Genetic relatedness is a fundamental concept in animal breeding and conservation genetics. Typically, pedigree information is available for calculating an additive relationship () matrix, while ancestors of founder individuals are assumed unrelated. Recently, genome-wide dense SNP markers have been available for measuring genetic similarity between all pairs of individuals, to construct a so-called matrix, and moreover, a hybrid () matrix of the and matrices as proposed for single-step GBLUP. A concept of metafounders has been advocated for constructing founder genetic relationships. Our objective was to investigate relationships between a matrix using all individuals in pedigree with , matrices and an matrix with metafounder (). We generated data having different two scenarios regarding relatedness among founders; linkage equilibrium (LE) and linkage disequilibrium (LD). Correlations of the matrix of whole individuals with the or matrices were better in the LE scenario than those in the LD scenario. On the other hand, in the LD scenario, regression coefficients of elements of on elements in or were less than the desired value of 1, and intercepts were higher than 0. In both scenarios, constructed using a small number of genotyped individuals departed from the matrix, whereas, that using a moderate number of individuals with the genotypes resulted in better adjusted matrices relative to . Keywords: conservation, genetic diversity, endangered local breeds, & metafounder

Aisaku Arakawa, Masaaki Taniguchi, Satoshi Mikawa

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Challenges - Species Conservation, , 414, 2018
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