A forum for debate and questions regarding molecular markers.

• Indra Bhatt

  Can anyone advise on the AFLP protocol? Silver staining of 7.5% Polyacrylamide gel.

  We are working on Valeriana species.

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  • 
    Indra Bhatt replied

    I will go through the paper and find any difficulty will let you know. Thanks once again for support and concern. Best regards,

    Apr 27, 2012
• Ramakrishna Goriparthi

  What is meant by scoring in marker assisted selection and how to do scoring? How to do dendrogram analysis?

  I am working in agricultural research in the field of marker assisted selection of rice varieties.

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  • 
    Vijayababu Tummala replied

    BARWALE FOUNDATION Knowledge and Study Centre Plot No. BT-4, Additional MIDC Areas, Phase II, Jalna-Aurangabad Road, Jalna – 431 203 , Maharashtra, India Tel. +91-2482-221191 / 92; Fax + 91 -2482 –BARWALE FOUNDATION Knowledge and Study Centre Plot No. BT-4, Additional MIDC Areas, Phase II, Jalna-Aurangabad Road, Jalna – 431 203 , Maharashtra, India Tel. +91-2482-221191 / 92; Fax + 91 -2482 – 220991 A Non- Profit Foundation Registered U/S 25 of the Companies Act 1956 Registered Office: 19, Raj Mahal, 84, Veer Nariman Road, Mumbai – 400 020, Maharashtra Hyderabad Branch : Barwale Chambers, Barwale Foundation, H.No. # 3-6-666, Street No. 10, Himayath Nagar , Hyderabad-500029, Tel. +91-040-27665871 to 76 Email: info@barwalefoundation.org; Website:www.barwalefoundation.org April 2, 2012 TRAINING ANNOUNCEMENT Dear All, GREETINGS FROM BARWALE FOUNDATION The Barwale Foundation, a non-profit organization, is planning to conduct a three day training program on “Statistical Tools for Molecular Breeding” from April 24-26, 2012. Course title Statistical Tools for Molecular Breeding Duration/Dates of course 3 days (April 24-26, 2012) Objective of course The course deals with analyses of molecular data generated from various experiments conducted towards enhancing breeding efficiency’s using software’s along with the interpretation of results Themes of program Theme 1: Diversity analyses Theme 2: QTL/Linkage mapping Theme 3: Association mapping, marker assisted backcross Theme 4: MARS, MAGIC and genome wide selection for breeding enhancement Venue of program Barwale Knowledge and Study Centre (BKSC) Plot # BT-4, Add. MIDC, Jalna-Aurangabad Road Jalna-431203, Maharashtra Fee details Rs 6742/- (Rs. 6000/ + 12.36 % service tax), per person Fees is exclusive of lodging and boarding Accepted as cash or Demand draft, drawn in favour of BARWALE FOUNDATION, payable at Jalna Contact persons 1. Mr.Vijayababu 09923002470 OR vijayababu@barwalefoundation.org 2. Dr. Neeru Jain 09860071192 OR neeru@barwalefoundation.org We anticipate nominations at your earliest, as we have limited seats only. Regards. Vinay Shenoy (Director Research) DAY SCHEDULE IS OVERLEAF BARWALE FOUNDATION Knowledge and Study Centre Plot No. BT-4, Additional MIDC Areas, Phase II, Jalna-Aurangabad Road, Jalna – 431 203 , Maharashtra, India Tel. +91-2482-221191 / 92; Fax + 91 -2482 – 220991 A Non- Profit Foundation Registered U/S 25 of the Companies Act 1956 Registered Office: 19, Raj Mahal, 84, Veer Nariman Road, Mumbai – 400 020, Maharashtra Hyderabad Branch : Barwale Chambers, Barwale Foundation, H.No. # 3-6-666, Street No. 10, Himayath Nagar , Hyderabad-500029, Tel. +91-040-27665871 to 76 Email: info@barwalefoundation.org; Website:www.barwalefoundation.org Statistical Tools for Molecular Breeding, April 24-26, 2012 Day Topics covered April 24, 2012 Approaches used for genetic diversity analyses Linkage mapping: concepts Hands On:  Genetic diversity analyses based on similarity matrix and clustering using NTSYS-pc software.  Principal component analyses using NTSYS-pc software  Linkage map generation using JoinMap  QTL detection using QTL cartographer April 25, 2012 Association mapping Marker Assisted backcrossing Hands on:  Evaluation of trait association and calculation of linkage disequilibrium using TASSEL  Analyses of population structure based on multi locus genotypic data using Structure software  Integration of genotypic, phenotypic and QTL mapping information for MABC pgm using ISMAB April 26, 2012 Application of MARS, MAGIC and Genome wide selection in enhancement of breeding programs Hands on:  Decision supporting in marker-assisted recurrent selection (MARS) and gene pyramiding using OptiMAS.

