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Pedigree analysis of genetic subdivision in a population of Japanese Black cattle

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ABSTRACT

Twenty-five subpopulations (i.e. populations of prefectures) of more than 2000 Japanese Black cows younger than or equal to 10 years of age were analyzed to evaluate the genetic relationships in the current population. The total number of cows analyzed was 392 346 and their pedigrees were traced back to 1944 or before. Using the pedigree records, the genetic relationships among the subpopulations were estimated by the two different measurements: (i) the average additive relationship coefficients and (ii) Nei's standard genetic distances. Principal component analysis (PCA) was performed to the matrix of the average additive relationship coefficients, and the factor loadings of subpopulations were plotted on the plane to visualize the genetic configuration of subpopulations. To understand the grouping process of the subpopulations, cluster analysis was applied to the matrix of the Nei's genetic distances, and a dendrogram was constructed. There was a high consistency between the results from PCA and cluster analysis. Eight subpopulations with relatively low migration rates showed their unique genetic compositions, and the other 17 subpopulations with high migration rates formed a single cluster. The major cause of the genetic similarity among the 17 subpopulations was inferred to be the strong genetic influence from one subpopulation (Hyogo prefecture) with prominent characteristics for meat quality.
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Keywords: Japanese Black; genetic relationships; genetic subdivision; multivariate analysis; pedigree analysis

Document Type: Research Article

Affiliations: 1: Faculty of Agriculture, Kobe University, Nada-ku, Kobe-shi, 2: Faculty of Engineering, Kyoto Sangyo University, Kita-ku, Kyoto-shi and 3: Wagyu Registry Association, Nakagyou-ku, Kyoto-shi, Japan

Publication date: 2002-12-01

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