# Development and Application of a 40 K Liquid Capture Chip for Beef Cattle

## TL;DR

A 40 K liquid SNP capture chip was developed for beef cattle to improve genetic understanding and breeding efficiency in China.

## Contribution

A new 40 K liquid SNP capture chip was developed for genotyping and analyzing genetic diversity in Hubei beef cattle breeds.

## Key findings

- The chip achieved a high SNP call rate of 99.48% when tested on 200 individuals.
- It successfully differentiated between foreign and indigenous cattle breeds in a population of 205 individuals.
- The chip identified 2547 ROH and genes linked to economically important traits in 195 local Hubei cattle.

## Abstract

The evaluation and utilization of local germplasm resources still pose limitations to the efficient and sustainable development of the beef cattle industry in China. With the increasing amount of sequencing data, the development of single-nucleotide polymorphism (SNP) chips has increased, enabling the evaluation, development, and utilization of local germplasm resources. Here, we developed a 40 K liquid SNP capture chip and evaluated its performance in genotyping, efficacy in population genetic studies, and practicality in identifying runs of homozygosity (ROH). These findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value.

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective genotyping platform essential for molecular breeding of livestock. In this study, we developed a liquid SNP capture chip suitable for five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. The panel consisted of 42,686 SNPs (~40 K). These SNPs were evenly distributed on each bovine chromosome, with the majority of SNPs having minor allele frequencies >0.05 and located within intergenic regions. The performance evaluation of this SNP chip panel was proceeded by genotyping 200 individuals, revealing that this panel has a high SNP call rate of 99.48%. The SNP chip panel was further used to examine the population structure of a beef cattle population with 205 individuals and demonstrated the ability to differentiate between foreign and indigenous cattle breeds. The SNP chip was also used to determine the runs of homozygosity (ROH) within a local Hubei beef cattle population of 195 individuals. We identified 2547 ROH and several genes associated with economically important traits in the study population. Our findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value.