Diversidade genética e identificação de duplicatas de Manihot esculenta Crantz com base em marcadores Single-Nucleotide Polymorphism (SNP)

Abstract

Cassava (Manihot esculenta Crantz) is one of the most important food sources in the tropics and much of their genetic diversity is preserved at germplasm collections. Therefore, the objective of this work was to analyze the genetic diversity and population structure of 1,580 cassava accessions, as well as to identify redundant genotypes from the analysis of 2,371 accessions preserved at different Embrapa research units. All these analysis were performed based on Single-Nucleotide Polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS). Mean genetic diversity parameters, polymorphic information content (PIC), inbreeding (f), observed heterozygosity (Ho) and expected heterozygosity (He) was 0.24; 0.21; 0.23; and 0.30 respectively, considered high, considering the predominant biallelic nature of the SNPs and the species reproductive system. The values of these parameters were quite similar throughout the 18 chromosomes of the species. At individual level, f values ranged from 0.49 to 0.97; with an average of 0.69, for three cassava accessions, being f > 0.90. The values of linkage disequilibrium (LD) extended between 15 and 20 kb (r2 = 0.20). The discriminant analysis of principal components (DAPC) indicated the formation of 22 groups, with individual allocation probability > 0.99. However, no association between the DAPC groups and the classification based on the phenotypic and genetic information, as well as the geographical origin, was identified. In order to identify duplicates a study was conducted based on the grouping of accessions according to multilocus analysis (MLGs) from different Embrapa units. 1,757 single and 614 duplicate accessions, approximately 25.89% of the total, with redundancy ranging from 22.47% (Embrapa Amazônia Oriental) to 40.0% (Embrapa Semiarido), were identified. These results will provide a better understanding of the preserved genetic variability and the germplasm population organization, since the presence of duplicates compromises germplasm development and increases the costs of proper conservation, characterization, evaluation and use of these materials.