Multiple marker effects of single nucleotide polymorphisms in three genes, AKIRIN2, EDG1 and RPL27A, for marbling development in Japanese Black cattle

Abstract

Marbling in beef, measured by Beef Marbling Standard (BMS) number, is an economically important trait for beef cattle breeding and markets in Japan. We previously detected three single nucleotide polymorphisms (SNPs) associated with BMS number of Japanese Black in Oita prefecture: c.*188G>A in AKIRIN2, g.1471620G>T in EDG1 and g.3109537C>T in RPL27A. Here, we carried out single and multiple marker association analyses for the three SNPs in a different commercial Japanese Black population of 892 genotyped animals. The single marker analyses with the model including a single SNP showed significant associations of all SNPs with BMS number. The multiple marker analysis with the model including the main effects of the three SNPs and their interactions detected only significant main effects of g.1471620G>T and g.3109537C>T and a significant interaction between c.*188G>A and g.1471620G>T. These findings suggest the presence of inter-allelic interactions among genes affecting the development of beef marbling. For effective marker-assisted selection for BMS number, interactions among these markers need to be considered.

The The favorable alleles of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN:g.231054C>T as candidate markers for high-marbling are very low in Bali cattle

“…The very high frequency of G allele in the present study was also detected in Japanese Shorthorn (0.975 to 0.981), Holstein (0.790) and Brown Swiss cattle (0.787) (Watanabe et al 2011). In contrast, the frequency of G allele tends to be less in Japanese Black cattle (0.262 to 0.568) (Sasaki et al 2009;Watanabe et al 2011;Sukegawa et al 2014) and Japanese brown (0.389 to 0.430) (Watanabe et al 2011). In the SNP of EDG1:c.-312A>G, all individuals of Bali cattle studied were detected to have AA genotype (100%) and consequently A allele was found to be fixed (1.000).…”

“…The genotype of AKIRIN2:c.*188G>A detected in Bali cattle were the GG (99.2%) and GA (0.8%), while AA genotype was not detected. The GG genotype was found to be the most frequent in Bali cattle, but not in Japanese Black and Korean cattle where the AG genotype was the most frequent genotype (48.0 to 52.3% and 64.7 to 73.2%, respectively) (Sasaki et al 2009;Watanabe et al 2011;Kim et al 2013;Sukegawa et al 2014). The G allele was to be the predominant allele in Bali cattle (0.996).…”

“…In bovine, the AKIRIN2, EDG1 and TTN genes have been mapped in Japanese Black cattle to chromosome 9, 3 and 2, respectively (Yamada et al 2006). Based on SNPs identification and association studies, the SNPs of c.*188G>A at 3'-untranslated region (3'UTR) of AKIRIN2 (AKIRIN2:c.*188G>A), c.-312A>G at 5'-untranslated region (5'UTR) of EDG1 (EDG1:c.-312A>G) and g.231054C>T at the promoter region of TTN gene B I O D I V E R S I T A S 20 (4): 965-970, April 2019 966 (TTN:g.231054C>T) have been found significantly associated to high-marbling breeding value (Sasaki et al 2009;Yamada et al 2009a, b;Sukegawa et al 2014).…”

Akirin2 promotes slow myosin heavy chain expression by CaN/NFATc1 signaling in porcine skeletal muscle satellite cells

“…Currently, Akirin2 has been reported to be located within genomic region of a quantitative trait locus for marbling, and has been shown to be differentially expressed in musculus longissimus muscle of low-marbled and high-marbled steer groups [8]. A number of studies showed that Akirin2 is associated with marbling based on single nucleotide polymorphisms analysis and may be considered as a positional functional candidate for the gene responsible for marbling [9–12]. …”

Genomic analysis of divergently selected experimental lines in rabbit

“…At genomic level, studies carried out in beef cattle suggest that IMF could be influenced by a large number of genes . Nevertheless, studies in Japanese Black cattle have reported genomic markers with large effects on IMF or marbling score around the SCD, FASN, AKIRIN2, EDG1 and RPL27A genes (Gotoh et al, 2014;Sukegawa et al, 2014). Genomic markers on the genes SCD and FASN have been incorporated into a breeding programme of this breed to select elite sires (Gotoh et al, 2018).…”