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Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication
Tuesday, 2021/05/04 | 08:37:38

Alex C. OgbonnaLuciano Rogerio Braatz de AndradeLukas A. MuellerEder Jorge de Oliveira & Guillaume J. Bauchet

Theoretical and Applied Genetics May 2021; vol. 134:1343–1362

Key message

Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.

Abstract

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 (Ho)(Ho), effective population size estimate (Neˆ(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 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.

 

See: https://link.springer.com/article/10.1007/s00122-021-03775-5

 

Figure 7:

Gene flow analysis using TreeMix (v1.12) for 419 Brazilian germplasm collected before the year 2000. Plotted is the structure of the graph inferred with gene flow events of 3 migration using Maximum likelihood. Individuals in the 5 populations from 5 different Brazilian Ecoregions. Migration arrows are colored according to their weight. Horizontal branch lengths are proportional to the amount of estimated genetic drift. Nodes robustness was estimated with 1000 bootstrap replicates. The analysis was carried out under the implementation of BITE R package version 1.2.0008

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