A Comparative Evaluation Of Genetic Diversity And Relationships Among The AA-genome Oryza Species Using SSR Markers

SSR marker and genetic analyses were employed to study the genetic diversity and relationships of AA-genome Oryza species with 87 representative accessions at the level of individual, species and population. DNA polymorphism analysis on 87 accessions showed that polymorphism with a 100% of polymorphic loci was detected by all 31 pairs of microsatellite markers distributed over 12 chromosomes of the whole rice genome. A total of 415 polymorphic bands were generated from these SSR primers, with an average of 13.38 bands per pair of primer. The amplified DNA fragments varied in size from 78 bp to 280 bp. The values of polymorphic information content (PIC) was 0.683808 on average. systematic analysis including Nei's expected heterozygosity ,Shannon's Information index , Gene flow estimated from Fst and clustering revealed that O. glaberrima had a closer relationship with O. barthii than with the others, confirming that O. glaberrima was derived from O. barthii in Africa. All of the Asian AA-genome Oryza species had much closer relationship. Of them, Asia cultivated species O. sativa had closer relationship with wild species O. rufipogon than with wild species O. nivara, supporting that O. sativa was derived from O. rufipogon. The genetic distance between the indica and japonica was lower than their distance with O. rufipogon,indicating that the differentiation between indica and japonica took place after the domestication of O. rufipogon . The relationship between O. spontanea and O. rufipogon was much closer than O. nivara,which suggested that O. spontanea was a weedy rice species between O. rufipogon and O.sativa under natural selection and artificial interference. Based on this study, O. rufipogon was one species with the richest genetic diversity and O. sativa was the second. Because no reproductive isolation existed between O. rufipogon and O. sativa, excellent germplasm of O. rufipogon could be directly used in enriching the rice gene bank for improvement. The genetic and evolutional relationships among the AA-genome Oryza species identified at DNA level by this study would be useful in modifying the taxonomical system of these rice species constructed by previous researchers. DNA polymorphism data of all the tested AA-genome germplasm would benefit the genetic resources conversation, core collection construction and genetic improvement of rice.