Chandima Ariyarathna

11 Questions 15 Answers 0 Followers

Questions related from Chandima Ariyarathna

What is the minimum number of polymophic markers needed for QTL mapping in rice?

Rice is a diploid species with 12 chromosomes. I plan to use a BC₂F₃ population of 100–130 individuals for mapping drought-associated QTLs. What is the minimum number of polymorphic markers and...

15 September 2024 8,522 4 View

Linkage disequilibrium in haploid populations?

Please suggest a tool to estimate linkage disequilibrium in haploid organisms like fungi

12 March 2024 9,399 3 View

Difference in Binary Diploid, Binary Haploid, Haploid data types in GenAlex 6.5?

Please help me understanding the difference in Binary Diploid, Binary Haploid, and Haploid data types in GenAlex 6.5. I want use a binary dataset (RAPD) from fungal species which has a haploid...

15 February 2024 9,318 3 View

Can there be Homothallic Magnaporthe grisea strains?

Magnaporthe grisea and M. oryza are heterothallic fungi. Mating type analysis using standard primer sets (Bao-Hua et, 2004) however, identify duel maters meaning the presence of both MAT1-1 and...

20 July 2022 2,134 0 View

Ho do I labe branches in newick ?

Hi I need to label 2 branches in a phylogenetic tree. Can somebody tell me if I have labelled the branches in these newick trees correctly. I need to use these trees in PAML to see positive...

05 January 2016 4,607 2 View

What is the easiest way to find a cDNA/genomic sequence of a gene when partial sequence available?

Hi, I am interested in an ortholog of rice OsHKT1;4 in wheat and found only a partial sequence (3' end) of the wheat gene on 2AL using IWGS survey sequence database. This gene is expressed through...

16 June 2015 3,618 7 View

What is the relationship between Gene islands an divergence of duplicated genes?

Dear friends Duplicated genes contribute to gene islands (high gene density regions) but at the same time undergo functional divergence. One feature of gene islands is that they co-express and...

23 February 2015 9,698 2 View

How to analyse duplication events in the promoter?

Hi, I made a sequence comparison of 5' UTR region of a membrane transporter protein gene (HKT) between rice and wheat . Around 500bp upstream there is 200bp tandem duplication. Is this a simple...

31 December 2014 4,976 3 View

Is there a relationship between the breakpoint intervals when quering insilico mtd to map markers into wheat deletion bin maps?

I queried a few (QTL) markers in GrainGene DB

26 June 2013 966 0 View

How to solve the problem with RT-PCR low copy number transcripts?

The gene I am working on has 6 copies. I have retrieved genomic DNA sequences of all of them from public domain. I also managed to get FL-cDNA of 5 of them. The missing one (I call it A-2) has...

20 May 2013 4,062 13 View

Genome specific primers non-specific on cDNA?

I have designed genome specific primers for a Na+ transporter gene in wheat. The primers work well on genomic DNA but on cDNA as a template they produce non-specific bands. I have synthesized...

30 March 2013 6,485 4 View