A molecular genetic map of cassava (Manihot esculenta Crantz)

Fregene, Martin A.; Fernando, A; Gómez, Rocío; Rodríguez, Fausto J.; Chavarriaga, Paul; Roca, W.; Tohmé, Joe; Bonierbale, Merideth

doi:10.1007/s001220050580

Cited by 154 publications

(154 citation statements)

References 32 publications

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“…Species of Manihot show disomic inheritance (33), such that individuals can be either homozygous or heterozygous at the G3pdh locus. For heterozygotes, the sequence of both haplotypes is shown on a single sequencing gel, resulting in double bands at sites that differ between the haplotypes.…”

Section: Methodsmentioning

confidence: 99%

Evidence on the origin of cassava: Phylogeography of Manihot esculenta

Olsen

Schaal

1999

Proc. Natl. Acad. Sci. U.S.A.

434

299

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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.

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Section: Methodsmentioning

confidence: 99%

Evidence on the origin of cassava: Phylogeography of Manihot esculenta

Olsen

Schaal

1999

Proc. Natl. Acad. Sci. U.S.A.

434

299

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“…The great need for crop improvement coupled with limitations imposed on traditional methods due to polyploidy have made cassava an ideal candidate for genomic approaches. Nuclear genetic maps collected from restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR), are available (Fregene et al 1997;Fregene 2000;Mba et al 2001), and recently advocated whole genome sequencing (Raven et al 2006) has been initiated (http://www.jgi.doe.gov/sequencing/cspseqplans2007.html).…”

Section: Introductionmentioning

confidence: 99%

The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron

et al. 2008

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The complete sequence of the chloroplast genome of cassava (Manihot esculenta, Euphorbiaceae) has been determined. The genome is 161,453 bp in length and includes a pair of inverted repeats (IR) of 26,954 bp. The genome includes 128 genes; 96 are single copy and 16 are duplicated in the IR. There are four rRNA genes and 30 distinct tRNAs, seven of which are duplicated in the IR. The infA gene is absent; expansion of IRb has duplicated 62 amino acids at the 3′ end of rps19 and a number of coding regions have large insertions or deletions, including insertions within the 23S rRNA gene. There are 17 intron-containing genes in cassava, 15 of which have a single intron while two (clpP, ycf3) have two introns. The usually conserved atpF group II intron is absent and this is the first report of its loss from land plant chloroplast genomes. The phylogenetic distribution of the atpF intron loss was determined by a PCR survey of 251 taxa representing 34 families of Malpighiales and 16 taxa from closely related rosids. The atpF intron is not only missing in cassava but also from closely related Euphorbiaceae and other Malpighiales, suggesting that there have been at least seven independent losses. In cassava and all other sequenced Malphigiales, atpF gene sequences showed a strong association between C-to-T substitutions at nucleotide position 92 and the loss of the intron, suggesting that recombination between an edited mRNA and the atpF gene may be a possible mechanism for the intron loss.

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“…DNA markers and statistical methods for mapping quantitative trait loci (QTLs) represent powerful tools for understanding the inheritance of quantitative traits (Rami et al 1998). The genetic map of cassava (Fregene et al, 1997;Mba et al 2001) provides DNA markers on genome wide basis to study the genetics of productivity and the plant architecture of cassava. Molecular information on the inheritance of traits will permit the design of appropriate breeding schemes to more efficiently produce improved genotypes and good parents.…”

Section: Introductionmentioning

confidence: 99%