Archaeological manioc (Manihot) from Coastal Peru

Ugent, Donald; Pozorski, Shelia; Pozorski, Thomas

doi:10.1007/bf02858949

Cited by 80 publications

(55 citation statements)

References 32 publications

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“…Esculenta (Euphorbiaceae) is an ancient crop species and starch grains or radiocarbon-dated macroscopic remains are in the archeological record from 1800-7500 BP (Ugent et al 1986;Dickau et al 2007). Molecular evidence based on the haplotypes of the single-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase and genetic variation in five microsatellite loci strongly support the view that cultivated cassava is most likely derived from wild populations referred to M. esculenta subsp.…”

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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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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“…flabellifolia (Pohl), a woody perennial shrub that is found throughout the Amazon basin [2][3][4][5] . Although domesticated over 6,000 years ago [6][7][8][9][10] , cassava cultivation spread beyond South America only in the past 500 years, exported by European colonialists and slave traders 11 . Nowadays, cassava is one of the most widely cultivated tropical crops, especially in sub-Saharan Africa where it has undergone additional improvement through introgression and focused breeding, with the primary aims of conferring disease tolerance and increasing yield 12,13 .…”

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confidence: 99%

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

et al. 2016

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Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. 13 International Institute of Tropical Agriculture (IITA), Nairobi, Kenya. 14 Dow AgroSciences, Indianapolis, Indiana, USA. 15 Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan. 16 In this report we use "cassava" to refer to cultivated and/or domesticated varieties of M. esculenta, and the shorthand M. esc. flabellifolia for wild accessions 3 . We also shotgun-sequenced five Manihot accessions related to cassava, including three from the wild species M. glaziovii Muell. Arg., one named M. pseudoglaziovii Pax & K. Hoffman, and "tree" cassava, a suspected hybrid sometimes called M. catingea Ule 12,18 . The Ceará or India rubber tree species M. glaziovii, also domesticated in South America, was imported to East Africa in the early twentieth century. It is interfertile with cassava and has been used in African breeding programs to exploit the natural resistance of M. glaziovii to cassava pathogens 18 . To analyze genetic variation present in African varieties, we also characterized 268 cultivars of cassava using reduced representation genotypingby-sequencing (GBS) 19 (Table 2). RESULTS Chromosome structureTo produce a high-quality chromosome-scale reference genome for cassava, we augmented our earlier draft sequence 20 of the reference genotype AM560-2 with additional whole genome shotgun sequencing and mate pair data, fosmid-end sequences, and a paired-end library developed using proximity ligation of in vitro reconstituted chromatin 21 (Methods and Supplementary Note 1). AM560-2 is an S3 line bred at Centro Internacional de Agricultura Tropical (CIAT) from MCOL1505 (also known as Manihoica P-12 (ref. 22). Compared with the previous draft 23 , the contiguity of our new shotgun assembly has more than doubled (N50 length 27.7 kb vs. 11.5 kb), and an additional 135 Mb is anchored to chromosomes 23 (Supplementary Note 1). To organize the sequence into chromosomes we integrated the shotgun ...

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“…They occur in large numbers in storage organs such as seeds, roots, and rhizomes, and these types of grains, called reserve starches, occur in a diverse array of forms that can be diagnostic to the genus and even species (18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Archaeological applications in southern Central America and South America have shown that the grains survive for long periods of time on stone implements used to process plants, allowing various aspects of prehistoric agriculture, including maize, to be documented (15,(23)(24)(25)(26)(27)(28)(29)(30)(31).…”

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confidence: 99%

Identification of teosinte, maize, and Tripsacum in Mesoamerica by using pollen, starch grains, and phytoliths

Holst

Moreno

Piperno

2007

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

125

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We examined pollen grains and starch granules from a large number of modern populations of teosinte (wild Zea spp.), maize (Zea mays L.), and closely related grasses in the genus Tripsacum to assess their strengths and weaknesses in studying the origins and early dispersals of maize in its Mesoamerican cradle of origin. We report new diagnostic criteria and question the accuracy of others used previously by investigators to identify ancient maize where its wild ancestor, teosinte, is native. Pollen grains from teosinte overlap in size with those of maize to a much greater degree than previously reported, making the differentiation of wild and domesticated maize in palynological studies difficult. There is presently no valid method for separating maize and teosinte pollen on a morphological basis. Starch grain analysis, a recently developed tool of archaeobotany, appears to be of significant utility in distinguishing the seeds of teosinte from maize. We propose that the differences in starch grain morphology and size between wild and domesticated maize defined in this study may be associated with domestication genes in Zea that have been documented in the starch biosynthesis pathway. As previously reported, phytoliths effectively discriminate the female reproductive structures of Tripsacum, teosinte, and maize. Multiproxy microfossil studies of archaeological and paleoecological contexts appear to be effective tools for investigating the earliest stages of maize domestication and dispersals.

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Archaeological manioc (Manihot) from Coastal Peru

Cited by 80 publications

References 32 publications

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

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

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Identification of teosinte, maize, and Tripsacum in Mesoamerica by using pollen, starch grains, and phytoliths

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