In House Generated SSR markers Reveals Genetic Variation and Population Structure in the Germplasm and Identification of Trait-Specific Markers that Enables Efficient Plant Breeding Program in Moringa (Moringa oleifera)

Abstract

Moringa oleifera Lam. leaves are rich in nutritionally and therapeutically important bioactive compounds. As the knowledge on natural population genetic diversity is a prerequisite for further leaf biomass improvement, the morphological and molecular diversity were assessed among 55 South Indian ecotypes of M. oliefera. Leaf traits such as leaf length, breadth, fresh weight, dry weight and number of leaves were evaluated for morphological diversity and for genetic diversity, a total of 116 Simple Sequence Repeats (SSR; including 75 Genomic- and 41 Genic-SSR) were used. Polymorphic information content (PIC) for those SSRs had ranged from 0.0 (for SSR19876) to 0.96 for (SSR25987) with an average of 0.886. The heterozygosity ranged from 0.0 to 0.96 with an average of 0.215 and those allelic data clustered the investigated accessions into three main clusters using the Unweighted Pair Group Method with Arithmetic mean (UPGMA). Analysis of molecular variance (AMOVA) indicated that 71% of diversity was attributed to differences among individuals of population. Cluster analysis, Principal coordinate analysis (PCoA) and structure-based population study showed that, there was no geographical distribution among the genotypes. Marker-trait associations was also implemented with general and mixed linear models and 65 SSR markers were found to be associated with investigated leaf traits at p < 0.05. Among them, six SSRs were linked to the investigated leaf biomass traits with more than 70% influence on the expression of those traits and shown to have putative functions in leaf biomass, which would be potential candidates for molecular breeding in Moringa.