction has been suggested to specifically promote IMF, whereas a polymorphism of the () gene has shown to specifically increase MUFA. The purpose of this study was to investigate the combined effects of provitamin A (PVA) carotenoid intake and genotype (>) on hepatic retinoid content and on the liver, muscle (LM and gluteus medius [GM]), and subcutaneous fat (SF) content and fatty acid composition. Following a split-plot design, 32 castrated Duroc pigs, half of each of the 2 homozygous genotypes (CC and TT), were subjected from 165 to 195 d of age to 2 finishing diets differing in the PVA carotenoid content (an enriched-carotene diet [C+] and a control diet [C-]). Both diets were identical except for the corn line used in the feed. The C+ was formulated with 20% of a carotenoid-fortified corn (M37W-Ph3) whereas the C- instead used 20% of its near isogenic M37W line, which did not contain PVA carotenoids. No vitamin A was added to the diets. The C- was estimated to provide, at most, 1,300 IU of vitamin A/kg and the C+ to supply an extra amount of at least 800 IU vitamin A/kg. Compared with the pigs fed the C-, pigs fed with C+ had 3-fold more retinoic acid ( < 0.01) and 4-fold more gene expression in the liver ( = 0.06). The diet did not affect performance traits and backfat thickness, but pigs fed the C+ had less fat (4.0 vs. 5.0%; = 0.07) and MUFA (18.3 vs. 22.5%; = 0.01) in the liver, less IMF (5.4 vs. 8.3%; = 0.04) in the GM, and more fat content (90.4 vs. 87.9%; = 0.09) and MUFA (48.0 vs. 46.6%; = 0.04) in SF. The TT genotype at the gene increased MUFA ( < 0.05) in all tissues (21.4 vs. 19.5% in the liver, 55.0 vs. 53.1% in the LM, 53.9 vs. 51.7% in the GM, and 48.0 vs. 46.7% in SF for TT and CC genotypes, respectively). Liver fat and MUFA content nonlinearly declined with liver all- retinoic acid, indicating a saturation point at relatively low all- retinoic acid content. The results obtained provide evidence for a complementary role between dietary PVA and genotype, in the sense that the TT pigs fed with a low-PVA diet are expected to show higher and more monounsaturated IMF without increasing total fat content.

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.