PLB143: Evolution of Crop Plants, UC Davis

A very recent paper on

The origin of cassava (Manihot esculenta)

Olsen KM, Schaal BA. 1999. Evidence on the origin of cassava: phylogeography of Manihot esculenta.

Proc. Nat. Acad. Sci. USA 96: 5586-5591

(Summary by P. Gepts )

Some links on cassava

Introduction

Phylogeography: "Use phylogenetically informative data (most often allele genealogies derived from DNA sequences) for investigating population divergence."
Cassava:

Crop:

staple root crop for > 500 million people living throughout the tropics
primary source of carbohydrates in subSaharan Africa and 6^th among crops worldwide

Its origin?

Genus Manihot (98 species): Neotropics
Wild M. esculenta: M. esculenta subsp. flabellifolia : South America

west central Brazil (south and east of Amazon basin) and eastern Peru (Fig. 1)

Fig. 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

forest patches in transition between cerrado (savanna scrub) and lowland rainforest

M. pruinosa: only wild species sympatric with M. esculenta

Used sequence variation of Glyceraldehyde 3-phosphate dehydrogenase (G3pdh): single-copy nuclear gene, highly polymorphic

Materials & Methods

2 transects:

southern, eastern; 157 individuals, 27 populations of M. esculenta ;
35 individuals, 6 populations of M. pruinosa

DNA extracted from dried leaves using a CTAB protocol
PCR amplification:

using primers designed for conserved regions from Arabidopsis thaliana and Ranunculis acris
three 50 µl reactions per individual; pooled for Geneclean II DNA purification

analysis of heterozygotes: "haplotype subtraction"?

Results & Discussion

Structure and variation of G3pdh

3 exons and 4 introns + 2 flanking exons
64 polymorphic sites: Table 1

Table 1. Variation in the G3pdh locus
Region	Mutation	No.
Exons	Nonsynonymous	1
	Synonymous	9
Intron	Substitutions	47
	Indels:	7
	1 bp	(2)
	3 bp	(3)
	19 bp	(1)
	25 bp*	(1)
* Minisatellite region with 1-5 repeats

Variation appears to be neutral: Tajima's and Fu and Li's criteria
Maximum parsimony tree: Fig. 2

28 haplotypes among 212 individuals (424 alleles)
3 sites were homoplasious (all single-base substitutions)

Fig. 2. 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.

Geographic origin of cassava

Of 28 haplotypes: 24 in M. esculenta, 6 in cassava; see reduction in diversity in other crops: 2 haplotypes represent 85% of haplotype variation in domesticated vs. only 9% in wild
Haplotypes shared by wild and domesticated cassava: only in southern border (6 sampled populations) (Fig. 1): between western Mato Grosso and western Rondônia = restricted area
Note: poor archaeological record: organ type, climate

Taxonomic relationships among haplotypes

no clustering of cassava accessions into monophyletic clade; same for wild: due to? Gene flow among taxa; lineage sorting (persistence and sorting of ancestral polymorphisms predating divergence of taxonomic lineages)