Diversidade e estrutura genética populacional em acessos de mandioca (Manihot esculenta Crantz) da Embrapa Amazônia Oriental por meio de marcadores SNPS.

Abstract

Cassava (Manihot esculenta Crantz) is a crop originating in the northern region of Brazil, widely used as a source of subsistence for families in this region and the world. It has high genetic variability, being cultivated throughout Brazil and in other countries. Despite the existence of several studies using cassava molecular markers, few are based on the identification of single nucleotide polymorphism markers (SNPs). The present study aims to evaluate the levels of diversity and the genetic structure of cassava accessions conserved in the Active Bank of Germplasm (BAG) of the Eastern Amazon using molecular SNPs markers. 397 cassava accessions belonging to the BAG were analyzed, which were collected mainly in areas in the state of Pará. Genomic DNA libraries were built and the fragments were sequenced using the Illumina platform. Using the Tassel-GBS V5.2.44 pipeline, the strings were identified and subjected to quality control analysis to remove low quality adapters and regions. Initially, 670,835 SNPs were identified, distributed in 18 chromosomes and 2 scaffolds. Subsequently, scaffolds, insertions and deletions, lost data retention and SNPs were removed according to the lower allele frequency of the alternative allele (MAF <0.05). Then, the data were exported to the R environment for additional filtering, considering the link imbalance, the Hardy-Weinberg balance and the external deviation of the FST using the R2vcftools package. After additional filtration, 3.300 neutrals and independents SNPs were identified, with an average density of 158.90kb per chromosome. The genetic structure was established through two complementary approaches, where three genetic groups (K = 3) were found in both analyzes and it was possible to observe correspondence with the classification regarding the type of cassava (wild, soft or sweet). The diversity parameters were the same, within the confidence interval, for groups 2 and 3 of two genetic groups and in the bravas and meek groups, however, groups 1 (HE = 0.48) and the sugary group (HE = 0.33) had lower values of genetic diversity compared to the other groups. The Molecular Variance Analysis (AMOVA) revealed that there is genetic differentiation considering all accessions (FST = 0.13; P <0.001) and from the group determined by the types of cassava it was 0.12; P <0.001. Analyzing the accessions collected in the state of Pará, the values were similar both for the genetic groups (FST = 0.15; P <0.001), and for the types collected in Pará (FST = 0.14; P <0.001). Therefore, the neutral SNPs markers were effective in studying the diversity and genetic structure of cassava, where it was possible to observe the genetic diversity and genetic structure present in the Active Germplasm Bank of Embrapa Amazônia Oriental, providing a better understanding of genetic variability and support for the development of genomic studies of cassava.