The T allele at the g.1471620G>T in the EDG1 gene associated with high marbling in Japanese Black cattle is at a low frequency in breeds not selected for marbling

Development of nutrigenomic based precision management model for Hanwoo steers

Focusing high marble deposition, Hanwoo feedlot system uses high-energy diet over the prolonged fattening period. However, due to the individual genetic variation, around 40% of them are graded into inferior quality grades (QG), despite they utilized the same resources. Therefore, focusing on development of a nutrigenomic based precision management model, this study was to evaluated the response to the divergent selection on genetic merit for marbling score (MS), under different dietary total digestible nutrient (TDN) levels. Total of 111 calves were genotyped and initially grouped according to estimated breeding value (high and low) for marbling score (MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2 × 2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness (BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p > 0.05) on the MS. Furthermore, no genetic-by-nutrition interaction for MS (p > 0.05) was also observed. The present results showed no correlation response on BFT (p > 0.05), which indicates that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1⁺⁺ and QG1⁺) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1⁺⁺ animals among the high-genetic group by further increasing the dietary energy content. Overall, this precision management strategy suggests the importance of adopting an MS based initial genetic grouping system for Hanwoo steers with a subsequent divergent management based on dietary energy level.

Association of SNPs in AKIRIN2, TTN, EDG1 and MYBPC1 genes with growth and carcass traits in Qinchuan cattle

Growth and carcass traits are the main breeding objectives in beef cattle. The aim of this study was to confirm genetic effects of the c.*188G>A SNP of AKIRIN2, the g.231054C>T SNP of TTN, the g.1471620G>T SNP of EDG1 and the g.70014208A>G SNP of MYBPC1 on growth and carcass traits in Chinese Qinchuan (QC) cattle, as well as to compare the frequencies of the well-characterized alleles of these SNPs among six Chinese cattle populations, three Japanese cattle populations, two European cattle populations and one Korean cattle population. In this study, a total of 665 cattle samples were genotyped using MassARRAY and PCR-RFLP. Association analysis explored effects of four SNPs on growth and carcass traits including body length, wither height, hip height, hip width, rump length, chest depth, chest circumference, back fat thickness, ultrasound longissimus muscle area and ultrasound longissimus muscle depth in QC (P<0.05 to P<0.001). The well-characterized A (c.*188G>A), T (g.231054C>T) and T (g.1471620G>T) alleles in Japanese Black cattle were significantly higher than Chinese cattle breeds, on the contrary, the G allele (g.70014208A>G) was markedly higher in Chinese cattle breeds than other cattle breeds. These results suggest that the four SNPs might be useful as a molecular marker for growth-related traits in Chinese QC cattle.

Effect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and quality

Carcass traits have been efficiently improved by recent selection using DNA markers in beef cattle. Additionally, DNA markers might have an effect on other traits such as fertility traits; therefore attention should also be paid to such pleiotropic effects. However, the effects of the markers on both carcass and fertility traits have never been evaluated in the same population, since they are generally measured in different populations. The objective in the current study was to discuss effectiveness of DNA markers developed for carcass traits through investigation of their effects on carcass and fertility traits in a population. We genotyped six markers SCD V293A, FASN g.841G>C, PLAG1 g.49066C>G, NCAPG I442M, DGAT1 K232A, and EDG1 g.1471620G>T in a Japanese Black cattle population (n=515). To investigate their effects on carcass and fertility traits, we performed statistical analysis (ANOVA and the Tukey–Kramer honestly significant difference (HSD) test). In the results, three of six markers, SCD V293A, NCAPG I442M, and EGD1 g.1471620G>T, were significantly associated with both carcass and fertility traits. Remarkably, the same allele for each marker had positive effects on both traits, suggesting that we would be able to simultaneously improve them using these markers in this population. However, previous studies reported that the effects of DNA markers could differ among populations. Therefore, it is necessary to confirm the effect of the marker in each population before it is used for improvement.

Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing

The native Japanese cattle Mishima-Ushi, a designated national natural treasure, are bred on a remote island, which has resulted in the conservation of their genealogy. We examined the genetic characteristics of 8 Mishima-Ushi individuals by using single nucleotide polymorphisms (SNPs), insertions, and deletions obtained by whole-genome sequencing. Mapping analysis with various criteria showed that predicted heterozygous SNPs were more prevalent than predicted homozygous SNPs in the exonic region, especially non-synonymous SNPs. From the identified 6.54 million polymorphisms, we found 400 non-synonymous SNPs in 313 genes specific to each of the 8 Mishima-Ushi individuals. Additionally, 3,170,833 polymorphisms were found between the 8 Mishima-Ushi individuals. Phylogenetic analysis confirmed that the Mishima-Ushi population diverged from another strain of Japanese cattle. This study provides a framework for further genetic studies of Mishima-Ushi and research on the function of SNP-containing genes as well as understanding the genetic relationship between the domestic and native Japanese cattle breeds.