Investigation of population structure and molecular genetic diversity under coastal agro-ecosystem in rice (Oryza sativa L.)

Abstract

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Thirty nine simple sequence repeat (SSR) markers were selected in order to evaluate the genetic diversity in 88 genotypes. A total of 115 alleles were detected in 39 SSR polymorphic markers. The number of alleles per marker ranged from 1 to 5, with an average of 3 alleles per locus. An average polymorphism information content value of 0.5615 was recorded. It ranged from zero (RM431, RM379 and RM262) to 0.6476 (RM324), indicating significant genetic diversity among and within the rice accessions of the present study. The average observed heterozygosity was 0.1136, while the average expected genetic diversity was 0.6105. A dendrogram constructed using the Unweighted Pair Group Method with Arithmetic means (UPGMA), grouped the 88 rice genotypes into three well differentiated major clusters. The structured program without prior information provided support for the existence of three genetically distinct clusters (K=3).

Keywords

• cluster analysis
• ssr marker
• oryza sativa
• rice breeding
• variability.