SNP Discovery and Genetic Clustering of Philippine 'Carabao' Mango (Mangifera indica L. cv. 'Carabao') using Genotype-By-Sequencing (DArTseq)

Understanding the genetic diversity of the Philippine 'Carabao' mango is important to identify possible genetic groups as source of traits for the improvement of the variety. Genotype-bysequencing (GBS) (using DArTseq molecular platform) was performed on 341 mango accessions from selected regions of the Philippines. Total single nucleotide polymorphisms (SNPs) numbered 31,208 which was filtered and imputed to 15,604 sequences. BLAST results for the SNPs show high homologies to genes from Citrus sinensis and Brassica sp. Functional variation was high on genes involved in cellular processes and signaling while 344 SNPs have no hits indicating possible novelty in M. indica. Homology of SNPs include agronomically important traits such as disease resistance and pathway genes for antioxidants and other secondary metabolites. Principal component analysis using the correlation of variances of the SNPs showed that genetic clustering of individuals accounted for 30% of the variation. There were four isolated groupings comprised of eight clusters based on locations and vaguely on their 'Carabao' characteristics. Group three clusters, VI and VII, contain most 'Carabao' accessions as well as red accessions, while isolated cluster VIII contains most commercial varieties such as Sweet Elena and Guimaras Super. Despite the high density of individuals and SNP markers found on all diversity analyses, consistent clustering of the 'Carabao' and non 'Carabao' accessions was not observed, but instead an increasing gradient of frequency can be traced in different groupings. Genomic clustering provided information on the relatedness of mango accessions across the Philippines while the SNPs provided genotypic information which can be utilized for marker-assisted selection in mango breeding.