New hyper-variable SSRs for diversity analysis in mango (Mangifera indica L.)

Abstract

Whole genome sequence in mango offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, simple sequence repeats (SSRs) were predicted from genome sequence of mango. Based on the SSR length (≤ 50 bp), highly-variable mango SSRs (MSSRs) were sorted. A sub-set of 129 MSSRs was validated on a set of 24 diverse mango genotypes yielding marker validation and polymorphism of 88.96 and 85.27 per cent, respectively. One hundred and ten polymorphic markers were identified for the present set of mango genotypes. Polymorphic information content (PIC) ranged from 0.10 to 0.78 and the highest value was observed with MSSR133. The mean PIC value was 0.40 but 33 MSSR markers showed PIC values ≥ 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs) in mango. MSSRs data was further used for diversity analysis of mango genotypes belonging to different agro-ecological conditions including chance seedlings, landraces, exotic and indigenous germplasm and hybrids. Cluster analysis using UPGMA of 24 mango genotypes revealed that these MSSRs were informative in diversity analysis and distinguished mango genotypes based on their origin, parentage and embryo types. A novel set of 110 hyper-variable SSR markers have been added to the mango repository depicting usefulness in discriminating closely related mango germplasm and their use in mango improvement programme.