Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis

Abstract

There are four unique cattle breeds in Japan: Japanese Black, Japanese Brown, Japanese Polled, and Japanese Shorthorn. The objective of this study was to comprehensively assess the genetic diversity, structure, relationship, and the degree of influence from foreign breeds (Angus, Simmental, Hanwoo, Shorthorn, Ayrshire, Brown Swiss, and Devon) in the Japanese cattle breeds using Illumina 50 K SNP array. In principal component analysis, each Japanese breed was separately clustered except for Japanese Shorthorn and Shorthorn. Japanese cattle breeds also showed different genetic components from each other at K ≥ 5 in population structure analysis. Japanese Shorthorn, on the other hand, had a very similar structure to Shorthorn at K ≤ 9, and Japanese Polled had a partially similar component with Angus at K = 3-7. Such close relationships were also observed in the phylogenetic tree. These findings imply that Japanese cattle breeds share genetic components with European cattle breeds to some extent while they have been almost differentiated. In population structure analysis, Japanese Black cattle shared little genetic component (3.5%) with European breeds. This is the first study to determine the extent to which European breeds impact Japanese breeds.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

“…Furthermore, the loss of population purity by gene introgression could affect the local fitness (outbreeding depression) of these valuable genetic resources. However, the present analysis shows that the studied populations still exhibit levels of genetic diversity (H E and H O ranging between 0.352 and 0.462), comparable with those reported for other cattle breeds (e.g., Cañas-Álvarez et al, 2015;Kawaguchi et al, 2022;McTavish et al, 2013;Michiels et al, 2023;Saravanan et al, 2022). In agreement with these relatively high values of genetic diversity, the Creole cattle populations showed low average inbreeding levels measured through two methods.…”

Causative alleles for chondrodysplastic dwarfism, factor XI deficiency, and factor XIII deficiency in the Kumamoto sub‐breed of Japanese Brown cattle

“…The Kumamoto sub-breed also shares the causative allele of factor XI deficiency with Japanese Black cattle. Genetic exchange has not been observed between these two breeds, and according to a recent SNP array analysis, the influence of foreign breeds is limited in Wagyu breeds (Kawaguchi et al, 2022), suggesting that common ancestors of the Wagyu breeds may possess the causative alleles of factor XI deficiency and factor XIII deficiency. DNA testing for these diseases is needed to prevent economic losses in beef production using the Kumamoto sub-breed.…”

“…Although all Wagyu breeds have distinct genetic characteristics, the Kumamoto sub-breed and Japanese Black cattle are relatively genetically close (Kawaguchi et al, 2022), suggesting that the Kumamoto sub-breed may contain animals with mutations responsible for the genetic diseases identified in Japanese Black cattle. Our previous studies detected mutations causing factor XI deficiency and Chediak-Higashi syndrome in the Kumamoto sub-breed (Kimura et al, 2021(Kimura et al, , 2022.…”

Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle

“…The quality of imputation using this reference population was valid for genomic prediction and genome-wide association study [ 35 , 36 ]. Moreover, several studies previously evaluated the genetic diversity and structure in Japanese Black cattle using BovineSNP50 BeadChip or GGP BovineLD v4.0 [ 37 – 39 ]. All SNP were filtered for call rate < 95%, minor allele frequency (MAF) < 0.01 and extreme deviation from Hardy–Weinberg equilibrium ( p < 0.0001).…”