The use of multiplexed simple sequence repeat (SSR) markers for analysis of genetic diversity in African rice genotypes

Abstract

Rice is an emerging food and cash crop in Eastern Africa. Thousands of germplasm accessions have been introduced from major rice breeding centers, such as the International Rice Research Institute (IRRI), and Africa Rice but the genetic variability among the introduced rice germplasm is unknown. Knowledge on genetic diversity would be useful in designing measures for comprehensive breeding and conservation. To address this knowledge gap, 10 highly polymorphic rice simple sequence repeat (SSR) markers were used to characterize 99 rice genotypes to determine their diversity and place them in their different population groups. The SSR markers were multiplexed in 3 panels to increase their throughput. An average of 15.9 alleles was detected, ranging from 6 alleles detected by marker RM7 to 30 by marker RM333. The UPGMA dendogram based on Nei’s genetic distance cluster analysis, revealed 5 genetic groups among the genotypes tested. Analysis of molecular variance indicated that 97% of the diversity observed was explained by differences in the genotypes themselves, and only 3% was due to the sources from which the genotypes were obtained. This study sets the stage for further diversity analysis of all the available germplasm lines using SSR markers to ensure effective utilization and conservation of the germplasm.

Keywords: Genetic diversity, simple sequences repeat (SSR) markers, multiplexing, rice genotypes, structure.

Abbreviation: IRRI, International Rice Research Institute; SSR, simple sequence repeat; NaCRRI, national crops resources research institute; RAPD, random amplified polymorphic DNA; AFLP, amplified fragment length polymorphisms; RFLP, restriction fragment length polymorphisms; SNP, single nucleotide polymorphisms; BAC, bacterial artificial chromosome; PAC, P1-derived artificial chromosome; PCR, polymerase chain reaction; Ho, heterozygosity; He, heterozygosity.