Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future

Ferguson, Morag; Rabbi, Ismail; Kim, Dong-Jin; Gedil, Melaku; López-Lavalle, Luís Augusto Becerra; Okogbenin, Emmanuel

doi:10.1007/s12042-011-9087-0

Cited by 42 publications

(46 citation statements)

References 107 publications

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“…Thus, clusters generated by Structure could not be associated to geographical area. Further studies are needed to try to correlate clusters with agromorphological characters, and verify if they represent heterotic groups, since the assignment of genotypes to heterotic groups is one of the goals of the use of molecular markers in cassava breeding (Ferguson et al 2012). However, bootstrap values of some clusters in the dendrogram revealed the most related accessions from the germplasm bank (Figure 1), and crossings among accessions from these clusters must be avoided.…”

Section: Resultsmentioning

confidence: 99%

Molecular characterization of 'sweet' cassavas (Manihot esculenta) from a germplasm bank in Brazilian Eastern Amazonia

Cunha

Silva

Albuquerque

et al. 2016

Crop Breed. Appl. Biotechnol.

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Section: Resultsmentioning

confidence: 99%

Molecular characterization of 'sweet' cassavas (Manihot esculenta) from a germplasm bank in Brazilian Eastern Amazonia

Cunha

Silva

Albuquerque

et al. 2016

Crop Breed. Appl. Biotechnol.

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“…The variants and population structure described here are essential inputs for marker-assisted and genomic selection-based approaches to improving disease resistance and yield for this staple crop 38,39 . Largescale breeding efforts, such as the NextGen Cassava program 40,41 , will need to incorporate the impact of common introgressions in predictive genotype-phenotype models to realize the full power of genome-enabled approaches.…”

Section: Discussionmentioning

confidence: 99%

“…These introgressed segments span substantial fractions of chromosomes, and additional effort will be needed to break these linkages and pinpoint causal variants. At least one unknown species of Manihot has contributed to the genetic diversity of cultivated South American cassava, suggesting the profitability of exploring additional interspecific breeding.The variants and population structure described here are essential inputs for marker-assisted and genomic selection-based approaches to improving disease resistance and yield for this staple crop 38,39 . Largescale breeding efforts, such as the NextGen Cassava program 40,41 , will need to incorporate the impact of common introgressions in predictive genotype-phenotype models to realize the full power of genome-enabled approaches.…”

mentioning

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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“…Genotype-by-environment (GxE) testing is used to verify that varieties proposed for release are widely adapted and stable across different environments [41]. Investments in marker-assisted selection have identified phytoene synthase 2 (PSY2) as one of the major alleles for provitamin A accumulation in cassava roots, and markers are beginning to be tested as a breeding tool, in addition to the ongoing phenotypic selection [42,43,44].…”

Section: Provitamin a Yellow Cassavamentioning

confidence: 99%

Progress update: Crop development of biofortified staple food crops under HarvestPlus

Andersson¹,

Saltzman²,

Virk³

et al. 2017

AJFAND

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Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future

Cited by 42 publications

References 107 publications

Molecular characterization of 'sweet' cassavas (Manihot esculenta) from a germplasm bank in Brazilian Eastern Amazonia

Molecular characterization of 'sweet' cassavas (Manihot esculenta) from a germplasm bank in Brazilian Eastern Amazonia

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

Progress update: Crop development of biofortified staple food crops under HarvestPlus

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