Molecular characterization of native corn populations in the Philippines based on SSR markers

Molecular characterization of native corn germplasm provides significant information useful for improved breeding program. Genetic variation and novel allelic differences cannot be fully determined by morphological characteristics only unless characterized at the DNA level. Genetic structure and variation among corn lines will provide relevant information on the degree of inheritance, genetic variation and level of heterosis. Several researches were conducted in CIMMYT inbred lines and populations, lowland tropics, subtropical mid-altitude, highland inbred lines and tropical corn germplasm. However, no study on the molecular diversity of corn native and traditional corn populations has been done. This study assesses the genetic diversity of 100 native corn populations collected across Luzon, Visayas and Mindanao [Philippines]. A total of 20 SSR markers with very distinct patterns distributed among the ten chromosomes of the corn genome were utilized in the genetic diversity assessment. At most 30 individual corn plants were sampled per population bulked into three sets consisting of ten plants per bulk to minimize allele dilution. An average of seven alleles were detected per bulk sample across the 20 SSR markers. A dendrogram was generated using R statistical software. Eighteen clusters were generated at a similarity coefficient of 0.43. The largest cluster comprised of 42 populations mostly coming from Mindanao. Moreover, APN 83 and APN 84 populations both collected from Leyte showed 95% similarity. Eight unique corn populations were generated wherein APN 138 collected from Bukidnon is the most different among the 100 native populations analyzed. The study provided key genetic information relevant in making decisions for corn native populations germplasm management and could be used by corn breeders to devise a more systematic and efficient breeding program for various traits of interest in corn.