Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa).

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (FIS and FROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Relationship between perilipin genes polymorphisms and growth, carcass and meat quality traits in pigs.

The perilipins (PLIN) belong to a family of structural proteins that play a role regulating intracellular lipid storage and mobilization. Here, PLIN1 and PLIN2 have been evaluated as candidate genes for growth, carcass and meat quality traits in pigs. A sample of 607 Duroc pigs were genotyped for two single-nucleotide polymorphisms, one in intron 2 of the PLIN1 gene (JN860199:g.173G>A) and the other at the 3' untranslated region of the PLIN2 gene (GU461317:g.98G>A). Using a Bayesian approach, we have been able to find evidence of additive, dominant and epistatic associations of the PLIN1 and PLIN2 polymorphisms with early growth rate and carcass length. However, the major effects were produced by the dominant A allele at the PLIN2 polymorphism, which also affected the carcass lean weight. Thus, pigs carrying an additional copy of the A allele at the g.98G>A PLIN2 polymorphism had a probability of at least 98% of producing carcasses with heavier lean weight (+0.41 kg) and ham weight (+0.10 kg). The results obtained indicate that the PLIN2 polymorphism could be a useful marker for lean growth. In particular, it may help to reduce the undesired negative correlated response in lean weight to selection for increased intramuscular fat content, a common scenario in some Duroc lines involved in the production of high quality pork products.

Five genomic regions have a major impact on fat composition in Iberian pigs.

The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content.

Association study highlights the influence of ELOVL fatty acid elongase 6 gene region on backfat fatty acid composition in Large White pig breed.

Dietary fatty acid (FA) composition has an impact on human health. There is an increasing request from consumers for healthier food and pork industry must respond to it without worsening performance and the technological properties of pork products. The inclusion of genetic markers for carcass FA composition in pig selection schemes could be a useful tool to reach the right balance between unsaturated and saturated FAs to satisfy market demands. With the aim of finding genomic regions associated with porcine backfat FA composition, a genome-wide association study was performed on 798 Italian Large White pigs genotyped using Illumina PorcineSNP60 k. The strongest associations with backfat contents of palmitic, palmitoleic, oleic, medium-chain and long-chain FAs were found for the Sus scrofa chromosome (SSC) 8 region located at 119 to 122 Mb, where the gene ELOVL FA elongase 6 is mapped. Palmitic, palmitoleic, stearic and oleic acid contents were also found associated with SSC14, in particular with the genomic region at 121 to 124 Mb, where stearoyl-CoA desaturase Δ9 gene lies. On the other hand, the genomic regions associated with backfat contents of arachidic, arachidonic, n-6 and n-3 FAs showed to harbour mainly genes involved in dietary lipids and carbohydrates digestion, absorption and utilisation. To our knowledge, this is the first study performed in Large White pigs identifying markers and genomic regions associated with backfat FA composition. The results validate in Large White some associations previously detected in other pig breeds and indicate the involvement of distinct metabolic pathways in the deposition pattern of essential and non-essential FAs.

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.

Genetic correlations of intramuscular fat content and fatty acid composition among muscles and with subcutaneous fat in Duroc pigs.

There is an increasing interest in including intramuscular fat (IMF) content and fatty acid composition, particularly oleic acid (C18:1) content, in the selection objectives of pig lines for quality pork markets. These traits are costly and can be measured in more than 1 location, so knowing their correlation structure across muscles and with subcutaneous fat (SF) is necessary for developing optimum sampling and recording schemes. We analyzed the genetic and phenotypic correlations of IMF content and composition among 3 of the most relevant muscles (LM, gluteus medius muscle [GM], and semimembranosus muscle [SM]) and with the fatty acid composition of SF. All genetic correlations were positive but variable. For IMF, the genetic correlation between GM and LM was 0.68, and for fatty acids, the genetic correlation ranged from 0.62 for C18:1 to 0.82 for total PUFA. Genetic correlations of GM and LM with SM were much lower: 0.13 to 0.19 for IMF and 0.10 to 0.54 for fatty acids. Correlations for fatty acid composition in SF with GM and LM were moderate to high (0.29-0.53 and 0.43-0.75, respectively) but were null with SM. The expected responses for IMF in the 3 muscles and for C18:1 in each muscle and in SF to selection on records taken from only a single muscle or SF were estimated. Selection for IMF and C18:1 in GM is expected to lead to positive responses in IMF and C18:1 in LM and vice versa, although this can entail genetic lags of 20 to 45% in the muscle not directly selected for. Selection for C18:1 in SF is more effective for C18:1 in LM than in GM and of very limited value for IMF. In conclusion, the genetic correlations of IMF content and fatty acid composition among muscles and with SF, although positive, are variable enough to influence the genetic evaluation scheme for IMF and fat quality. They also indicate that GM and LM can be used alternatively for selection purposes.

