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

Abstract

The objectives of this study were to estimate genetic parameters and to perform a genome‐wide association study (GWAS) for predicted methane‐related traits in Japanese Black steers. The methane production and yield traits were predicted using on‐farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane‐related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed‐efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome‐wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed‐efficiency traits were located on the regions. Our results suggest that the predicted methane‐related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.

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

“…In particular, our estimates for the heritability of RFI appeared to be notably low. Comparatively, somewhat disparate findings have been reported for the heritability of RFI in Japanese Black cattle, with Okanishi et al (2008) detecting low heritability, whereas Hoque and Oikawa (2004) and Uemoto et al (2020) have observed moderate heritability. In this regard, from 2002, the protocol of the performance test used for Japanese Black bull calves was modified with respect to the provision of concentrate based on BW, given the preponderance of excessively fat bulls obtained under the previous protocol, in which bull calves had ad libitum access to concentrate for 1 h twice daily (Okanishi et al, 2008).…”

“…Therefore, we can speculate that the higher heritabilities reported in previous studies could be attributable to an increase in the genetic variation for RFI in response to ad libitum access to feed. In addition, the higher heritability reported by Uemoto et al (2020) could also be attributed to the results obtained in Japanese Black steers with a long fattening period.…”

“…Using records based on the revised protocol, Okanishi et al (2008) reported that heritability estimates were moderate for DG and FI (ranging from 0.26 to 0.37) but low with respect RFI T (0.10), whereas Hoque and Oikawa (2004) reported a heritability of 0.24 for RFI S using records based on the previous protocol. More recently, Uemoto et al (2020) have reported heritabilities of 0.38, 0.43, 0.29, and 0.34 for FCR S , RFI S , RG S , and RIG S, respectively, in Japanese Black steers that were fattened for 52 weeks with ad libitum access to roughage and concentrate. In the present study, we found that the heritability estimate of RFI S was slightly higher than that of RFI T , which is assumed to reflect the fact that the percentage of roughage in FI S was higher than that in FI T .…”

“…The abbreviations used for traits are shown in Table 3. The standardized annual genetic gains, which were calculated as annual genetic gains divided by their genetic standard deviation, are shown Hoque and Oikawa (2004) and Uemoto et al (2020) have observed moderate heritability. In this regard, from 2002, the protocol of the performance test used for Japanese Black bull calves was modified with respect to the provision of concentrate based on BW, given the preponderance of excessively fat bulls obtained under the previous protocol, in which bull calves had ad libitum access to concentrate for 1 h twice daily (Okanishi et al, 2008).…”

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

“…Interestingly, more selection sweep regions were identified in the DM sheep relative to the AFR and Meatmaster. DM shared two sweeps with AFR, one on chromosome 1 in regions 119, 0–121, and 0 Mbs, which harbours IFNAR1, IL10RB, SLC5A3 , and CRYZL1 associated with anti-inflammatory and immune response ( Uemoto et al, 2020 ) and reproductive traits such as implantation of the conceptus to the uterus (Zhang et al , 2013), and one on chromosome 19 position in regions 46, 7–48, and 1 Mbs, which harbours the gene WNT5A (45 and 5 Mb), important in morphology, particularly the development of limbs and skeleton ( Fariello et al, 2014 ) and reproductive traits (including mammary gland development) (Hao et al , 2019). Other sweeps on chromosome 6 (93, 5–95, and 2 Mb) associated with the FGF5 gene are reported as a signature of selection in worldwide sheep breeds by Kijas et al (2012 ) and Fariello et al (2014 ), and the ANTXR2 gene is associated with adaptation to variation in climatic conditions ( Lv et al, 2020 ).…”