Bivariate GWAS performed on rabbits divergently selected for intramuscular fat content reveals pleiotropic genomic regions and genes related to meat and carcass quality traits Bolívar Samuel Sosa-Madrid, Agostina Zubiri-Gaitán, Noelia Ibañez-Escriche, Agustín Blasco, Pilar Hernández Genetics Selection Evolution, 2025 Background Meat quality plays an important economic role in the meat industry and livestock breeding programmes. Intramuscular fat content (IMF) is one of the main meat quality parameters and its genetic improvement has led breeders to investigate its genomic architecture and correlation with other relevant traits. Genetic markers associated with causal variants for these traits can be identified by bivariate analyses. In this study, we used two rabbit lines divergently selected for IMF to perform bivariate GWAS with the aim of detecting pleiotropic genomic regions between IMF and several weight, fat, and meat quality traits. Additionally, whole-genome sequencing data from these lines were used to identify potential causal variants associated with the genetic markers. Results The main pleiotropic region was found on Oryctolagus cuniculus chromosome (OCC) 1 between 35.4 Mb and 38.2 Mb, explaining up to 2.66% of the IMF genetic variance and being associated with all traits analysed, except muscle lightness. In this region, the potentially causal variants found pointed to PLIN2, SH3GL2, CNTLN, and BNC2 as the main candidate genes affecting the different weight, fat depots and meat quality traits. Other relevant pleiotropic regions found were those on OCC3 (148.94–150.89 Mb) and on OCC7 (27.07–28.44 Mb). The first was associated with all fat depot traits and explained the highest percentage of genetic variance, up to 10.90% for scapular fat. Several allelic variants were found in this region, all located in the novel gene ENSOCUG00000000157 (orthologous to ST3GAL1 in other species), involved in lipid metabolism, suggesting it as the main candidate affecting fat deposition. The region on OCC7 was associated with most meat quality traits and explained 8.48% of the genetic variance for pH. No allele variants were found to segregate differently between the lines in this region; however, it remains a promising region for future functional studies. Conclusions Our results showed that bivariate models assuming pleiotropic effects are valuable tools to identify genomic regions simultaneously associated with IMF and several weight, fat and meat quality traits. Overall, our results provided relevant insights into the correlations and relationships between traits at the genomic level, together with potential functional mutations, which would be relevant for exploration in rabbit and other livestock breeding programmes.
Correlated Responses to Selection for Intramuscular Fat on the Gut Microbiome in Rabbits Marina Martínez-Álvaro, Agostina Zubiri-Gaitán, Pilar Hernández, Cristina Casto-Rebollo, Noelia Ibáñez-Escriche, Maria Antonia Santacreu, Alejandro Artacho, Vicente Pérez-Brocal, Agustín Blasco Animals, 2024 Intramuscular fat (IMF) content is important for meat production and human health, where the host genetics and its microbiome greatly contribute to its variation. The aim of this study is to describe the consequences of the genetic modification of IMF by selecting the taxonomic composition of the microbiome, using rabbits from the 10th generation of a divergent selection experiment for IMF (high (H) and low (L) lines differ by 3.8 standard deviations). The selection altered the composition of the gut microbiota. Correlated responses were better distinguished at the genus level (51 genera) than at the phylum level (10 phyla). The H-line was enriched in Hungateiclostridium, Limosilactobacillus, Legionella, Lysinibacillus, Phorphyromonas, Methanosphaera, Desulfovibrio, and Akkermansia, while the L-line was enriched in Escherichia, Methanobrevibacter, Fonticella, Candidatus Amulumruptor, Methanobrevibacter, Exiguobacterium, Flintibacter, and Coprococcus, among other genera with smaller line differences. A microbial biomarker generated from the abundance of four of these genera classified the lines with 78% accuracy in a logit regression. Our results demonstrate different gut microbiome compositions in hosts with divergent IMF genotypes. Furthermore, we provide a microbial biomarker to be used as an indicator of hosts genetically predisposed to accumulate muscle lipids, which opens up the opportunity for research to develop probiotics or microbiome-based breeding strategies targeting IMF.
