The Wagyu breed of cattle, known for its marbled and high-quality beef, commands a significant premium in global markets, underlining the importance of investigating the Wagyu population in the United States. This small population of Red Wagyu (Akaushi) and Black Wagyu were imported to the United States from Japan in the early 1990’s and since then has not had any more live animals, semen, or embryos available. This strange introduction of this cattle breed to the US and the unique selection pressures on a relatively un-researched breed demands further investigation through genomic technologies. In the U.S. market, Wagyu beef products are becoming increasingly commonplace. However, there is a notable absence of standardization to these products which carry high price tag due to the breed's reputation for superior quality and taste. Verifying products through genotype is the most straightforward approach, yet sequencing methods have been largely inaccessible, limited to specialists in molecular genetics. Oxford Nanopore's new mobile sequencing tools aim to increase sequencing capabilities for anyone. An initial trial run with inexperienced user conducted seven flow cell sequencing runs on the handheld MinION sequencer to sequence a single animal's genome. Results achieved good breadth and a low depth coverage across the genome, with each run generating more data. While ONT promises over 50 GB per run, the highest run achieved ~6 GB, signaling a significant gap between expected and actual output. Despite this difference, the technology's novelty and the user's inexperience didn't prevent successful sequencing. This emphasizes the potential of ONT's products for mobile sequencing, particularly for newcomers, extending beyond traditional lab settings. Enabling the mobility of this sequencer for on-site product verification necessitated developing a mobile genomic sequencing kit for field use. Establishing an out-of-lab protocol was essential to swiftly identify breeds, with a specific focus on identifying Wagyu animals in this study. Sam Red (Akaushi) Wagyu and Black Wagyu animals were sequenced using the mobile kit. Breed verification of all animals was initially done with principal component analysis (PCA), but due to low output and sporadic coverage of the genome, PCA showed to be a poor way to identify breed of origin. Another method of directly matching haplotypes to a reference population was employed which was successful and boasted high correlation (0.55) and concordance rates (0.94) of sample haplotypes to the correct reference breed. These identification methods successfully verified Wagyu samples and hold potential for broader application in field product verification. However, the genomic landscape of US Wagyu largely remains unexplored. While the traditional Wagyu breeds from Japan are well-documented, the genetic composition of American Wagyu is not yet fully grasped. Initial explorations into this breed revealed inbreeding and extensive linkage disequilibrium within the genome. A particularly intriguing finding emerged in Akaushi animals: they exhibited a close genetic relation to the Korean Hanwoo breed, as evidenced by a Principal Component Analysis (PCA). This correlation isn't entirely surprising, given the historical understanding that Japanese animals have roots tracing back to inland Korea. This connection sheds light on the genetic affinity between Red Wagyu and the Hanwoo breed, offering insights into their shared ancestry. Further connections between the Black Wagyu, Red Wagyu, the RedBlack cross between the two Wagyu groups and Korean Hanwoo were tested through estimating the accuracy of predicting phenotype between the breeds. The accuracy between Red and Black Wagyu was low, approximately 0.10 and increased when using the RedBlack or the Korean Hanwoo, ranging from 0.23 to 0.27. To address unbalanced breed group sizes (~150 Black Wagyu versus ~5000 Red Wagyu), the total population was divided into 10 balanced groups based on animal relatedness via the first principal component. Testing prediction accuracies within these splits revealed higher accuracies, especially between closely related splits, reaching up to 0.45. Notably, the split involving Red Wagyu (1st PC split) and Korean Hanwoo (10th PC split) demonstrated this heightened accuracy, reinforcing the close genetic relationship between these breeds. Lastly, a comprehensive genome-wide association study across all breeds identified new genomic regions on chromosomes 6, 10, and 14 associated with growth in Asian cattle. The uncovered genomic architecture of US Wagyu can aid in understanding the unusual introduction of US Wagyu and small number of animals available that have shaped the Wagyu population today. This understanding will pave the way for enhanced breeding programs, enabling producers to further refine and optimize the desirable traits of Wagyu beef, ultimately improving its quality and consistency. The exploration of US Wagyu's genomic landscape further contributes to the authenticity and traceability of Wagyu products in the market. By establishing a comprehensive genetic profile, it is easier to verify and certify the quality of Wagyu beef, thereby ensuring transparency and trust for consumers.
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