Hi,
any one please guide me; SSR primers are species specific or trait specific. i have few primer which was reported in articles for wheat yield can i use these similar primer for lentil yield or other yield related traits.
Thank you
Hi Syed,
SSRs divides into two classes:
1. expressed sequence tag (EST)-SSRs and
2. genomic SSRs (gSSRs)
ESTs are more reliable.
I did a long time ago EST-SSR. Now not on track. However, it's ideal to have species-specific SSR markers.
Poaceae and Leguminosae are not genetically related, so not sure if you can go for SSR. I presume if it's from the same genus, there'd be more chances.
Check the below protocols. and worth checking with a molecular breeder if they have done this kind of work before.
Article Development of EST-SSR markers and their application in the ...
Article Development of a set of SSR markers for genetic polymorphism...
Article SSR marker development and intraspecific genetic divergence ...
Article An analysis of genetic diversity in coconut (Cocos nucifera)...
Hi Syed,
SSRs divides into two classes:
1. expressed sequence tag (EST)-SSRs and
2. genomic SSRs (gSSRs)
ESTs are more reliable.
I did a long time ago EST-SSR. Now not on track. However, it's ideal to have species-specific SSR markers.
Poaceae and Leguminosae are not genetically related, so not sure if you can go for SSR. I presume if it's from the same genus, there'd be more chances.
Check the below protocols. and worth checking with a molecular breeder if they have done this kind of work before.
Article Development of EST-SSR markers and their application in the ...
Article Development of a set of SSR markers for genetic polymorphism...
Article SSR marker development and intraspecific genetic divergence ...
Article An analysis of genetic diversity in coconut (Cocos nucifera)...
I guess that SSR primers for wheat will not amplify similar target in lentil. More, if the SSR locus was reported as wheat yield-associated marker, it hardly will be linked to yield in other crops.
Hello,
SSR markers have a certain range, which could be archived by in silico analysis with programs like CLC or similar or even simplier on NCBI with the primer test function.
I would suggest you to stay as close as possible since the already published material could give you some hints about what to expect and how to proceed with your research.
As dr. Akila Wijerathna Yapa suggested, EST-SSRs are indeed better both qualitatively and quantitatively in my opinion but sometimes simple SSR could be good enough if you are trying to analysie the same crop family.
Poliploidism is also another factor quite important for SSR which could increase or decrease the number of bands you could find.
As dr. Alex Ignatov suggested, the expected outcome would be quite far from the wheat, and I agree with him.
I rather suggest you to use SSR primers (EST if possible) that are already available for lentils and from those one try to understand the correlation with the yield.
I would suggest you to have a look at the following material:
http://nopr.niscair.res.in/handle/123456789/34324
Chapter Sourcing SSR markers from related species
https://pubmed.ncbi.nlm.nih.gov/20453299/
https://www.frontiersin.org/articles/10.3389/fpls.2015.00078/full
" GENETIC DIVERSITY IRON AND ZINC CONTENT IN LENTIL (LENS CULINARIS MEDIKUS SUBSP.CULINARIS) AS ASSESSED BY SSR MARKER Reena Mehra*1 , Ashutosh Sarker1 , Harsh K Dixit2 , Muraleedhar Aski2 , Rekha Khandia3 , Ashok Munjal3 "
Best
- Badges
- Science method