Genome‐wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single‐step genomic best linear unbiased prediction method

Abstract

The current beef production system of Japanese Black cattle is highly dependent on imported high-concentrate feed, which is given for long fattening periods of 19 months (Gotoh, Nishimura, Kuchida, & Mannen, 2018). In order to reduce production costs and ensure sustainability, genetic improvement of feed efficiency during the fattening period is necessary. Residual feed intake (RFI) is defined as the difference between actual and predicted feed intake (Koch, Swiger, Chambers, & Gregory, 1963), and this has previously been studied in other cattle breeds and livestock (Berry & Crowley, 2013). In addition, residual intake and body weight gain (RIG) has been proposed as an indicator of efficiency (Berry & Crowley, 2012). Thus, animals with a lower RFI and higher residual body weight gain (RG) (Berry & Crowley, 2012) are desirable. The heritabilities for RFI ranged from 0.07 to 0.62 in growing animals across different breeds (Berry & Crowley, 2013). Recently, the genetic parameters for RFI, RG, and RIG during different fattening periods were studied in 4,578 Japanese Black steers tested for a year, suggesting that these traits are moderately heritable and different genetic background could

Effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci detection and genomic evaluation in a simulated cattle population

“…One of the reasons is that the real data had SNP genotypes based on an imputed BovineHD SNP array (Takeda et al, 2020), whereas the simulated data had SNP genotypes based on a 50 K SNP array.…”

“…The GWAS and genomic evaluation were performed using the BLUPF90 family of programs (Aguilar et al, 2018). The detailed description of the statistical models used is in Takeda et al (2020), and a brief description is as follows. The single-trait animal model was used for the genomic analyses as follows:…”

Genetic and genomic analyses for predicted methane‐related traits in Japanese Black steers

“…All animals were cared for and slaughtered according to Japanese animal welfare regulations. A complete description of the experimental population was previously reported by Inoue, Kobayashi, Shoji, and Kato (2011) and Takeda et al (2018Takeda et al ( , 2020. Briefly, a total of 4,578 Japanese Black steers raised by the Livestock Improvement Association of Japan, Inc. (LIAJ) from 1998 to 2008 were used in this study, and a total of 30,012 animals were used for pedigree information.…”

“…Thus, this is a good example of a trait to use to evaluate the difference in the power of QTL detection between both methods. In our population, more than 27% of genetic variance were obtained near the pleomorphic adenoma gene 1 (PLAG1) gene, which is one of the candidate genes for CW in Japanese Black cattle (Nishimura et al, 2012), using ssGWAS with two iterative procedures (Takeda et al, 2020; Figure S1). Genome-wide significant SNPs were also detected around the same region by the ssGWAS with frequentist p value tests ( Figure S1).…”

“…Recently, Uemoto, Ogawa, Satoh, Abe, and Terada (2020) developed prediction equations for CH 4 and methane yield traits, which could account for beef cattle fed with high-concentrate diets by including dietary and animal characteristic variables in the prediction equation. In addition, Takeda et al (2018Takeda et al ( , 2020 reported results of genetic and genomic analyses for feed-efficiency traits measured for approximately a year fattening period in Japanese Black steers; thus, it is possible to evaluate the genetic effects of predicted methane-related traits over long fattening periods using a dataset and prediction equations. Therefore, the objectives of this study were to clarify and better understand the genetic architecture of predicted methane-related traits by performing (a) genetic parameter estimation and (b) a genome-wide association study (GWAS) in Japanese Black steers.…”