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Genetic diversity of Manihot esculenta Crantz germplasm based on single‐nucleotide polymorphism markers

de Albuquerque, Hilçana Ylka Gonçalves, Carmo, Catia Dias do, Brito, Ana Carla, Oliveira, Eder Jorge de
Annals of applied biology 2018 v.173 no.3 pp. 271-284
Manihot esculenta, cassava, chromosomes, color, discriminant analysis, genetic variation, germplasm, heterozygosity, inbreeding, linkage disequilibrium, phenotype, phenotypic variation, population structure, provenance, pulp, reproductive system, single nucleotide polymorphism, Brazil
Cassava (Manihot esculenta Crantz) is a species whose natural diversity has great food, industrial and energy potential. This study aimed to evaluate the genetic diversity, and population structure of 1,580 accessions belonging to the international germplasm conserved in Brazil using 20,601 single‐nucleotide polymorphism markers. The average values of polymorphic information content (PIC), inbreeding (f), observed heterozygosity (Ho) and expected heterozygosity (He) were 0.24, 0.21, 0.23 and 0.30, respectively, presenting levels of genetic diversity compatible with the nature of the marker (predominantly biallelic) and with the species reproductive system. The mean values of He, Ho, PIC and f were similar for the 18 chromosomes of the species. At the individual level, f values ranged from 0.49 to 0.97, with an average of 0.69, whereas some cassava accessions showed f > 0.90. The values of linkage disequilibrium ranged from 15 to 20 kb (r² = 0.20). In the discriminant analysis of principal components (DAPC), 22 groups were formed with probabilities of assignment of individuals above 0.99. No association was observed between DAPC grouping and clusters based on phenotypic data (cyanogenic compound content and colour of the root pulp) and on genetic and geographic origin. However, the DAPC grouping resulted in greater variation between groups (14.85%). This information suggests extensive exchange of cassava germplasm in Brazil and wide molecular and phenotypic diversity. These results will provide a better understanding of the preserved genetic variability and the population organisation of the germplasm.