CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Blenda, Anna V.; Scheffler, Jodi A.; Scheffler, Brian E.; Palmer, Michael; Lacape, Jean-Marc; Yu, John Z.; Jesudurai, Christopher; Jung, Sook; Muthukumar, Sriram; Yellambalase, Preetham; Ficklin, Stephen P.; Staton, Margaret; Eshelman, Robert E.; Ulloa, Mauricio; Saha, Sukumar; Burr, Benjamin; Liu, Shaolin; Zhang, Tianzhen; Fang, David D.; Pepper, Alan E.; Kumpatla, Siva P.; Jacobs, John; Tomkins, J. P.; Cantrell, R. G.; Main, Dorrie

doi:10.1186/1471-2164-7-132

Cited by 107 publications

(77 citation statements)

References 19 publications

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“…The Wrst step was to identify cotton simple sequence repeat (SSR) markers identiWed as polymorphic in previous studies identiWed in the Cotton Marker Database (Blenda et al 2006). From the pool of polymorphic markers identiWed, the second step was to select markers to ensure complete coverage of each cotton linkage group or chromosome.…”

Section: Molecular Marker Analysismentioning

confidence: 99%

Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources

Campbell¹,

Williams

Park³

2009

Euphytica

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Knowledge of genetic relationships in crop breeding programs provides valuable information that can be used by plant breeders as a parental line selection tool. In Upland cotton (Gossypium hirsutum L.), the Pee Dee germplasm program represents one of the most historically signiWcant Upland cotton breeding programs and is known as a key source of Wber quality genes for commercial cultivars. The foundation of the Pee Dee germplasm is known to represent an array of genetic diversity involving the hybridization of G. hirsutum L., G. barbadense L., and triple hybrid strains (G. arboreum L. £ G. thurberi Todaro £ G. hirsutum L.). In this study, we characterized genetic relationships within the Pee Dee germplasm collection using molecular marker and Weld performance data. Molecular marker and Weld performance data showed the Pee Dee germplasm collection still maintains useful amounts of genetic diversity. The methods described provide plant breeders of cotton and other crops a strategy to develop a parental line selection tool based on genotypic and phenotypic information. Cotton breeders can directly use the information provided to select speciWc Pee Dee germplasm parental line combinations based on genotypic (molecular marker) and phenotypic (Weld performance) information rather than relying on pedigree and phenotypic information alone.

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Section: Molecular Marker Analysismentioning

confidence: 99%

Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources

Campbell¹,

Williams

Park³

2009

Euphytica

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“…The recent discovery and advances on the analysis of polymorphism in cotton SSRs (Blenda et al, 2006;Chen & Du, 2006;Kebede et al, 2007;Lacape et al, 2007) led to the choice of high polymorphic markers. Microsatellites may be chosen instead of markers based on random PCR amplification because they are relatively easy to reproduce and their location in the genome can also be determined (Blenda et al, 2006).…”

Section: Resultsmentioning

confidence: 99%

“…Microsatellites may be chosen instead of markers based on random PCR amplification because they are relatively easy to reproduce and their location in the genome can also be determined (Blenda et al, 2006). Furthermore, microsatellites are easy to perform and cost-effective, in comparison to SNP high-throughput technologies, because they are multiallelic (Gupta et al, 2005) and only a small number of markers are required for the analyses.…”

Section: Resultsmentioning

confidence: 99%

“…Currently, most of the available polymorphic molecular markers for cotton varieties are interspecific, and genetic diversity, as well as molecular mapping in cotton, has frequently been done with more than one species or race (Blenda et al, 2006;Menezes et al, 2008). Despite the high diversity of SSR markers in Gossypium genomes (Lacape et al, 2007), the documentation of markers that are intraspecifically polymorphic in G. hirsutum is still incipient.…”

Section: Introductionmentioning

confidence: 99%

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Optimal use of SSR markers for varietal identification of upland cotton

Pereira

Cazé

Silva

et al. 2015

Pesq. agropec. bras.

