Genetic diversity, genomics and phylogeography of manioc (Manihot esculenta Crantz): implications for the dispersion of the crop along the main fluvial axes in Brazilian Amazon basin

Abstract

Manioc (Manihot esculenta ssp. esculenta Crantz) was domesticated in the southwestern Amazon basin and currently is the main source of calories for more than 800 million people in the world. After its initial domestication, divergent selective pressures gave rise to two major groups of varieties (sweet and bitter manioc), which differ in their contents of toxic compounds. Although there is some overlap, these groups of varieties have distinct patterns of distribution, which may be the outcome of limited processes of contact and interchange between varieties along the crop's domestication history. The evolutionary history of a crop may be better understood by studying the organization of genetic diversity within and between its domesticated populations. Few studies evaluated how the genetic diversity of manioc is organized across its geographic distribution, and there are no genomic population studies with manioc varieties. The main goal of this proposal is to evaluate, with different molecular markers, the genomic and genetic diversity and structure, and the phylogeography of manioc varieties traditionally grown along the major rivers of Brazilian Amazon basin. The current genetic diversity and structure will be evaluated with nuclear microsatellites markers (ncSSR), while historical patterns of the organization of genetic diversity (phylogeography) will be evaluated with chloroplastidial microsatellites (cpSSR). Novel information on the genomic basis for distinction between sweet and bitter varieties, as well as possible distinct patterns of dispersion, will be generated with SNPs detected with Restriction-site associated DNA sequencing (RAD-seq). We expect to contribute to the understanding of manioc's dispersal across the Amazon basin after its initial domestication, as well as to the understanding of the genomic basis for the differentiation between sweet and bitter manioc. This information may help identify centers of genetic diversity of the crop, which in turn may be useful for the conservation of genetic resources, and also for manioc's breeding programs.