Development and characterization of microsatellite markers for castor (Ricinus communis L.), an important oleaginous species for biodiesel production

Bajay, Miklos Maximiliano; Pinheiro, José Baldin; Batista, Carlos Eduardo de Araújo; Nóbrega, Márcia B.M.; Zucchi, Maria Imaculada

doi:10.1007/s12686-009-9058-z

Cited by 40 publications

(27 citation statements)

References 5 publications

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“…Allan et al (2008) reported 9 genomic SSR markers, 0.403 gene diversity (PIC) with an average of 3.01 alleles per locus. Bajay et al (2009) developed 12 genomic SSR markers with an average of 0.416 gene diversity (He) and 3.3 alleles per locus. Qiu et al (2010) reported 118 polymorphic SSR loci, 0.36 PIC and 2.97 alleles per locus which suggested that EST-SSR markers developed had moderate level of polymorphism.…”

Section: Polymorphism Of Est-ssrsmentioning

confidence: 99%

“…Gajera et al (2010) reported 5 polymorphic ISSRs with an average PIC value of 0.88. Pecina-Quintero et al (2013) used the proven SSRs of Bajay et al (2009) and obtained PIC values that ranged from 0.5 to 0.812 and 5.5 alleles per marker. Data indicated that genetic variation was mostly due to variation within populations, 10.5 % to among populations and 0.5 % to among regions.…”

Section: Polymorphism Of Est-ssrsmentioning

confidence: 99%

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Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta¹,

Sankar²,

Sreelakshmi³

et al. 2016

Physiol Mol Biol Plants

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Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSRcontaining ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.

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Section: Polymorphism Of Est-ssrsmentioning

confidence: 99%

Section: Polymorphism Of Est-ssrsmentioning

confidence: 99%

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta¹,

Sankar²,

Sreelakshmi³

et al. 2016

Physiol Mol Biol Plants

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“…Apenas o par de iniciadores RcoM30 amplificou um produto acima de 300 pb; os demais amplificaram produtos abaixo desse valor. Bajay et al (2009), Qiu et al (2010) e Bajay et al (2011, respectivamente, também obtiveram, por meio de marcadores microssatélites, para mamoneira, produtos de amplificação cujo tamanho variou entre 100 e 300, 130 e 288, 170 e 320.…”

Section: Resultsunclassified

“…Resultados semelhantes foram obtidos por Bajay (2009), que desenvolveu 41 pares de iniciadores para mamoneira, dos quais 70,73% foram classificados como perfeitos; 19,51%, como compostos; e apenas 9,75% como interrompidos.…”

Section: Resultsunclassified

“…Embora o sequenciamento do genoma da mamoneira (Ricinus communis L.) já tenha sido realizado , até o momento, o número de microssatélites disponíveis para a espécie é baixo para o mapeamento de QTLs, com um total de 51 pares de iniciadores SSR (Bajay et al, 2009(Bajay et al, , 2011Seo et al, 2011) e 118 EST-SSR (Qiu et al, 2010). Assim, é necessário o desenvolvimento e a otimização de mais iniciadores SSR para saturação do genoma da mamoneira.…”

Section: Introductionunclassified

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Desenho e validação de iniciadores microssatélites SSR para mamoneira

Machado

Silva

2013

Pesq. agropec. bras.

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Resumo -O objetivo deste trabalho foi desenhar, validar e otimizar pares de iniciadores microssatélites SSR para mamoneira. O desenho dos pares de iniciadores foi feito por meio do aplicativo Websat, a partir de sequências depositadas no GenBank do National Center for Biotechnology Information (GenBank/NCBI), e a sua qualidade foi aferida com uso do aplicativo web NetPrimer. Foram utilizadas diferentes concentrações de DNA, cloreto de magnésio, pares de iniciadores, dNTPs e temperatura de anelamento para otimização das condições de PCR. Um total de 30 pares de iniciadores SSR foi desenhado, sintetizado e otimizado. O gel de agarose foi utilizado para detecção dos produtos amplificados, e o gel desnaturante de poliacrilamida, na otimização das condições de PCR e na identificação de polimorfismo. Os pares de iniciadores apresentaram percentagem média de guanina/citosina (GC) igual a 47,29% e produtos amplificados com tamanhos entre 128 e 381 pb. Vinte e nove pares de iniciadores SSR (96,7%) foram validados, dos quais nove foram polimórficos (23,3%). As concentrações otimizadas para amplificação são: DNA, 25 ng; cloreto de magnésio, 1,2 mmol L -1 ; iniciadores Forward e Reverse, 0,4 mmol L -1 ; dNTPs, 0,1 mmol L -1 ; e temperatura de anelamento, 62 a 64ºC. As ferramentas de bioinformática Websat e Net Primer podem ser utilizadas para desenvolver iniciadores microssatélites de qualidade, para a mamoneira, a partir de sequências depositadas no GenBank/NCBI.Termos para indexação: Ricinus communis, GenBanK/NCBI, genoma. Design and validation of SSR microsatellite primers for castor beanAbstract -The objective of this work was to design, validate, and optimize pairs of SSR microsatellite primers for castor bean. The design of the primer pairs was done by means of the Websat application from sequences deposited in the GenBank of the National Center for Biotechnology Information (GenBank/NCBI), and its quality was assessed using the NetPrimer web application. Different concentrations of DNA, magnesium chloride, primer pairs, dNTPs, and annealing temperatures were used for the optimization of PCR conditions. A total of 30 primer pairs were designed, synthesized, and optimized. Agarose gel was used for detection of the amplified products, and denaturing polyacrylamide gel for the optimization of PCR conditions and the identification of polymorphism. The primer pairs presented average guanine/cytosine (GC) percentage of 47.29% and amplified fragment sizes varying from 128 to 381 bp. Twenty-nine pairs of SSR primers (96.7%) were validated, of which nine were polymorphic (23.3%). The concentrations optimized for amplification are: DNA, 25 ng; magnesium chloride, 1.2 mmol L -1 ; Forward and Reverse primers, 0.4 mmol L -1 ; dNTPs, 0.1 mmol L -1 ; and annealing temperature, 62 to 64°C. The bioinformatic tools Websat and Net Primer can be used to develop quality microsatellite primers for castor bean from sequences deposited at the GenBank/NCBI.Index terms: Ricinus communis, GenBanK/NCBI, genome. IntroduçãoO desenvolvimento de mar...

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Castor

Fernández‐Martínez

Velasco

2011

Technological Innovations in Major World Oil Crops, Volume 1

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Development and characterization of microsatellite markers for castor (Ricinus communis L.), an important oleaginous species for biodiesel production

Cited by 40 publications

References 5 publications

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Desenho e validação de iniciadores microssatélites SSR para mamoneira

Castor

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