Isolation and characterization of 28 polymorphic SSR loci from castor bean (Ricinus communis L.)

Seo, Kyoung‐In; Lee, Gi-An; Ma, Kyung‐Ho; Hyun, Do-Yoon; Park, Yong‐Jin; Jung, Jin-Woo; Lee, Sok-Young; Gwag, Jae‐Gyun; Kim, Chung-Kon; Lee, Myung Chul

doi:10.1007/s12892-010-0107-7

Cited by 24 publications

(12 citation statements)

References 35 publications

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“…Least present were CA/TG and AC/ GT (Supplementary Table 2). The result confirms the finding that AG/CT repeat motif occurs predominantly with a frequency of about twice that of AC/GT (Seo et al 2011). Abundance of AG/CT regions can be explained by the fact that they were the preferred regions for amplification.…”

Section: Genetic Diversitysupporting

confidence: 89%

“…DNRs were present in non genic regions, introns, 5 0 UTRs and 3 0 UTRs. Earlier Seo et al (2011) observed dinucleotide repeats to range from 4 to 52 (mean 12.4). Generally AG/CT and AC/GT abundance has been common in plant genome.…”

Section: Genetic Diversitymentioning

confidence: 97%

“…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. Seo et al (2011) developed 28 polymorphic SSR loci with PIC value of 0.26 and an average of 3.18 alleles per locus. Gajera et al (2010) reported 5 polymorphic ISSRs with an average PIC value of 0.88.…”

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: Genetic Diversitysupporting

confidence: 89%

Section: Genetic Diversitymentioning

confidence: 97%

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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“…Different types of molecular markers have been used to study the genetic variability of castor bean: amplified fragment length polymorphism (AFLP) (Pecina-Quintero et al, 2013), random amplified DNA polymorphism (RAPD) (Gajera et al, 2010;Silva et al, 2012;Vivodík et al, 2014Vivodík et al, , 2015Lakhani et al, 2015), single nucleotide polymorphism (Foster et al, 2010), simple sequence repeats (SSR) (Bajay et al, 2009(Bajay et al, , 2011Seo et al, 2011;Tan et al, 2013Tan et al, , 2014Gálová et al, 2015;Machado et al, 2016), and inter-simple sequence repeats (ISSR) Tomar et al, 2014;Goodarzi et al, 2015;Kallamadi et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Development of TRAP primers for Ricinus communis L.

et al. 2017

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ABSTRACT. The objective of this article was to develop TRAP (target region amplification polymorphism) primers for castor bean, with the goal of making functional markers available for genetic studies about the species. To do this, oligonucleotides were designed based on ESTs, obtained from the NCBI (National Center for Biotechnology Information) databank, which code enzymes involved in metabolic routes of fatty acid synthesis, ricin synthesis, and resistance to castor bean pathogens. The forward primers were designed with the help of the Primer3 software and, for the reverse, six arbitrary primers were used. To standardize the amplification reactions, the following criteria were used to select the primers: sizes between 18 and 20 bp, guanine/ cytosine (GC) in the range of 40 to 60%, and average annealing temperature between 55° and 62°C. The design quality of the primers was verified using the Net Primer application. Fifty-six primers were designed, which had an average GC percentage of 53.2%. A total of 336 combinations were obtained using the 56 fixed and 6 arbitrary primers. Based on polymerase chain reaction, 330 combinations (89%) presented good amplification patterns for the genomic DNA of castor bean. The size of the fragments amplified varied between 50 and 2072 bp. The TRAP primers designed and validated in this study are the first for castor bean and represent a significant increase in the molecular markers for this species.

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“…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

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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Isolation and characterization of 28 polymorphic SSR loci from castor bean (Ricinus communis L.)

Cited by 24 publications

References 35 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.)

Development of TRAP primers for Ricinus communis L.

Desenho e validação de iniciadores microssatélites SSR para mamoneira

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