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Fundraiser for whole-genome sequencing of figs
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FruitGardener
Vista, CA, USA
22 Posts
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April 7, 2022 - 11:12 pm

The geneticists from AGI in Tucson were here today obtaining leaf samples from 9 cultivars! In a few weeks they'll obtain 6 more from NCGR Davis. To help defray the costs of this project I've set up a fundraiser here:

https://gofund.me/71166cea

Thanks!

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jafar
549 Posts
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April 8, 2022 - 1:19 pm

What do you hope to learn from the testing and how much is the cost?

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FruitGardener
Vista, CA, USA
22 Posts
(Offline)
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April 8, 2022 - 6:02 pm

Jafar,

My goal is to determine a set of genetic markers which can be measured in a PCR test that will (a) uniquely identify F. carica cultivars and (b) identify morphology including sexual type (there are 12) and primary flavor (there are at least six). In addition, I hope to gain insights to markers distinguishing F. carica from F. palmata. To accomplish this I have selected 13 F. carica specimens with differing morphology plus two F. palmata cultivars for chromatin whole-genome sequencing. Six of the specimens are coming from NGCG Davis so I can correlate with the coarse 15 SSR measurements taken there in 2009 which I re-evaluated last year (https://journals.plos.org/plos.....ne.0263715). A 2016 report by Mathi Thumilan details 206 markers for the Moraceae family of which 58 are applicable to F. carica and at least 41 to F. palmata (https://doi.org/10.1371/journa.....ne.0162909). The primer sequences are provided in the publication. Hopefully I can find them within my sequences and evaluate their suitability for my goals above. I will also correlate with a large dataset from Kazuki Mori published in 2017 which contains RNA sequences from 136 male and female F. carica specimens at the Fukuoka repository (https://doi.org/10.1038/srep41124). Overall it will be a collaborative effort involving researchers on several continents.

The sequencing will be performed by a robotic PacBio Sequel II device at the Arizona Genomics Institute. It is currently the most accurate device for nucleotide sequencing. The specimen leaf samples must first be processed in 1-2 weeks of laboratory procedures to isolate cell nuclei. It will then take the machine about 6-8 days per specimen. The total laboratory cost is $101,600, of which I've made the 50% down payment.

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