# Paternal Lineage and Genetic Diversity of Jiuzhi Yaks Revealed by Y-Chromosome SRY Sequencing

## TL;DR

This study reveals that Jiuzhi yaks have two paternal lineages and moderate genetic diversity, which helps in selecting breeding bulls to preserve unique traits and improve productivity on the Qinghai-Tibetan Plateau.

## Contribution

The study provides the first quantitative analysis of paternal lineages in Jiuzhi yaks using Y-chromosome SRY sequencing.

## Key findings

- Jiuzhi yaks have two paternal lineages and twelve haplotypes, six with private alleles.
- Jiuzhi yaks show moderate genetic diversity and close affinities with Jinchuan, Yushu, and Huanhu breeds.
- F_ST values show strong divergence from Tianzhu White and Wild yaks but little from Qinghai Plateau and Yushu yaks.

## Abstract

Accurate knowledge of male lineages helps herders select bulls that keep unique traits while boosting herd productivity. We sequenced the SRY gene in 117 male yaks from eight breeds and found that Jiuzhi yaks derive from two paternal lineages with moderate diversity. Breeds such as Tianzhu White and Wild yaks are genetically distant, so that uncontrolled crossbreeding could erode rare alleles. Our results guide producers in choosing sires that safeguard local genes and improve performance under plateau conditions.

Yak husbandry on the Qinghai–Tibetan Plateau relies on genetically resilient sire lines, yet the paternal ancestry of the locally prominent Jiuzhi breed has never been quantified. To resolve this gap, a 690 bp fragment of the Y chromosomal SRY gene was sequenced in 117 males spanning Jiuzhi (n = 12) and five neighboring Qinghai breeds and compared with three single individual public records that represent Qinghai Plateau, Tianzhu White, and Wild yaks. Alignment, haplotype calling, diversity indices, F_ST differentiation, AMOVA, multidimensional scaling, and TCS network analysis were performed. Thirty-two haplotypes were recovered; Jiuzhi yaks possessed twelve, and six of them had private alleles. Mean A + T content was 53.8%. Haplotype diversity was highest in Qinghai Plateau, Tianzhu White and Wild yaks and lowest in Larima yaks, while Jiuzhi diversity resembled that of Huanhu. Pairwise F_ST values indicated negligible differentiation between Jiuzhi and either Qinghai Plateau or Yushu yaks (F_ST ≈ 0) but pronounced divergence from Tianzhu White and Wild yaks (F_ST ≈ 0.97–0.99). AMOVA attributed 90.7% of molecular variance to among-breed differences, and multidimensional scaling clustered Jiuzhi with Jinchuan, Yushu and Huanhu. Network topology resolved two patrilineal clades, confirming dual paternal origins for Jiuzhi yaks. These data provide the first quantitative baseline for sire selection and conservation of Jiuzhi yaks and highlight close affinities with adjacent plateau breeds. Limitations include the use of single individual public sequences for Qinghai Plateau, Tianzhu White and Wild yaks (employed solely as phylogenetic anchors) and reliance on a single Y-linked locus; broader sampling and multilocus approaches will refine within-breed estimates.