    Apr 3, 2012
• Iván Carreño

  Additive effect in QTL analysis.

  When analysing QTLs mainly with MapQTL, we get an ADDITIVE EFFECT as a result. I think that the higher the value (in absolute terms) of the additive effect, the more dominant the effect of the geneWhen analysing QTLs mainly with MapQTL, we get an ADDITIVE EFFECT as a result. I think that the higher the value (in absolute terms) of the additive effect, the more dominant the effect of the gene (or genes) underlying the QTL. Is that true? Thank you very much.

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    Ramakrishna Goriparthi replied

    Thank you

    Mar 13, 2012
• Bing Liu

  Tools of converting illumina genotyping data?

  Can anyone suggest tools that I can use to convert illumina genotyping data into ANCESTRYMAP or PED or PACKEDPED format?

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    Nikolay Chekanov replied

    Oh, I tried it back in 2009 and strongly disliked it then, however can't remember why in particular. Maybe now it's already usable and stable enough.

    Mar 11, 2012
• Sümeyra Çetinkaya

  My problem is restriction enzymes for RFLP

  Hi! I'm looking for LYS109ARG and LYS656ASN polimorphisms.I found FASTA squence and portable primers.But these are not compatible with restriction enzymes.I have a problem about enzyme for RFLP.InHi! I'm looking for LYS109ARG and LYS656ASN polimorphisms.I found FASTA squence and portable primers.But these are not compatible with restriction enzymes.I have a problem about enzyme for RFLP.In article they use respectively HaeIII and BstUI. If you know how to use them please share to me. I'm use web cutter and neb cutter.Thanks in advance

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    Linda Piekuse replied

    Hello, We are now meeting the same problem - but what is interesting that the same problem repeats in many scientific articles. Did You solve this problem?

    Feb 29, 2012
• Susana Molina

  Methods for genotyping

  Hi! I'm looking for methods for genotyping, any suggestions? Thanks!

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    Ekrem Ayna replied

    Sequencing is not genotyping and conventional genotyping is not effective in species discrimination, if we are speaking in the terms modern molecular genetics. please check Applied Biosystem web pageSequencing is not genotyping and conventional genotyping is not effective in species discrimination, if we are speaking in the terms modern molecular genetics. please check Applied Biosystem web page to get the definition of genotyping.

    Feb 26, 2012
• Keya Mukherjee

  Question related to marker

  Is there is anybody can tell me that "how SNP is used to identify alleles for traits contributing to higher yield in crop?"

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    Ekrem Ayna replied

    Woww, can be long as two semesters. I advise you to separate your question into four tiny ones? 1) How do we genotype SNPs (well by sequencing off course) ? This is molecular part that you can findWoww, can be long as two semesters. I advise you to separate your question into four tiny ones? 1) How do we genotype SNPs (well by sequencing off course) ? This is molecular part that you can find every where. 2) What is trait (genotypical traits) and how come associated with phenotypes ? 3) How these variations ( defined by SNPs) are correlated with functional genes or traits what ever so? 4) How do we predict the distribution of some SNPs (which we believe that are linked with some good phenotypes) ? As soon as you get an answer to these question you would be dealing with linkage association (QTLs) and using medium resolution SNPs maps for the desired trait of interest.

    Feb 26, 2012
• Nguyen Minh

  Mashine for polyacrylamide electrophoresis

  Hello! What mashine for polyacrylamide electrophoresis can be used in the analysis of a large number of markers and plants?

