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, 96 (10), 5586-91

Evidence on the Origin of Cassava: Phylogeography of Manihot Esculenta

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Evidence on the Origin of Cassava: Phylogeography of Manihot Esculenta

K M Olsen et al. Proc Natl Acad Sci U S A.

Abstract

Cassava (Manihot esculenta subsp. esculenta) is a staple crop with great economic importance worldwide, yet its evolutionary and geographical origins have remained unresolved and controversial. We have investigated this crop's domestication in a phylogeographic study based on the single-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (G3pdh). The G3pdh locus provides high levels of noncoding sequence variation in cassava and its wild relatives, with 28 haplotypes identified among 212 individuals (424 alleles) examined. These data represent one of the first uses of a single-copy nuclear gene in a plant phylogeographic study and yield several important insights into cassava's evolutionary origin: (i) cassava was likely domesticated from wild M. esculenta populations along the southern border of the Amazon basin; (ii) the crop does not seem to be derived from several progenitor species, as previously proposed; and (iii) cassava does not share haplotypes with Manihot pruinosa, a closely related, potentially hybridizing species. These findings provide the clearest picture to date on cassava's origin. When considered in a genealogical context, relationships among the G3pdh haplotypes are incongruent with taxonomic boundaries, both within M. esculenta and at the interspecific level; this incongruence is probably a result of lineage sorting among these recently diverged taxa. Although phylogeographic studies in animals have provided many new evolutionary insights, application of phylogeography in plants has been hampered by difficulty in obtaining phylogenetically informative intraspecific variation. This study demonstrates that single-copy nuclear genes can provide a useful source of informative variation in plants.

Figures

Figure 1
Figure 1
Sampling locations for populations of M. esculenta subsp. flabellifolia (squares) and M. pruinosa (circles) in Brazilian states surrounding the Amazon basin. Black squares indicate populations of subspecies flabellifolia found to share one or more haplotypes with cassava (M. esculenta subsp. esculenta) accessions. Populations within the oval together contain all of the shared cassava haplotypes (see Results and Discussion). TO, Tocantins; GO, Goiás; MT, Mato Grosso; RO, Rondônia; AC, Acre.
Figure 2
Figure 2
Structure of the G3pdh region in Manihot. Numbers 1–4 indicate the positions of primers: GPDX7F (1), GPD9R2 (2), GPD9R4 (3), and GPDX9R (4). Uppercase and lowercase letters designate exons and introns, respectively, as follows: partial exon A (52 bp), intron a (84 bp), exon B (98 bp), intron b (265 bp), exon C (143 bp), intron c (101 bp), exon D (84 bp), intron d (101 bp), and partial exon E (34 bp). The cross-hatched region within intron b indicates a variable minisatellite.
Figure 3
Figure 3
The G3pdh gene tree. Haplotype letters correspond to those in Table 2. Shapes around letters indicate the taxa in which haplotypes were found. Each line between haplotypes represents a mutational step, with numbers on lines indicating the variable base pair position. For branches of more than one mutational step without intermediate haplotypes (or side branches), the relative placement of the mutations along the branch is arbitrary. Insertions (i) and deletions (d) relative to the center of the tree are indicated after the base pair number, followed by the number of bases involved. Two different substitutions at position 463 are designated as a and b. Homoplasious (H) mutations are indicated after the base pair number. Numbers in bold print indicate the number of 25-bp minisatellite motifs associated with each haplotype.

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