Relationship between gilt behavior and meat quality using principal component analysis.

Pig on-farm behavior has important repercussions on pig welfare and performance, but generally its relationship with meat quality is not well understood. We used principal component analysis to determine the relationship between meat quality traits, feeding patterns, scale activity, and number of conflict-avoidance interactions. The first principal component indicated that gilts with greater daily feed intake stayed longer in the feeder and their meat had increased intramuscular fat (IMF), was lighter in color, and, in the second principal component, had better juiciness, tenderness, chewiness, and flavor. Meat from gilts with lower scale activity scores appeared to have more IMF but greater drip losses (DL). The third principal component suggested that dominant gilts could gain priority access to the feeder, eating more and growing fatter. In conclusion, except for the slight associations with IMF and DL, gilt scale activity and conflict-avoidance behaviors were not good indicators of final meat quality attributes.

Response to selection for decreased backfat thickness at restrained intramuscular fat content in Duroc pigs.

Intramuscular fat (IMF) content is a relevant trait for the pig industry and consumers. However, selection for IMF has the undesired correlated effect of decreasing lean growth. A selection experiment was performed to investigate the effects of selection against backfat thickness (BT) at restrained IMF. Barrows from a purebred Duroc line were allocated into a selected (n = 165) or a control (n = 185) group based on their litter predicted EBV. Litters in the selected group were selected against BT at 180 d at restrained IMF in gluteus medius (GM) whereas those in the control group were chosen randomly. Realized selection intensities and genetic responses for BT, IMF in GM, and BW were estimated using a 3-trait multivariate animal mixed model under a Bayesian setting. Correlated responses for other traits were estimated similarly but using a 4-trait model, where other traits were added to the previous 3-trait model 1 at a time. Selected pigs had less BT than control pigs [-1.22 mm, with highest posterior density interval at 95% (HPD95; -2.47, -0.75)] with restrained decrease in IMF, both in GM [-0.16%; HPD95 (-0.36, +0.05)] and in LM [-0.15%; HPD95 (-0.37, +0.09)]. However, the realized selection intensity for IMF in GM denotes that the restriction on IMF was incomplete [-0.18; HPD95 (-0.36, +0.02)]. Selection decreased BW [-1.64 kg; HPD95 (-2.47, -0.75)] but increased carcass lean weight [+0.66 kg; HPD95 (+0.14, +1.22)], indicating that the response in BT offsets the unfavorable correlated response in BW. Selected pigs were shorter [-0.50 cm; HPD95 (-0.81, -0.20)] but with similar ham weight and loin depth. These results provide evidence that lean weight can be improved restraining the genetic change in IMF. However, they also stress that a complete restriction on IMF is difficult to achieve unless selection is practiced on a big population where IMF is accurately predicted.

Expected genetic response for oleic acid content in pork.

Intramuscular fat (IMF) and oleic acid (C18:1) content in pork are important issues for the pig industry and consumers. Data from a purebred Duroc line were used to i) estimate the genetic parameters of IMF and C18:1 and their genetic correlations with lean growth components, and ii) evaluate the opportunities for genetically improving C18:1 in IMF. The data set used for estimating genetic parameters consisted of 93,920 pigs, from which 85,194 had at least 1 record for BW or backfat thickness (BT) at 180 d and 943 for IMF and C18:1 at 205 d. Intramuscular fat content and C18:1, expressed as percentage of total fatty acids, were determined in the gluteus medius muscle by gas chromatography. Genetic parameters for C18:1 were estimated under a Bayesian 4-trait multivariate animal mixed model. Heritability of C18:1 was 0.50, with a probability of 95% of being greater than 0.37. Genetic correlations of C18:1 with BW, BT, and IMF were 0.11, 0.22, and 0.47, respectively (with a probability of 95% of being greater than -0.07, 0.04, and 0.27, respectively). Genetic responses were evaluated by deterministic simulation using a half-sib recording scheme for C18:1 and the previously estimated parameters. The C18:1 content is expected to exhibit only minor changes in selection programs directed at growth rate but to decrease in those focusing on lean content. Maximum expected response in C18:1 at no lean growth loss (i.e., at no change in BW and BT) was 0.44%, with a resulting correlated response in IMF of 0.15%. However, because lean growth is emphasized in the breeding goal, the resulting response scenarios are more constrained. We concluded that there is evidence to support the idea that C18:1 in IMF is genetically determined and defined selection strategies can lead to response scenarios in which C18:1, IMF, BT, and BW can be simultaneously improved. However, if adopted, the potential for lean growth would be reduced. The extent to which it is affordable relies on how much consumers are prepared to pay for high-C18:1 pork products.