Conservation & local programs

Evaluation of genetic structure and effective population size in Japanese Shorthorn cattle using pedigree and genomic data

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Abstract

The Japanese Shorthorn cattle is the Japanese wagyu breeds that are maintained at a small population size, and the pedigree-based inbreeding coefficient is increasing in this population. Thus, the evaluation of genetic structure and controlling of effective population size (Ne) are essential. Single nucleotide polymorphism (SNP) information can be used to estimate genetic structure and Ne. Therefore, the objective of this study is to investigate the genetic structure and Ne in Japanese Shorthorn cattle using pedigree and SNP information. The population size of this breed in Iwate Prefecture, which has the largest number of animals in Japan, were approximately 8,000 and 2,000 in 1999 and 2022, respectively. From the population, a total of 1,226 individuals, which were composed of 74 bulls and 1,152 cows and were born from 1999 to 2022, were genotyped using the Illumina LIAJ custom_50v1 array (50K). The genotyped cattle possessed pedigree information for 5,254 individuals traced back as far as possible. First, the genetic structure was evaluated using the F-statistics (FIT, FST and FIS), which were calculated with pedigree information. Principal component analysis (PCA) was also performed by using VanRaden's genomic relationship matrix. Secondly, the Ne was estimated from the rate of inbreeding and coancestry, which were calculated using two approaches: the pedigree-based (ΔFPED and ΔCPED), SNP-based (ΔFGRM and ΔCGRM), and homozygous segments-based approaches (ΔFROH and ΔCSEG). Furthermore, the realized Ne was also estimated based on individual increase in inbreeding and coancestry using pedigree information, which let NeFi and NeCij. For the genetic structure, the FIT was increased from 0.03 in 1999 to 0.059 in 2022, while the FIS remained negative or almost zero over the observed years. The results of PCA revealed that the group with earlier birth years exhibited a wider range of principal component scores compared to the group with later birth years. Consequently, the inbreeding is increased in this population, yet the population was not genetically subdivided. The Ne based on ΔFPED, ΔFGRM, ΔFROH, ΔCPED, ΔCGRM, and ΔCSEG was estimated to be 148, NA, NA, 82, 372, 207, respectively, for the periods 1999-2009. For the periods 2010-2022, corresponding Ne was estimated to be 58, 82, 192, 57, 76, 118, respectively. Additionally, NeFi and NeCij were 90 and 86, respectively, for the periods 1999-2009. For the periods 2010-2022, NeFi and NeCij were 81 and 78, respectively. These results suggest that SNP-based Ne is the closest to realized Ne compared with pedigree-based and homozygous segments-based approaches. The results of this study revealed that Japanese Shorthorn cattle exhibit reduced genetic diversity at both the pedigree and genome levels. The results also suggested that genetic structure and Ne could be evaluated using SNP information alone in populations with incomplete pedigree information.

Keywords: 2026

How to Cite:

Ara, Y., Yamagata, K., Yasuda, J., Saito, O., Nagai, R., Hara, K., Sasaki, S. & Uemoto, Y., (2026) “Evaluation of genetic structure and effective population size in Japanese Shorthorn cattle using pedigree and genomic data”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283818. doi: https://doi.org/10.31274/wcgalp.23515

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