Pheno-genetic studies of apple varieties in northern Pakistan: A hidden pool of diversity.

• First application of alpha- and beta-diversity approach for apple accessions in N-Pakistan. • High numbers of rare phenotypes and private alleles suggest high potential for conservation. • Remoteness and distance of regions is not necessarily responsible for genetic sub-structuring. • Lack of awareness and management forces decline of local apple varieties. Apple (Malus × domestica) is a main fruit crop of cold temperate regions and traded globally. Despite being a comparatively well documented plant cultigen, available germplasm in many remote regions is still unexplored and threatened. Increasing market demands for modern cultivars and farmers' preference for high yields may lead to the gradual loss of indigenous varieties. Gilgit-Baltistan in northern Pakistan – a mountainous and remote apple growing region – was selected to study local cultigen diversity by assessing varietal richness and diversity, arboriculture activities as well as phenotypic and genotypic characters of available germplasm. In total, 106 individual apple trees were sampled, and 35 tree owners from seven villages of the two valleys Ishkoman and Baltistan were interviewed. Dendrometric parameters, fruit traits (qualitative and quantitative), and varietal diversity in each village were measured. Genetic variation was estimated using eleven SSR markers and synonyms and homonyms were identified based on cluster analysis. Sixty-one multi-locus genotypes (MLG; mean genotype diversity: 58 %) and 18 putative clones (comprising 2 to 9 ramets) were identified. Varietal diversity was highest in Baltistan where even a wild apple relative (Malus baccata) was discovered. Mean genetic diversity was moderate (H e = 0.677), while negative inbreeding coefficients indicated excess of heterozygotes in three genetic clusters. A moderate correlation (r = 0.627, p = 0.001) between phenotypic and genetic dendrograms suggested genetically linked fruit traits, which merits further exploration. Considering the high genetic and phenotypic variability, Gilgit-Baltistan appears a promising source of apple germplasm for future breeding programs. The promotion of local varieties may allow farmers to diversify their produce and derived sources of income as well as to maintain a historically important bio-cultural heritage of Gilgit-Baltistan. To this end, comprehensive conservation strategies combined with further participatory research will be needed. [ABSTRACT FROM AUTHOR]