Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data.

Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China. It is bred by crossing the Brahman, the Murray Grey and the Yunnan Yellow cattle. Yunling cattle can adapt to the tropical and subtropical climate environment, and has good reproductive ability and growth speed under high temperature and high humidity conditions, it also has strong resistance to internal and external parasites and with good beef performance. In this study, we generated a high-quality chromosome-level genome assembly of a male Yunling cattle using a combination of short reads sequencing, PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly(3.09 Gb) is anchored to 31 chromosomes(29 autosomes plus one X and Y), with a contig N50 of 35.97 Mb and a scaffold N50 of 112.01 Mb. It contains 1.62 Gb of repetitive sequences and 20,660 protein-coding genes. This first construction of the Yunling cattle genome provides a valuable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate Yunling cattle breeding efforts.

Population Structure and Genetic Diversity of Yunling Cattle Determined by Whole-Genome Resequencing.

The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and rough feed. It can be rightfully stated that Yunling cattle serve as vital genetic repositories of the local Yunnan cattle. Gaining insights into the genetic information of Yunling cattle plays a significant role in the formulation of sound breeding strategies for this breed, safeguarding genetic resources and mitigating the risks associated with inbreeding depression. In this study, we constructed the Yunling cattle standard reference genome and aligned the whole genomes of 129 Yunling cattle individuals to the constructed reference genome to estimate the current genetic status of Yunling cattle in Yunnan Province, China. The average alignment rate and the average percentage of properly paired are both 99.72%. The average nucleotide diversity in Yunling cattle is 0.000166, which indicates a lower level of diversity. Population structure analysis classified Yunling cattle into two subgroups. Inbreeding analysis revealed that inbreeding events did occur in the Yunling cattle, which may have contributed to the low genetic diversity observed. This study presents a comprehensive assessment of the genetic structure and diversity among the Yunling cattle and provides a theoretical foundation for the preservation and exploitation of these precious germplasm resources.