Cecal metabolomics of 2 divergently selected rabbit lines revealed microbial mechanisms correlated to intramuscular fat deposition Agostina Zubiri-Gaitán, Marina Martínez-Álvaro, Agustín Blasco, Pilar Hernández Journal of Animal Science, 2024 The gastrointestinal microbiota plays a key role in the host physiology and health through a complex host–microbiota co-metabolism. Metabolites produced by microbial metabolism can travel through the bloodstream to reach distal organs and affect their function, ultimately influencing the development of relevant production traits such as meat quality. Meat quality is a complex trait made up of a number of characteristics and intramuscular fat content (IMF) is considered to be one of the most important parameters. In this study, 52 rabbits from 2 lines divergently selected for IMF (high-IMF (H) and low-IMF (L) lines) were used to perform an untargeted metabolomic analysis of their cecal content, with the aim to obtain information on genetically determined microbial metabolism related to IMF. A large, correlated response to selection was found in their cecal metabolome composition. Partial least squares discriminant analysis was used to identify the pathways differentiating the lines, which showed a classification accuracy of 99%. On the other hand, 2 linear partial least squares analyses were performed, one for each line, to extract evidence on the specific pathways associated with IMF deposition within each line, which showed predictive abilities (estimated using the Q2) of approximately 60%. The most relevant pathways differentiating the lines were those related to amino acids (aromatic, branched-chain, and gamma-glutamyl), secondary bile acids, and purines. The higher content of secondary bile acids in the L-line was related to greater lipid absorption, while the differences found in purines suggested different fermentation activities, which could be related to greater nitrogen utilization and energy efficiency in the L-line. The linear analyses showed that lipid metabolism had a greater relative importance for IMF deposition in the L-line, whereas a more complex microbial metabolism was associated with the H-line. The lysophospholipids and gamma-glutamyl amino acids were associated with IMF in both lines; the nucleotide and secondary bile acid metabolisms were mostly associated in the H-line; and the long-chain and branched-chain fatty acids were mostly associated in the L-line. A metabolic signature consisting of 2 secondary bile acids and 2 protein metabolites was found with 88% classification accuracy, pointing to the interaction between lipid absorption and protein metabolism as a relevant driver of the microbiome activity influencing IMF.
Plasma metabolomic profiling in two rabbit lines divergently selected for intramuscular fat content Agostina Zubiri-Gaitán, Agustín Blasco, Pilar Hernández Communications Biology, 2023 This study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity supported its relevant role in the lipid deposition. Future research will focus on the analysis of the metabolomic profile of the cecum content, and on the integration of the several -omics datasets available for these lines, to help disentangle the host and microbiome biological mechanisms involved in the IMF deposition.
Intramuscular Fat Selection in Rabbits Modifies the Fatty Acid Composition of Muscle and Liver Tissues Agostina Zubiri-Gaitán, Agustín Blasco, Ruth Ccalta, Katy Satué, Pilar Hernández Animals, 2022 This study was conducted on two rabbit lines divergently selected for intramuscular fat (IMF) content in the Longissimus thoracis et lumborum (LTL) muscle. The aim was to estimate the direct response to selection for IMF after 10 generations, and the correlated responses in carcass quality traits, meat fatty acid content, liver fat and its fatty acid content, and in plasma metabolic markers related to liver metabolism. Selection for IMF content was successful, showing a direct response equivalent to 3.8 SD of the trait after 10 generations. The high-IMF line (H) showed a greater dissectible fat percentage than the low-IMF line (L), with a relevant difference (DH-L = 0.63%, Pr = 1). No difference was found in liver fat content (DH-L = −0.04, P0 = 0.62). The fatty acid content of both LTL muscle and liver was modified after selection. The LTL muscle had greater saturated (SFA; DH-L = 5.05, Pr = 1) and monounsaturated fatty acids (MUFA; DH-L = 5.04, Pr = 1) contents in the H line than in the L line. No relevant difference was found in polyunsaturated fatty acids content (PUFA; Pr = 0.05); however, greater amounts of C18:2n6 (DH-L = 3.03, Pr = 1) and C18:3n3 (DH-L = 0.56, Pr = 1) were found in the H than in the L line. The liver presented greater MUFA (DH-L = 1.46) and lower PUFA (DH-L = −1.46) contents in the H than in the L line, but the difference was only relevant for MUFA (Pr = 0.86). The odd-chain saturated fatty acids C15:0 and C17:0 were more abundant in the liver of the L line than in the liver of the H line (DH-L = −0.04, Pr = 0.98 for C15:0; DH-L = −0.09, Pr = 0.92 for C17:0). Greater concentrations of plasma triglycerides (DH-L = −34) and cholesterol (DH-L = −3.85) were found in the L than in the H line, together with greater plasma concentration of bile acids (DH-L = −2.13). Nonetheless, the difference was only relevant for triglycerides (Pr = 0.98).
Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment Marina Martínez-Álvaro, Agostina Zubiri-Gaitán, Pilar Hernández, Michael Greenacre, Alberto Ferrer, Agustín Blasco Communications Biology, 2021 Our study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from −0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.
Novel genomic regions associated with intramuscular fatty acid composition in rabbits Houda Laghouaouta, Bolívar Samuel Sosa-Madrid, Agostina Zubiri-Gaitán, Pilar Hernández, Agustín Blasco Animals, 2020 Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0–37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0–48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.