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-The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.Index terms: Gossypium hirsutum, cultivar discrimination, intraspecific polymorphism, microsatellite. Uso otimizado de marcadores SSR para identificação varietal de algodoeiro herbáceoResumo -O objetivo deste trabalho foi identificar marcadores polimórficos de sequências simples repetidas (SSR) para identificação varietal de algodão e avaliação da distância genética entre as variedades. Inicialmente, 92 marcadores SSR foram genotipados em 20 cultivares de algodão do Brasil. Desse total, 38 locos foram polimórficos, dos quais dois deles foram amplificados por um único par de iniciadores; o número médio de alelos por loco foi 2,2. Os conteúdos de informação polimórfica (PIC) e de poder de discriminação (DP) foram, em média, 0,374 e 0,433, respectivamente. A distância genética média foi de 0,397 (mínima de 0,092 e máxima de 0,641). Um painel de 96 variedades originárias de diversas regiões do mundo foi avaliado por 21 locos polimórficos derivados a partir de 17 pares de iniciadores selecionados. Entre essas variedades, a distância genética média foi de 0,387 (mínima de 0 e máxima de 0,786). Os dendrogramas elaborados a partir de média aritmética não ponderada (UPGMA) não refletiram as regiões do Brasil (20 genótipos) ou do mundo (96 genótipos), onde as variedades ou linhagens foram selecionadas. O procedimento de reamostragem bootstrap mostra que a identificação dos genótipos é viável com 19 locos. Os marcadores polimórficos avaliados são úteis na identificação varietal de um painel amplo de variedades de algodão e podem ser aplicados em estudos de diversidade da espécie.Termos para indexação: Gossypium hirsutum, discriminação de cultivares, polimorfismo intraespecífico, microssatélite.

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“…SSR markers have proven utility for the resolution diVerences between individuals, mapping traits of interest in experimental populations, analysis of genome evolution and comparative genomics, and for the eYcient utilization of wild and primitive germplasm resources in MAS (Bell and Ecker 1994;Akkaya et al 1995;McCouch et al 1997). A number of cotton SSR containing loci, including more than 500 BNL SSRs (Brookhaven National Laboratory, NY, USA; Blenda et al 2006), 309 JESPR SSRs (Reddy et al 2001) and 418 CIR SSRs (Nguyen et al 2004;Lacape et al 2005) have been identiWed and made available for cotton genome research. Also, EST speciWc microsatellite markers (Qureshi et al, 2004;Han et al 2004;Han et al 2006;Blenda et al 2006), and SSRs derived from bacterial artiWcial chromosomes (BACs) (Yu et al 2002;Yu et al 2004a;Blenda et al 2006) have recently been identiWed in cotton.…”

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Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum

et al. 2007

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Molecular markers associated withWber development traits have the potential to play a key role in understanding of cotton Wber development. Seventeen SSRs out of 304 markers tested from MGHES (EST-SSR), JESPR (genomic SSR), and TMB (BAC-derived SSR) collections showed signiWcant linkage associations (using a Kurskal-Wallis non-parametric test) with lint percentage QTL in a set of recombinant inbred cotton lines (RILs) segregating for lint percentage. The permutation test of these potential markers associated with lint percentage QTL(s) determined that 12 SSR markers have stable estimates, exceeding empirically chosen threshold signiWcance values at or above = 0.01. Interval mapping demonstrated that 9 SSRs with stable critical LOD threshold values at = 0.01 have signiWcant QTL eVect. Multiple QTL-mapping (MQM) revealed that at least, two highly signiWcant Wber development QTLs exist around regions TMB0471 and MGHES-31 (explained about 23-59% of the phenotypic variation of lint percentage) and around markers MGHES-31 and TMB0366 (accounted for 5.4-12.5% phenotypic variation of lint percentage). These markers, in particular Wber-speciWc EST-SSRs, might be the possible 'candidate' loci contributing for Wber development in cotton. BAC-derived SSRs associated with Wber trait are the possible markers that are useful for the identiWcation of physical genomic contigs that contain Wber development genes. Several lint percentage trait associated SSR markers have been located to chromosomes 12, 18, 23, and 26 using deletion analysis in aneuploid chromosome substitution lines. Outcomes of the work may prove useful in understanding I. Y. Abdurakhmonov and S. Saha contributed equally to the work

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CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Abstract: Background: The Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding.

Cited by 107 publications

References 19 publications

Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources

Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources

Optimal use of SSR markers for varietal identification of upland cotton

Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum

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