<i>In Silico</i>Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

Vásquez, Andrea; López, Camilo

doi:10.1155/2014/471461

Cited by 5 publications

(3 citation statements)

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“…SSRs have been comprehensively characterized for some plant species after their genome sequences were published, including in Brachypodium [ 10 ], foxtail millet [ 12 , 35 , 36 ], Brassica [ 13 ], and cassava [ 37 ]. Currently, SSR DNA entries from 110 plant species with sequenced genomes are available in a plant microsatellite DNAs database (PMDBase) [ 38 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

et al. 2018

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BackgroundSimple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.ResultsHere, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.ConclusionsThe present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.htmlElectronic supplementary materialThe online version of this article (10.1186/s12864-018-4878-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

et al. 2018

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“…The percentages of each motif are generally as expected in plants [ 43 , 44 ], and a high percentage of tetramers is not uncommon in plants [ 35 ]. An elevated number of tetramer repeats is thought to be an indication that the majority of this motif length may be found in non-coding regions of the expressed genes [ 43 ].…”

Section: Resultsmentioning

confidence: 53%

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

et al. 2015

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BackgroundDue to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders.MethodsLeaf and meristem tissue from ‘Heritage’ red raspberry (Rubus idaeus) and ‘Bristol’ black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database.ResultsTo accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species.ConclusionThis resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0629-8) contains supplementary material, which is available to authorized users.

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“…AFLPs and SSR markers have been used on cassava genetic diversity studies and exploitation of gene sequence variation for important traits, such as CMD (Akano et al 2002) and CBB (Fregene et al 2003, López et al 2007, Vásquez and López 2014. These molecular marker technologies have been largely superseded with the rapid identification of a large number of SNP variants through nextgeneration sequencing (Rabbi et al 2015, Soto et al 2015 and subsequent release of the first draft of the cassava genome (Prochnik et al 2012, UANews 2009.…”

Section: Research Initiatives To Accelerate Cassava Breeding In Asiamentioning

confidence: 99%

Cassava breeding and agronomy in Asia: 50 years of history and future directions

Malik¹,

Kongsil

Nguyen

et al. 2020

Breed. Sci.

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In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.

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In SilicoGenome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

Cited by 5 publications

References 53 publications

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

Cassava breeding and agronomy in Asia: 50 years of history and future directions

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