Whole-genome Sequence and Genetic Variant Analysis of the Tankwa Feral Goat of South Africa

The Tankwa is a South African feral goat breed that has survived several generations in the Karoo desert without human intervention, before it was transferred to Carnavon Research Station in South Africa as a conservation flock. The unique phenotypic and genetic features of the Tankwa are the reason why the breed is regarded as a suitable candidate for screening for novel genetic variants that can be used in goat improvement programs. Analysis using the 60K SNP chip data has confirmed that the Tankwa breed has unique genetic characteristics compared to other South African breeds. Since the SNP chip was designed using exotic goat breeds and may not necessarily contain all the polymorphic sites found in the African breeds, it has become important to unravel the Tankwa genome further. This study was aimed at screening and annotating genetic variants in the Tankwa goat genome using Illumina HiSeq2500 paired-end whole-genome sequence data. In total, 20 goats were used. Approximately 112 million reads were generated for one Tankwa goat at 60x and an average of 148 million reads were generated for 10 pooled individuals from both Boer and Tankwa breeds at 10x coverage. After quality control, alignment of the reads to domestic goat reference genome (CHIR1.0) resulted in mapping between 97.70 and 99.51%. Genome Analysis ToolKit-3.3.5, HaplotypeCaller was used for variant discovery and over 1 million variants were identified. On average, approximately 44 % of the variants were SNPs and 54 % were INDELs. In addition, 13,711 multi allelic SNPs and complexes were recovered for both the Tankwa and the Boer genomes. Novel variants were discovered predominantly in the Tankwa breed. Gene annotation and pathway analysis suggested association of the single nucleotide polymorphisms with immune functions and general cellular mechanisms, both processes that could be of importance in the viability of the feral goats.