Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

Abstract

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N ge ) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

“…Our primary objective was to develop the method to calculate genetic contributions with respect to genes on sex chromosomes and mitochondrial DNA, and as a further challenge, we extended the concept of CV of genetic contribution with respect to autosomal genes to those with respect to sex chromosomes and mitochondrial DNA. Our method developed in this study might also contribute the expansion of other indicators for genetic diversity, such as the number of founder alleles [48,50]. Further study would be valuable to develop an indicator to monitor the genetic diversity with respect to genes on sex chromosomes and mitochondrial DNA.…”

“…However, in livestock populations where selection based on pedigree information has been conducted for many years, it is often more difficult to use genotype information closer to the base population, and thus approaches based on pedigree data are still useful. It should be noted that the indicators proposed do not consider mutations, recombination, or mitochondrial DNA heteroplasmy, as is the case with the genetic contribution with respect to autosomal genes [48][49][50][51]. This study developed the novel method to calculate the genetic contributions with respect to genes on sex chromosomes and mitochondrial DNA.…”

“…The genetic contribution of a particular individual can be used as an indicator to monitor the pattern of gene transmission in a population with pedigree information (e.g., [45][46][47]). In Japan, the genetic contribution has been used for line maintenance and brand identification in pigs and for genetic diversity management in Wagyu cattle populations (e.g., [48][49][50][51]). For example, different pig strains have been developed through closed-line breeding with widely collecting animals and semen as a base population and strict selection of several generations (e.g., [8,52,53]), and the coefficient of variation (CV) of genetic contribution has been used to keep the genetic composition of the population after approving it as a distinct strain (e.g., [51,54,55]).…”

Genetic relationships of feed efficiency and growth traits with carcass traits in Japanese Shorthorn cattle

“…Consequently, selection of 33% of bulls with phenotypic value (selection intensity = 1.1) and no selection of cow was assumed, and thus, an average selection intensity of 0.55 was used in the analysis. In recent years, the average generation interval of cattle in the Japanese Shorthorn population has been estimated to be approximately 7.5 years (Uemoto et al, 2021), and thus, we used a GI value of 7.5 in the present study. In each case, favorable selection was performed, which corresponds to positive selection for DG, RG, and RIG and negative selection for BF, FI, FCR, and RFI.…”

“…The Japanese Shorthorn is a Japanese Wagyu breed of cattle raised in the Tohoku and Hokkaido regions of northern Japan (Motoyama et al, 2016). Although the size of the Japanese Shorthorn population is currently small, comprising approximately 7000-8000 individuals (National Livestock Breeding Center [NLBC], 2021), these cattle retain an appreciable genetic diversity compared with other Japanese Wagyu breeds (Uemoto et al, 2021). One of the characteristic features of Japanese Shorthorns is their efficient roughage utilization, which enables to breed to adapt well to diverse grazing conditions and harsh environments, and most Japanese Shorthorn cattle are grazed on pastures during summer (Kondo et al, 2005).…”