Microsatellites and agronomic traits for assessing genetic relationships among 18 New Rice for Africa (NERICA) varieties

The Africa Rice Center (WARDA) has developed several interspecific rice varieties by crossing the high yielding Asian rice (Oryza sativa subsp. japonica) with the locally adapted African rice (Oryza glaberrima). Eighteen varieties were named with the prefix NERICA (New Rice for Africa) but their genetic difference and patterns of relationship is largely unknown. A total of 102 polymorphic microsatellite markers were used to genotype 18 NERICAs. A subset of seven NERICAs (NERICA 1 to 7) was further characterized for 10 agronomic traits. The microsatellites data revealed no genetic difference between NERICA 8 and 9. The absence of genetic distance and identical SSR haplotype distribution (banding pattern) observed between NERICAs 8 and 9 is highly likely to be due to lack molecular difference at the DNA level but the possibility for seed admixture remains to be explored. This study, however, revealed the presence of a wide range of genetic differences among all other NERICAs, with the highest being between NERICA 6 and 17. Cluster and principal component analyses of the SSR data revealed distinct separation of NERICA 1 to 7 from NERICA 8 to 18. The possible reasons for such separation and the implications for breeding programs are discussed.