María Saura, Beatriz Villanueva, Miguel Toro, Jesús J. Fernández, Elisabeth Morales-González, Almudena Fernández, Ricardo Pong-Wong, Armando Caballero, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Xunta de Galicia, Biotechnology and Biological Sciences Research Council (UK), Villanueva, Beatriz [0000-0003-4645-8853], Saura, María [0000-0002-2744-2840], Caballero, Armando [0000-0001-7391-6974], Fernández, Jesús [0000-0001-8269-1893], Morales-González, Elisabeth [0000-0002-5614-5044], Toro, Miguel A [0000-0001-7460-2483], Pong-Wong, Ricardo [0000-0001-9808-2742], Villanueva, Beatriz, Saura, María, Caballero, Armando, Fernández, Jesús, Morales-González, Elisabeth, Toro, Miguel A, and Pong-Wong, Ricardo
17 Pág. Departamento de Mejora Genética Animal (INIA), Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs., This work was carried out with funding from the Ministerio de Ciencia e Innovación, Spain (CGL2016-75904-C2, PID2020-114426GB-C22), the European Commission Horizon 2020 (H2020) Framework Programme through grant agreement no 727315 MedAID project (Mediterranean Aquaculture Integrated Development), Xunta de Galicia (ED431C 2020-05) and Fondos FEDER.R. Pong-Wong is funded by the European Union’s Horizon 2020 research and innovation program under the Grant Agreement n°772787 (SMARTER) and the Biotechnology and Biological Sciences Research Council through Institute Strategic Programme Grant funding (BBS/E/D/30002275)