The genetic diversity of Japanese Wagyu using molecular markers

Abstract

We have investigated the genetic diversity and structure using several DNA markers, such as mtDNA, Sry gene in Y chromosome and autosomal SNPs for Japanese Wagyu and native cattle in the North Eastern Asia. Most of Japanese cattle mtDNA belonged to Bos taurus mtDNA haplogroups T1, T2, T3 and T4. All Japanese populations included Asian unique mtDNA haplogroup T4 with high frequencies (0.43-0.81). The predominant T4 haplogroup may be a result of founder effect when ancestral cattle were introduced to Japan Islands at the immigration. We found that Mongolian cattle have Bos indicus mtDNA with the genetic frequency of 0.20, but no Bos indicus Y chromosome. No Bos indicus mtDNA in both Japanese and Korean samples suggested that the introgression may be a secondary phenomenon, with the earlier cattle in the region being purely Bos taurus. We analyzed 117 SNPs to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations. The results could suffi ciently explain the genetic construction of Asian cattle populations. These results reflected to the geographical and historical background in each population. The genetic information would contribute to understanding origin of North Asian native cattle, in addition to the origin of Japanese Wagyu cattle.

Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis

“…In the current study, we investigated on genetic diversities, structures, and relationships in Japanese cattle breeds using 50 K SNP array data. Although they have been reported in prior research, based on sequences of mtDNA D‐loop region, SNPs on Y chromosome, and several hundred autosomal SNPs (Mannen, 2006; Mannen et al, 2004, 1998, 2017; Noda et al, 2018; Sasazaki et al, 2006; Yonesaka et al, 2016), this is the first study to comprehensively investigate using 50 K SNP array data in all four Japanese cattle breeds. We also used 50 K SNP datasets of foreign cattle breeds downloaded from a database to compare the genetic diversity and survey the genetic relationship between Japanese and foreign breeds.…”

“…Although they have been reported in prior research, based on sequences of mtDNA D-loop region, SNPs on Y chromosome, and several hundred autosomal SNPs (Mannen, 2006;Mannen et al, 2004Mannen et al, , 1998Mannen et al, , 2017Noda et al, 2018;Sasazaki et al, 2006;Yonesaka et al, 2016), this is the first study to comprehensively investigate using 50 K SNP array data in all four Japanese cattle breeds.…”

Mass spectrometry-based untargeted metabolomics approach for differentiation of beef of different geographic origins

“…Meanwhile, Mannen used mitochondrial DNA to classify Wagyu cattle from Japan (Mannen, 2017). Although these studies demonstrated the utility of the genomics approach in determining the geographical origin of beef, no studies have compared DNA profiles among beef from different countries.…”