The GGP indicus chip consists of 35,090 SNPs that are optimally selected for Bos indicus breeds using the SelectSNP software package that features MOLO optimization (Wu et al., 2016). The chip also includes Bos indicus specific SNPs for parentage testing, and causative assays for genetic diseases.
The Bos indicus optimal 35K SNP panel features:
- 19K multi- indicus breed specific backbone SNP targets, highly informative according to weighted MAF
- 3K highly informative (breed-specific MAF > 0.40) SNPs specifically for Brahman and Nellore respectively
- 2K highly informative (breed-specific MAF > 0.40) SNPs for Guzzera and Gyr, respectively
- 3K highly informative (breed-specific MAF > 0.40) SNPs for DroughtMaster, Santa Gertrudis and Tropical Composites, respectively
- An additional set of 1000 map-optimal SNPs (chosen to fill chromosomal gaps)
- Imputation accuracy (to the Illumina Bovine HD) averages greater than 97% for all evaluated breeds