IN SILICO VALIDATION OF MICROSATELLITE MARKERS USING LARGE-SCALE GENOTYPING (DDRADSEQ) DATA IN AGAVE PLANTS, AN EMERGING ENERGY CROP.

João Vitor Rodrigues Mio; Marina Pupke Marone; Lucas Miguel de Carvalho; Gonçalo Amarante Guimarães Pereira; Marcelo Falsarella Carazzolle

Paper Title

Authors

João Vitor Rodrigues Mio
Marina Pupke Marone
Lucas Miguel de Carvalho
Gonçalo Amarante Guimarães Pereira
Marcelo Falsarella Carazzolle

Modality

Poster

Subject area

DNA and Genomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/831981-in-silico-validation-of-microsatellite-markers-using-large-scale-genotyping-(ddradseq)-data-in-agave-plants-an-e

ISBN

978-65-272-0843-3

Keywords

Sisal, SSR, Molecular Markers, Genetic Diversity

Summary

The genus Agave is composed of succulent and herbaceous monocotyledonous angiosperm plants, with most of its species endemic to Mexico, in addition they are drought-resistant plants, highly productive even without irrigation, making them promising for biofuel generation in semi-arid regions. Some agave species are used for sisal fiber production in semiarid areas, with Brazil being the world's largest producer of this fiber, cultivated in the Northeast of Brazil and extremely important for the local population’s income and survival. However, the lack of molecular markers to identify genotypes of interest has slowed the growth of this culture in the region. Microsatellites (SSRs) are molecular markers used for genotyping plant species, but their in vitro validation is laborious. Developing a methodology for in silico validation of SSRs can expedite their application in the field and save resources for standardization. In this study, ddRAD-seq data for 77 individuals of Agave sisalana and 18 hybrid 11648 ((A. amaniensis x A. angustifolia) x A. amaniensis)) were used to predict polymorphic SSRs among these plants. In our pipeline, we start by predicting SSRs and primers flanking these regions from a draft and incomplete genome. We also align ddRAD-seq sequences to this same genome. We filter the ddRAD data to obtain only the SSR regions in the ddRAD data. This is used as input to a Python script to identify polymorphic loci based on the presence of insertions or deletions (indels) within the SSR repeats, through calculations of the start and end positions of these markers. We then generate a table of polymorphic individuals per SSR region. Applying this to our agave dataset, after aligned in reference genome we identified a total of 5,720 and 5,092 regions in A. sisalana and hybrid 11648, respectively. Further on, we determined a minimum coverage criterion of 5 reads to identify the indels in these intersection regions and these numbers decreased to 586 and 602 polymorphic regions. From these, 5 regions of each agave type were selected for wet lab validation through conventional PCR and parallel capillary electrophoresis. After validating these primers in samples from many Agave individuals, we expect to have a toolkit to distinguish individuals from the same species to accelerate agave production in Brazil.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

MIO, João Vitor Rodrigues et al.. IN SILICO VALIDATION OF MICROSATELLITE MARKERS USING LARGE-SCALE GENOTYPING (DDRADSEQ) DATA IN AGAVE PLANTS, AN EMERGING ENERGY CROP... In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/831981-IN-SILICO-VALIDATION-OF-MICROSATELLITE-MARKERS-USING-LARGE-SCALE-GENOTYPING-(DDRADSEQ)-DATA-IN-AGAVE-PLANTS-AN-E. Access in: 27/04/2025