Genetic diversity and population structure analysis of wild Malus genotypes including the crabapples (M. baccata (L.) Borkh. & M. sikkimensis (Wenzig) Koehne ex C. Schneider) collected from the Indian Himalayan region using microsatellite markers

The inadequate information on genetic diversity and population structure of wild Malus genotypes including indigenous Himalayan crabapples [M. baccata (L.) Borkh. and M. sikkimensis (Wenzig) Koehne ex C. Schneider] collected and maintained at different field gene banks of apple necessitated this study. A set of 31 SSR loci covering all the linkage groups of apple genome was successfully used in this study. The average number of alleles at per locus, major allelic frequency, expected heterozygosity, observed heterozygosity and PIC values were 3.29, 0.592, 0.506, 0.271 and 0.438, respectively among the studied SSR loci. The set of SSR loci yielded 8 unique and 11 rare alleles among the wild Malus genotypes. These wild Malus genotypes were grouped into seven distinct clades, where the indigenous Himalayan M. baccata (L.) Borkh. ecotypes were grouped in separate clades confirming them to be genetically distinct. Furthermore, model based population structure differentiated the wild apple genotypes into three populations of which one was indigenous Himalayan M. baccata (L.) Borkh. ecotypes. The high allele-frequency divergence among populations revealed high genetic differences between them. The AMOVA revealed high genetic diversity between populations of wild Malus genotypes; and within; and among the individuals of the populations. The PCoA validated and reconfirmed the three groups of the population as differentiated by model based population structure. The genetic uniqueness of indigenous Himalayan M. baccata (L.) Borkh. ecotypes can further add the new genes in the global gene pool of apple. This study could serve as base information for future exploration and collection of more accessions of indigenous Himalayan crabapples from the region extending to about 7000km in the Indian Himalayan region. The existing high degree of genetic diversity among the studied wild apple genotypes could be the valuable genetic resource for the apple improvement programmes.