New softwares for automated microsatellite marker development

Martins, Wellington Santos; Sousa, Daniel de; Proite, Karina; Guimarães, P. M.; Moretzsohn, Márcio de Carvalho; Bertioli, David J.

doi:10.1093/nar/gnj030

Cited by 45 publications

(36 citation statements)

References 13 publications

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“…MISA (Perl script, Thiel et al 2003), TRA (visual C++ program, Bilgen et al 2004), TROLL (Tcp/Tk script, Martins et al 2006), SSRIT (Perl script, Temnykh et al 2001) and SSR primer (Perl script, Robinson et al 2004). We identified class 1, or hypervariable markers, consisting of SSRs ≥ 20 bp.…”

Section: Methodsmentioning

confidence: 99%

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Riju

Rajesh

Sherin

et al. 2009

J Genet

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Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.

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Section: Methodsmentioning

confidence: 99%

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Riju

Rajesh

Sherin

et al. 2009

J Genet

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“…Microsatellites are currently the markers of choice for peanut since they are co-dominant, highly polymorphic, transferable among related species, PCR-based and work easily in the tetraploid. Now more than 3000 markers are available (Hopkins et al, 1999;Palmieri et al, 2002Palmieri et al, , 2005He et al, 2003He et al, , 2005Moretzsohn et al, 2004Moretzsohn et al, , 2005Moretzsohn et al, , 2009Ferguson et al, 2004b;Bravo et al, 2006;Budiman et al, 2006;Martins et al, 2006;Gimenes et al, 2007;Proite et al, 2007;Wang et al, 2007;Cuc et al, 2008;Guo et al, 2008;Liang et al, 2009;Moretzsohn MC, de Macedo SE, Leal-Bertioli SCM, Guimarães PM and Bertioli DJ, unpublished data). Furthermore, reference genetic maps, both in diploid A and B and in tetraploid genomes, have been created enabling the comparison of different peanut maps, and even allowing the alignment of maps with other legume species (Hougaard et al, 2008;Bertioli et al, 2009;Leal-Bertioli et al, 2009;Moretzsohn et al, 2009;Varshney et al, 2009a).…”

Section: The Use Of Wild Germplasm In Peanut Breedingmentioning

confidence: 99%

An overview of peanut and its wild relatives

Bertioli

Seijo

Freitas

et al. 2011

Plant Genet. Resour.

136

113

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The legume Arachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and sub-tropics. The genus is endemic to South America being mostly associated with the savannah-like Cerrado. All species in the genus are unusual among legumes in that they produce their fruit below the ground. This profoundly influences their biology and natural distributions. The species occur in diverse habitats including grasslands, open patches of forest and even in temporarily flooded areas. Based on a number of criteria, including morphology and sexual compatibilities, the 80 described species are arranged in nine infrageneric taxonomic sections. While most wild species are diploid, cultivated peanut is a tetraploid. It is of recent origin and has an AABB-type genome. The most probable ancestral species are Arachis duranensis and Arachis ipaënsis, which contributed the A and B genome components, respectively. Although cultivated peanut is tetraploid, genetically it behaves as a diploid, the A and B chromosomes only rarely pairing during meiosis. Although morphologically variable, cultivated peanut has a very narrow genetic base. For some traits, such as disease and pest resistance, this has been a fundamental limitation to crop improvement using only cultivated germplasm. Transfer of some wild resistance genes to cultivated peanut has been achieved, for instance, the gene for resistance to root-knot nematode. However, a wider use of wild species in breeding has been hampered by ploidy and sexual incompatibility barriers, by linkage drag, and historically, by a lack of the tools needed to conveniently confirm hybrid identities and track introgressed chromosomal segments. In recent years, improved knowledge of species relationships has been gained by more detailed cytogenetic studies and molecular phylogenies. This knowledge, together with new tools for genetic and genomic analysis, will help in the more efficient use of peanut's genetic resources in crop improvement.

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“…1,039 clones from A. cytherea, F. scutaria and M. capitata were amplified and submitted for sequencing at the Hawai'i Institute of Marine Biology EPSCoR Facility, while 384 clones from P. lobata were amplified and Table 1 Locus name, repeat motif, primer sequences, annealing temperature (T a ) and approximate size of expected product for one nuclear coding region and eight microsatellites for M. capitata and seven microsatellites from A. cytherea Taxa Conservation Genet Resour (2010) 2:11-15 13 sequenced at the Huck Institute for the Life Sciences, Pennsylvania State University. The STADEN-TROLL pipeline (Martins et al 2006) was used to identify tandem repeats. Primers were designed using PRIMER3 for each of 50, 118, 140, and 149 sequences from A. cytherea, F. scutaria, M. capitata and P. lobata, respectively.…”

mentioning

confidence: 99%

Development of microsatellite markers from four Hawaiian corals: Acropora cytherea, Fungia scutaria, Montipora capitata and Porites lobata

Concepcion¹,

Polato

Baums

et al. 2009

Conservation Genet Resour

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Comprehensive population genetic studies of coral communities are comparatively rare, because of the scarcity of population genetic markers. The Hawaiian archipelago offers a unique perspective into understanding the population genetic structuring of this ecologically important group of organisms. Here we report the development of microsatellite marker libraries from holobiont extracts of four corals: Acropora cytherea (n = 50), Fungia scutaria (n = 118), Montipora capitata (n = 140) and Porites lobata (n = 149). Blast searches indicate that these libraries contain microsatellites from both the coral host and Symbiodinium endosymbionts from each coral. In addition, we also present redesigned primers for the nuclear coding region (atpsb) for use in M. capitata. We report testing and optimization for seven of these microsatellites from A. cytherea, and eight microsatellites and the atpsb locus from M. capitata. Using 25 individuals per species collected from each French Frigate Shoals (FF) and Johnston Atoll (JO), the number of alleles per locus ranged from 2 to 9. Expected heterozygosities ranged from 0.38 to 0.85 and 0.08 to 0.87 for A. cytherea and M. capitata, respectively. We expect that these libraries will be a valuable resource and provide additional useful microsatellite markers for both the coral host and zooxanthellae.

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New softwares for automated microsatellite marker development

Cited by 45 publications

References 13 publications

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

An overview of peanut and its wild relatives

Development of microsatellite markers from four Hawaiian corals: Acropora cytherea, Fungia scutaria, Montipora capitata and Porites lobata

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