YGEP: An Integrated Web Platform for Genomic Evaluation and Intelligent Breeding in Yak

The yak, a vital livestock species in high-altitude alpine ecosystems, plays crucial roles in meat, milk, and wool production while also contributing to ecological balance. Traditional yak breeding systems, however, encounter several challenges such as scattered herd data management, inefficient phenotypic data collection, absent pedigree records, and complex technical barriers when implementing genomic technologies.

These issues limit the widespread adoption of modern genetic evaluation methods in yak breeding initiatives.

To address these limitations, researchers have developed the Yak Genomic Evaluation Platform (YGEP), a comprehensive digital system designed for yak genetic selection and herd management. YGEP unifies three essential analytical modules: pedigree reconstruction, genotype imputation, and genomic breeding value estimation. When tested on a dataset of 706 yaks, the platform demonstrated impressive results, with GBLUP achieving a prediction accuracy of r = 0.96 for cannon bone circumference (CCB) and KBeagle achieving 84.0% imputation accuracy using a combined reference panel.

By integrating these advanced genomic functionalities into a user-friendly cloud-based platform, YGEP effectively eliminates technical and data bottlenecks that have historically hindered the application of genomic technologies in yak breeding. As a result, YGEP offers an accessible, scalable, and standardized solution to enhance digital herd management and precision genetic improvement in alpine livestock, ultimately overcoming the constraints faced by traditional yak breeding systems.