Longitudinal genome-wide association analysis using a single-step random regression model for height in Japanese Holstein cattle

Toshimi Baba; Gota Morota; Junpei Kawakami; Yusaku Gotoh; Taro Oka; Yutaka Masuda; Luiz F Brito; Rebbeca R Cockrum; Takayoshi Kawahara

doi:10.3168/jdsc.2022-0347

Longitudinal genome-wide association analysis using a single-step random regression model for height in Japanese Holstein cattle

JDS Commun. 2023 Jul 13;4(5):363-368. doi: 10.3168/jdsc.2022-0347. eCollection 2023 Sep.

Authors

Toshimi Baba^{1

2}, Gota Morota², Junpei Kawakami¹, Yusaku Gotoh¹, Taro Oka³, Yutaka Masuda⁴, Luiz F Brito⁵, Rebbeca R Cockrum², Takayoshi Kawahara¹

Affiliations

¹ Holstein Cattle Association of Japan, Hokkaido Branch, Sapporo, Hokkaido, Japan 001-8555.
² School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061.
³ Holstein Cattle Association of Japan, Tokyo, Japan 164-0012.
⁴ Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan 069-8501.
⁵ Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.

Abstract

Growth traits, such as body weight and height, are essential in the design of genetic improvement programs of dairy cattle due to their relationship with feeding efficiency, longevity, and health. We investigated genomic regions influencing height across growth stages in Japanese Holstein cattle using a single-step random regression model. We used 72,921 records from birth to 60 mo of age with 4,111 animals born between 2000 and 2016. The analysis included 1,410 genotyped animals with 35,319 single nucleotide polymorphisms, consisting of 883 females with records and 527 bulls, and 30,745 animals with pedigree information. A single genomic region at the 58.4 megabase pair on chromosome 18 was consistently identified across 6 age points of 10, 20, 30, 40, 50, and 60 mo after multiple testing corrections for the significance threshold. Twelve candidate genes, previously reported for longevity and gestation length, were found near the identified genomic region. Another location near the identified region was also previously associated with body conformation, fertility, and calving difficulty. Functional Gene Ontology enrichment analysis suggested that the candidate genes regulate dephosphorylation and phosphatase activity. Our findings show that further study of the identified candidate genes will contribute to a better understanding of the genetic basis of height in Japanese Holstein cattle.