Comprehensive genotyping of Brazilian Cassava (Manihot esculentaCrantz) Germplasm Bank: insights into diversification and domestication

Abstract

Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonas region. In this study, 3,354 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 1,536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, 1,300 to 4,700 SNP markers were selected for large quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity (Ho), effective population size estimate (Ne) 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 suggest earliest population split from Amazonas to Atlantic forest and Caatinga eco-regions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava 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.

Large‐scale genome‐wide association study, using historical data, identifies conserved genetic architecture of cyanogenic glucoside content in cassava (Manihot esculenta Crantz) root

“…Broad‐sense heritability ( H 2 ) was calculated as 0.82 for HCN content, similar to previous observations reported on several species (Barnett and Caviness, 1968; Goodger et al ., 2004; Gleadow and Møller, 2014). Using genotyping data previously recorded for this population (Ogbonna et al ., 2020), we observed genotype variance ( V g ) that was higher than genotype‐by‐year variance ( V g × y ), with the V g × y / V g ratio showing a year interaction value of 0.29. HCN‐deregressed best linear unbiased prediction (BLUP) shows a very high correlation with non‐deregressed BLUP, with a Pearson’s correlation coefficient of 0.99, indicating a balanced replication of individuals among the population studied (see deregressed BLUPs, Table S3).…”

“…We represented the geographical distribution and HCN content of Brazilian germplasm recently characterized by Ogbonna et al . (2020) and presented a contrasted distribution (Figure 4a). Accessions with high HCN‐contributing alleles are grouped mostly around the Amazonas and low HCN‐contributing alleles are grouped in other areas of Brazil.…”

“…As a validation step, we used a subset of 523 unique individuals (from the core panel of 1536 unique individuals; Ogbonna et al ., 2020) with phenotypic and genotypic information to perform GWAS. Our results (Figure 3, Unique HCN; Table S5) revealed the same loci (as was observed in the larger data set of 1246 individuals) associated with HCN variation in our initial GWAS data set, indicating that the core unique panel represents the overall genetic variation for HCN in the Brazilian germplasm collection.…”

“…This region spans over 54 biallelic ancestry‐informative single‐nucleotide markers fixed or nearly fixed between M. esculenta and M. esculenta subsp . flabellifolia (Ogbonna et al ., 2020), suggesting that domestication can impact metabolic content targeting transport regulation (Wang et al ., 2019), as earlier reported in maize and Oryza sativa (rice) (Sosso et al ., 2015). In view of the above findings, we speculate that cassava domestication may have specifically targeted downstream genetic regulation steps of HCN biosynthesis.…”

“…(2018) and Ogbonna et al . (2020) on the Embrapa CGB collection. Briefly, DNA was extracted from young leaves according to the cetyltrimethylammonium bromide (CTAB) protocol, as described by Doyle and Doyle (1987).…”