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This research has received funding from the Spanish Ministry of Economy and Competitiveness and the European Union Regional Development Funds (AGL2015–65846-R grant) and was partially supported by the Centre for the Development of Industrial Technology (IDI-20150115 project). SG is recipient of a PhD scholarship from the Spanish Ministry of Science and Innovation (BES-2014-FPU13/04975). We acknowledge the staff at Selección Batallé for their cooperation.

This research was funded by the Spanish Ministry of Science, Innovation and Universities and the European Regional Development Funds, ERDF, a way of making Europe (grant PID2021-124149OB-I00). H.L. is a recipient of a PhD scholarship from the Department of Research and Universities of the Government of Catalonia.

Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48-0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.

The authors acknowledge the financial support from the Spanish Ministry of Science, Innovation and Universities and European Union Regional Development Funds (grants AGL2015–65846-R and RTI2018-101346-B-I00; https://www.ciencia.gob.es) and Selección Batallé (https://www.batalle.com).

In rabbit breeding, selection for production efficiency traits has been successful but has reduced rabbit functional longevity. The gut microbiota, which influences host health, is linked to longevity and undergoes significant changes with age. While previous studies have focused on young rabbits, research on gut microbiota changes in adult rabbits is limited. Understanding how gut microbiota evolves with age and its impact on longevity of does during reproductive life could offer insights into improving productivity, health and welfare. This study aims to investigate the evolution of gut microbiota through age and to compare different functional longevity groups between and within two maternal rabbit lines with different longevities; a standard commercial line (A) and another founded using longevity criteria (LP). Our analysis demonstrated a significant impact of age on the gut microbiome of does during their reproductive lifespan, with a decline in alpha diversity and change in beta diversity composition as age progressed. Differential abundance analysis revealed that 20% and 16% of taxa in lines A and LP, respectively, were influenced by age, predominantly showing a negative correlation. In terms of functional longevity, differences in abundance between groups were more pronounced within line A, with up to 16% of taxa differing between high-longevity HL (females with more than 10 parities) and low-longevity LL (females died/culled before 5th parity) groups, compared to only 4% within line LP, highlighting the role of genetic background in shaping microbiota composition and its potential influence on longevity. Finally, differences in microbiome between the two lines A and LP were consistent and maintained through their lifespan independently from their longevity. This study reveals that age significantly influences gut microbiome diversity and composition in adult female rabbits, leading to decreased alpha diversity and notable shifts in composition. Microbiome also differs according to functional longevity, with differences varying by genetic line. This suggests that using microbiome through selection or using specific taxa within it as biomarkers could be a promising avenue for improving longevity. Moreover, microbiome differences between genetic lines persist throughout life, even among animals with the same longevity.

In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into two groups fed either a standard-protein (SP) or a low-protein (LP) diet. In the last month (165-195 days), all pigs received a LP diet, either carotene- enriched (CE) or not (NC). Significant differences were observed between T1 and T2 at Amplicon Sequences Variants (ASVs), phylum and genus levels. In T1 group, Prevotella, Faecalibacterium and Treponema were the genera most influenced by dietary protein, together with predicted functions related with the degradation of protein. In contrast, the CE diet did not impact the microbiome diversity, although 160 ASVs were differentially abundant between CE and NC groups at T2. Weak stability of enterotype clusters across time-points was observed as consequence of medium-term dietary interventions. Our results suggest that during the last month of fattening, dietary protein have a stronger effect than carotenes on the modulation of the compositional and functional structure of the pig microbiota.

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.

Fundação para a Ciência e a Tecnologia (FCT), I.P., is acknowledged for funding A. Usié through Contrato–Programa (CEECINST/00100/2021/CP2774/CT0001) and for Projects UIDB/05183/2020 to Mediterranean Institute for Agriculture, Environment and Development (MED), and LA/P/0121/2020 to CHANGE—Global Change and Sustainability Institute. Fundación Universitat Rovira i Virgili funded the sequencing (grant no. 2060-398-454-455). The authors are member of 2021SGR135.

There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.

Breeding animals to produce more robust and disease-resistant pig populations becomes a complementary strategy to the more conventional methods of biosecurity and vaccination. The objective of this study was to explore the ability of a panel of genetic markers and immunity parameters to predict the survival rates during a natural PRRSV outbreak. Ten-week-old female Duroc pigs (n = 129), obtained from 61 sows and 20 boars, were naturally infected with a highly pathogenic PRRSV genotype 1 strain. Prior to infection, piglets were screened for immunity parameters (IgG levels in plasma and SOX13 mRNA expression in blood) and genetic markers previously associated to PRRSV immune response and immunity traits. Additionally, the 20 boars were genotyped with a panel of 132 single nucleotide polymorphisms (SNPs). Survival analysis showed that mortality was significantly higher for animals with low basal IgG levels in plasma and/or high SOX13 mRNA expression in blood. The genotypes of sires for SNPs associated with IgG plasma levels, CRP in serum, percentage of γδ T cells, lymphocyte phagocytic capacity, total number of lymphocytes and leukocytes, and MCV and MCH were significantly associated with the number of surviving offspring. Furthermore, CD163 and GBP5 markers were also associated to piglet survival. The effects of these SNPs were polygenic and cumulative, survival decreased from 94 to 21% as more susceptible alleles were accumulated for the different markers. Our results confirmed the existence of genetic variability in survival after PRRSV infection and provided a set of genetic markers and immunity traits associated with PRRS resistance.