Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation.

This study explores the decreasing genetic diversity and increasing inbreeding amongst a breed of native Japanese horses, the Hokkaido. It suggests that counteracting these trends is vital for the breed’s conservation and offers specific considerations for breeding plans.

Objective and Methodology

• The aim of this research study was to investigate the genetic diversity and level of inbreeding in Japanese Hokkaido native horses. This breed is known for adapting well to cold climates and roughage diets.
• The researchers used pedigree analysis to conduct the study. This technique employed detailed family trees to study the transmission and inheritance of genetic characteristics.

Findings on Genetic Diversity

• Genetic diversity was measured using several metrics, such as the number of founder horses, effective number of founders, ancestors, and genomes.
• All the applied metrics indicated a decrease in genetic diversity over time. Factors contributing to this reduction included pedigree bottlenecks (situations where the population is drastically reduced for a brief period). The study proposed that such bottlenecks had a larger contribution to decreasing diversity than random gene losses.
• The study identified that these bottlenecks were primarily caused by the use of related stallions for breeding, reducing the effective population size.

Findings on Inbreeding

• There was observed evidence suggesting a trend towards increasing inbreeding among the Japanese Hokkaido horses. Inbreeding refers to the mating of closely related individuals, which can lead to reduced genetic diversity and increased chances of unwanted genetic traits.
• The F-statistics, a technique for analyzing variation in genetics within and among populations, revealed that increased inbreeding was mostly attributed to a small effective population size. Some cases of non-random mating in specific regions also contributed to this increase.

Recommendations for Conservation

• The research implies that mitigating bottlenecks is crucial to conserving the breed. As pedigree bottlenecks were found to have reduced the effective population size, boosting the diversity and number of breeding stallions is recommended.
• The study also suggests formulating mating plans with careful consideration of kinships to prevent non-random mating in specific regions, another factor contributing to increased inbreeding and loss of genetic diversity.