Whole-genome variants resource of 298 Saanen dairy goats

Abstract

The Saanen breeds are often used as terminal sires for hybridization and play an important role in the global dairy food industry. However, there is still a lack of genomics information on the Saanen dairy goats. Whole-genome sequencing offers a promising approach to identify genetic markers associated with economic traits and discover new candidate genes. This can effectively utilize genetic resources to accelerate breeding processes and improve lactation performance in Saanen dairy goats. In this study, we present the genomes of 298 Saanen dairy goats. Through rigorous sequencing and quality control, we achieved an average sequencing depth of 14.6X, with 92.3% of high-quality (Q30 > 90%) data and an average mapping ratio of 99.9%, indicating reliable results. By comparing our data to a reference genome of Saanen dairy goats, we identified14.59 million single nucleotide polymorphisms (SNPs) and 1.34 million insertions-deletions (InDels). This dataset significantly contributes to enriching public databases in dairy goats and provides valuable resources for studying genetic diversity, improving breeds, and developing new varieties.

Fig. 1

Sample quality control, data processing, and variant filtering general workflow. This process is consistent with the variant calling scheme recommended by GATK.

Fig. 2

Boxplots showing the average sequencing depth, raw base and raw Q30 for Chinese Saanen samples (n = 298).

Fig. 3

Statistics for the SNP Fraction in depth (a), neighbouring SNP distance (b). The different colour indicated the various individual.

Fig. 4

Distribution of SNP and InDels across the whole-genome of 298 Chinese Sannen goat. (a) SNP density statistics across the whole-genome. (b) SNP and InDel density statistics across the whole-genome.