Phylogenetic assessment of selected Ghanaian groundnuts, in reference to U.S. mini-core based on Kompetitive allele-specific PCR (KASP) and axiom single nucleotide polymorphism (SNP) array protocols

Groundnut farming has always been an essentially major agricultural venture, both commercially and in subsistence, to the inhabitants of the Northern Regions of Ghana. The current study sought to assess the relationship and genetic diversity, through a phylogenetic analysis, among twenty-five (25) Ghanaian groundnut genotypes, in reference to US groundnut mini-core collection, based on the Kompetitive allele-specific PCR (KASP) protocol (a high throughput genotyping platform for marker-assisted selection, studies [LightCycler 480II]) and axiom single nucleotide polymorphism (SNP)  array version 2 (48,000 SNP features). It further sought to classify the groundnuts into sub-species based on botanical types, market types, general uses as well as genetic diversity to late leaf spot resistance. The Qiagen Dneasy DNA extraction Kit was used for DNA extraction. Results of the study indicate that majority of the Ghanaian groundnuts evaluated belonged to the Virginia (hypogaea) (large-seeded), Spanish/Valencia (vulgaris/fastigiata) and Mixed (Virginia x Valencia) types based on characteristics, including growth habit (erect/semi-erect/upright/bunch or trailing/spreading) seed or pod size/shape and disease resistance. Thus, significant genetic diversity in morphological characteristics, botanical and market varieties, growth habit and seed size were found among the groundnuts studied. Information generated from this study can be used to develop new groundnut breeding lines that combine these traits to produce higher yields. Marker-assisted selection procedures could help enhance this process based on the availability of QTLs and genes for the traits and markers developed in that regard. Key words: Axiom, genetic diversity, genotypes, groundnut, Kompetitive allele-specific PCR (KASP), mini-core collection, phylogenetic analysis, disease resistance, single nucleotide polymorphism (SNP).