Genomic regions influencing intramuscular fat in divergently selected rabbit lines

[EN] Intramuscular fat (IMF) is one of the main meat quality traits for breeding programs in livestock species. The main objective of this study was to identify genomic regions associated with IMF content comparing two rabbit populations divergently selected for this trait, and to generate a list of putative candidate genes. Animals were genotyped using the Affymetrix Axiom OrcunSNP Array (200k). After quality control, the data involved 477 animals and 93,540 single nucleotide polymorphisms (SNPs). Two methods were used in this research: single marker regressions with the data adjusted by genomic relatedness, and a Bayesian multi-marker regression. Associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU8 and OCU13. The highest value for the percentage of the genomic variance explained by a genomic region was found in two consecutive genomic windows on OCU8 (7.34%). Genes in the associated regions of OCU1 and OCU8 presented biological functions related to the control of adipose cell function, lipid binding, transportation and localization (APOLD1, PLBD1, PDE6H, GPRC5D, and GPRC5A) and lipid metabolic processes (MTMR2). The EWSR1 gene, underlying the OCU13 region, is linked to the development of brown adipocytes. The findings suggest that there is a large component of polygenic effect behind the differences in IMF content in these two lines, as the variance explained by most of the windows was low. The genomic regions of OCU1, OCU8 and OCU13 revealed novel candidate genes. Further studies would be needed to validate the associations and explore their possible application in selection programs.The work was funded by project AGL2014-55921-C2-1-P from National Programme for Fostering Excellence in Scientific and Technical Research -Project I+D. BSS was supported by a FPI grant from the Ministry of Economy and Competitiveness of Spain+ (BES-2015-074194). NIB was supported with a "Ramon y Cajal" grant provided by Ministerio de Ciencia e Innovacion (RYC-2016-19764). CSH and PN were supported by the Medical Research Council (United kingdom, grants MC_PC_U127592696 and MC_PC_U127561128). CSH was supported by Biotechnology and Biological Sciences Research Council (United Kingdom, Grant/Award Number: BBS/E/D/30002276).Sosa-Madrid, BS.; Hernández, P.; Blasco Mateu, A.; Haley, CS.; Fontanesi, L.; Santacreu Jerez, MA.; Pena, RN.... (2020). Genomic regions influencing intramuscular fat in divergently selected rabbit lines. Animal Genetics. 51:58-69. https://doi.org/10.1111/age.12873586951Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., … Searle, S. M. J. (2016). The Ensembl gene annotation system. Database, 2016, baw093. doi:10.1093/database/baw093Aloulou, A., Ali, Y. B., Bezzine, S., Gargouri, Y., & Gelb, M. 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Efficient generation of transgenic pigs using equine infectious anaemia virus (EIAV) derived vector

AbstractTraditional methods of transgene delivery in livestock are inefficient. Recently, human immunodeficiency virus (HIV-1) based lentiviral vectors have been shown to offer an efficient transgene delivery system. We now extend this method by demonstrating efficient generation of transgenic pigs using an equine infectious anaemia virus derived vector. We used this vector to deliver a green fluorescent protein expressing transgene; 31% of injected/transferred eggs resulted in a transgenic founder animal and 95% of founder animals displayed green fluorescence. This compares favourably with results using HIV-1 based vectors, and is substantially more efficient than the standard pronuclear microinjection method, indicating that lentiviral transgene delivery may be a general tool with which to efficiently generate transgenic mammals

Quantitative trait loci analysis of a Duroc commercial population highlights differences in the genetic determination of meat quality traits at two different muscles

We performed a whole-genome scan with 110 informative microsatellites in a commercial Duroc population for which growth, fatness, carcass and meat quality phenotypes were available. Importantly, meat quality traits were recorded in two different muscles, that is, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), to find out whether these traits are determined by muscle-specific genetic factors. At the whole-population level, three genome-wide QTL were identified for carcass weight (SSC7, 60 cM), meat redness (SSC13, 84 cM) and yellowness (SSC15, 108 cM). Within-family analyses allowed us to detect genome-wide significant QTL for muscle loin depth between the 3rd and 4th ribs (SSC15, 54 cM), backfat thickness (BFT) in vivo (SSC10, 58 cM), ham weight (SSC9, 69 cM), carcass weight (SSC7, 60 cM; SSC9, 68 cM), BFT on the last rib (SSC11, 48 cM) and GM redness (SSC8, 85 cM; SSC13, 84 cM). Interestingly, there was low positional concordance between meat quality QTL maps obtained for GM and LTL. As a matter of fact, the three genome-wide significant QTL for colour traits (SSC8, SSC13 and SSC15) that we detected in our study were all GM specific. This result suggests that QTL effects might be modulated to a certain extent by genetic and environmental factors linked to muscle function and anatomical location. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.This study was funded with grants AGL2002-04271-C03 and AGL2007-66707-C02-01 (Ministerio de Ciencia e Innovación, Spain).Peer Reviewe

Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects

Intramuscular fat (IMF) storage is a biological process with a strong impact on nutritional and technological properties of meat and also with rel- evant consequences on human health. The genetic ar- chitecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the iden- tification of QTL and the estimation of genetic param- eters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, have broad effects on the whole skeletal muscle compartment. We have ad- dressed this question by generating lipid QTL maps for 2 muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (n = 350). Our data support a lack of concordance between the GM and LTL QTL maps, suggesting that the effects of poly- morphisms influencing IMF, cholesterol, and fatty acid contents are modulated to some extent by complex spa- tial factors related to muscle location, metabolism, and function. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat. © 2011 American Society of Animal Science, All rights reserved.This study was funded with grants AGL2007-66707-C02-01 and AGL2010-22208-C02-01 (Ministerio de Ciencia e Innovación, Spain). D. Gallardo and A. Cánovas were supported by fellowships from the Universitat Autònoma de Barcelona and the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria of Spain, respectively.Peer Reviewe