Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

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henry kuska
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Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67666Post henry kuska
Sat Apr 21, 2018 12:20 am

Abstract
"Roses are well known for commercial floriculture and greatly used in the field of perfumery, soap, cosmetics, jams & jelly and essential oil production. Due to interspecific hybridization, a large number of hybrids and cultivated varieties of rose are recognized which reveals distinguishable features in flowers such as size, shape, and color. Apart from this, the geographical distribution and polyploidy also make Rose genus more complex. Therefore, the present study was undertaken for the identification and characterization of genetic variation within 29 rose accessions through Start codon targeted polymorphism (SCoT) markers. Out of 36 primers, 32 revealed polymorphic amplification profile in 29 rose accessions with amplification ranging from 150bp to 1.2kb. A total of 299 polymorphic amplicons were obtained, ranging from 4 to 19 amplicons with an average of 9.34 amplicons per primer. The polymorphic information content (PIC) ranged from 0.42 to 0.92 with an average of 0.78. The dendrogram was constructed to establish genetic relationship among 29 different accessions using Neighbor-joining and Nei-Li matching coefficient. The distinguishable genetic background and a high degree of variation in the rose genotypes successfully exhibited by the SCoT markers may serve as a valuable aid in Rose improvement strategy."

I am going to put 2 different links here. After the post comes up I will see if one or both will work.

Apparently both will work. The PDF is 28 pages.

See:

https://ac.els-cdn.com/S101836471730791 ... 94f33e98ae

https://www.sciencedirect.com/science/a ... 7-main.pdf

Larry Davis
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Re: Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67676Post Larry Davis
Sat Apr 21, 2018 10:35 pm

I would be very cautious about this one. There is a built-in control with radnectar and apricot nectar CV purchased from the same nursery being compared. They come out at very different places in the dendrogram. Seems the authors did not realize the synonymy. So either the CV sold were poorly labeled, or the techniques were poorly executed. Really the level of informativeness in this work is very low, no better than the average eyeball.

I haven't yet read the cited articles but start codon polymorphism is actually methionine associated polymorphism. Proteins contain methionine many places besides the start codon. Unless there is something else special about their PCR primers not mentioned in this study it has little to do with start codons. Upstream of the start, yes there is considerable variation. Downstream maybe, maybe not. But variation is true of the surroundings of any methionine in the protein.

Thanks for posting. I will look at some of the cited articles. Perhaps there is something novel there but poorly described in the present article.

Peter Harris
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Re: Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67686Post Peter Harris
Sun Apr 22, 2018 3:54 pm

I have read the article in question. It is incoherent, without plan, or nearly so, and generally not worth the time one might spend in reading it. It reaches no meaningful conclusions. Apparently it will go on the co-authors' resumes as if it were of scientific value.

Peter

henry kuska
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Re: Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67688Post henry kuska
Sun Apr 22, 2018 4:53 pm

It is not uncommon for new techniques /applications to be greeted with some skepticism. There is often a trade off of being one of the first and having errors and publishing a perfect "me too" paper.

This is a reviewed scientific paper(Received 2 August 2017, Accepted 16 April 2018) published by a respectable publishing house Elsevier: "Production and Hosting by Elsevier B.V. on behalf of King Saud University".

Below is a link to a similar recent paper:

https://www.bjbabe.ro/wp-content/upload ... _SAIDI.pdf

Peter Harris
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Re: Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67698Post Peter Harris
Sun Apr 22, 2018 10:55 pm

Henry,

What did you learn from reading the paper? Maybe I missed something meaningful. Perhaps you can explain it better than the authors did.

As I see it, the problems with the paper have much to do with unclear plan and poor writing, nothing to do with new techniques/applications. Elsevier is simply hosting and producing--not deciding what is worth being published.

Peter

henry kuska
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Re: Assessment of genetic diversity in 29 Rose germplasms using SCoT marker

Post: # 67699Post henry kuska
Mon Apr 23, 2018 12:55 am

Peter I am not in the field. I depend on the reviewers and editor to determine what is publishable. Of course others may have different opinions. In science this is normally handled by the others publishing follow up papers with their opinions/analysis. The editor normally allows the authors of the original paper to reply to the points of the critical paper.

Dave Byrne had earlier used RAPD to look at genetic diversity. Perhaps he will comment in this thread. And Larry Davis has indicated that he also may have further comments after he reads more of the backup material. I was hoping that the reference that I gave on Sunday April 22 would help the reader(s) see how this technique is expected to contribute.

"Molecular markers that are extended in genome across different plant species, such as SCoT and CDDP, and have longer primers with higher annealing temperature will be more trustworthy and reproducible than arbitrary markers such as RAPDs or ISSR."

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Concerning how the present rose hybridizer could utilize the paper. If he/she was conservative, one could pick a mother and father that were close in Figure 3. If one wanted to "shoot for the stars", one could trying crossing 2 very dissimilar roses in hope of taking hybridizing in a new direction (of course the crosses could be sterile or only lead to very weak offspring).

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