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    Anand A Khot replied

    @Rallapalli R,.....Vertical units are better....even multiplexing can be done in PCR also, but it depends on the primer size and tm . If we can optimize these two the work will be much more@Rallapalli R,.....Vertical units are better....even multiplexing can be done in PCR also, but it depends on the primer size and tm . If we can optimize these two the work will be much more easier.....

    Feb 10, 2012
• Alexander Petrenko

  Could somebody recommend a protocol for GFP transduction of human or rat adipose tissue derived mesenchymal stromal cells

  I am looking for a simple and reproducible protocol for GFP transduction of human or rat adipose tissue derived mesenchymal stromal cells
• Chamila Adhikaram

  any of you have worked with RFLP analysis

  any of you have worked with RFLP analysis

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    Chamila Adhikaram replied

    Dear Flavio, thank you very much for your reply. I will try on your information.

    Jan 24, 2012
• Nagaveni C Kumbar

  What are the methods to recognize Genomic changes between in-vitro and in-vivo plants...?

  Hi, Friends I have been in Tissue culture field from 2years and i need to analyze the variations between tissue cultured plant and the wild one... So i wanted to go for RAPD first and then SSR.... AmHi, Friends I have been in Tissue culture field from 2years and i need to analyze the variations between tissue cultured plant and the wild one... So i wanted to go for RAPD first and then SSR.... Am I right or are there any other methods? If so please advice me and also give information where it can be done?

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    Nagaveni C Kumbar replied

    Thank You Mr. Rallapalli Ravikiran for your worthful ideas. I tried RAPD and have got variations so now i'm going for gene cloning and sequencing. Thanks to all others who have given valuableThank You Mr. Rallapalli Ravikiran for your worthful ideas. I tried RAPD and have got variations so now i'm going for gene cloning and sequencing. Thanks to all others who have given valuable suggestions.

    Jan 19, 2012
• Hyba abbas Ibrahim

  am looking for a good video lectures about genetic polymorphism and a RFLP genotype technique?

  Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species
• Ashok Sharma

  Can anyone suggest me the online tools for designing of peptidomimetics.....

  Peptidomimetics can be defined as “a molecule bearing identifiable resemblance to a peptide that, as a ligand of a biological receptor, can imitate or inhibit the effect of a natural peptide”. i wantPeptidomimetics can be defined as “a molecule bearing identifiable resemblance to a peptide that, as a ligand of a biological receptor, can imitate or inhibit the effect of a natural peptide”. i want to design peptidomimetics for inhibitory peptides ..........

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    Rajashri Bhairamadgi replied

    Protein Design as peptidomimetics With Rosetta have look on the below page https://files.nyu.edu/rb133/public/design.html http://www.rosettacommons.org/software/ may both links are useful toProtein Design as peptidomimetics With Rosetta have look on the below page https://files.nyu.edu/rb133/public/design.html http://www.rosettacommons.org/software/ may both links are useful to you.... thank you

    Dec 30, 2011
• Sapan Tailor

  Information about Molecular marker technology

  Hi Can anybody suggest me a good book or research article from which I can get knowledge about molecular marker technology and marker assisted selection of genotype? I also want to know how molecularHi Can anybody suggest me a good book or research article from which I can get knowledge about molecular marker technology and marker assisted selection of genotype? I also want to know how molecular biology make map of the plant DNA?

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  • 
    Sasan Shadpour replied

    Very thanks best regards sasan shadpour research tobacoo center-rasht - iran

    Dec 13, 2011
• Endang Anggarwulan

  Rflp

  Hello friends, can anybody tell me the RFLP procedure especially for Araceae family

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  • 
    Endang Anggarwulan replied

    As Rivard,Cappadocia and Landry (1996) said in their paper, ................... RFLPs have several advantages over morphological and isozyme markers and have greatly contributed to the constructionAs Rivard,Cappadocia and Landry (1996) said in their paper, ................... RFLPs have several advantages over morphological and isozyme markers and have greatly contributed to the construction of detailed genetic maps. Detection of allelic variation for RFLP markers in plant populations is much greater than for morphological or isozyme markers (Tanksley 1983; Helentjaris et al. 1985). In addition, RFLP markers are generally codominant, apparently free of epistatic effects, and, quite importantly, are developmentally stable (Beckman and Soller 1983). So what your suggestion if I want to study a species that has several tuber colour. Thank's a lot for your response.

    Nov 15, 2011