Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

摘要: Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. recurrent parents, rice breeders at the Africa Rice Center developed several ‘New for (NERICA)’ improved varieties. A smaller number of intraspecific varieties have also been released ‘Advanced (ARICA)’. Here, we studied genetic variation, relatedness, population structure 331 widely used genotypes in using DArTseq-based single nucleotide polymorphisms (SNP). sample 1 aus, 11 ARICAs, 85 NERICAs, 62 japonica, 172 indica were genotyped with 26,260 SNPs, which 15,020 SNPs polymorphic. Genetic distance between pairs that belong to indica, ARICA NERICA varied from 0.015 0.624, 0.020 0.661, 0.075 0.763, 0.014 0.644, respectively. The proportion > 0.400 was largest within NERICAs (35.1% pairs) followed by japonica (22.6%), ARICAs (18.2%), (7.8%). We found one pair 35 differing < 2% total scored alleles, due 26 identical pedigrees. Cluster analysis, principal component model-based analysis all revealed two distinct groups corresponding lowland (primarily NERICAs) upland (japonica growing ecologies. Most formed a sub-group, likely caused differences genome compared genotypes. Analysis molecular variance very great differentiation (FST = 0.688) ecologies, 31.2% variation attributable cluster groups. About 8% (1,197 15,020) polymorphic significantly (P 0.05) different contrasting haplotypes could clearly discriminate This is first study high density markers characterized comparison Africa.