Abstract
Key messageBrazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity ({H}_{o}), effective population size estimate widehat{{(N}_{e}}) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
Highlights
Cassava (Manihot esculenta ssp. esculenta) domestication resulted from human-mediated selection in the Amazonian region and adjacent areas of northern Bolivia (Clement et al.Communicated by Emma Mace.USA 3 Embrapa Mandioca E Fruticultura, Cruz de Almas, BA, Brazil2010), initially in the early Holocene period (Lombardo et al 2020), with significant changes in root size
For IBS analysis on the GA panel, 9686 single-nucleotide polymorphisms (SNPs) remained after Hardy–Weinberg filtering, while 8242 SNPs remained after additional minor allele frequency (MAF) filtering on the IBS-selected unique set (GU)
Using 27,045 SNP markers obtained from the Genotypingby-sequencing (GBS) method, we identified and characterized genetic groups of the Embrapa Brazilian cassava germplasm collection and inferred the parameters describing genetic diversity, population structure and linkage disequilibrium
Summary
Cassava (Manihot esculenta ssp. esculenta) domestication resulted from human-mediated selection in the Amazonian region and adjacent areas of northern Bolivia (Clement et al.Communicated by Emma Mace.USA 3 Embrapa Mandioca E Fruticultura, Cruz de Almas, BA, Brazil2010), initially in the early Holocene period (Lombardo et al 2020), with significant changes in root size. Evidence suggests that cultivated cassava was domesticated once from M. esculenta subsp. Flabellifolia (Olsen and Schaal 1999; Olsen 2004; Schaal et al 2006) This hypothesis was further supported by Léotard and colleagues studying the G3pdh gene diversity among six wild Manihot species (Léotard et al 2009). Domesticated cassava has been further separated into two groups, sweet and bitter cassava, based on root cyanogenic potential (Elias et al 2004; Clement et al 2010). Sweet cassava is generally cultivated throughout the Neotropics, but dominates the western and southern water-heads of the Amazon river basin; the bitter cassava type dominates Amazon’s northern water-heads and central portion where it is predominantly used for starch extraction and cassava flour production (Nordenskiold 1924; Renvoize 1972; Fraser et al 2012; Mühlen et al 2019; Ogbonna et al 2020).
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