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In silico validation of microsatellite markers using large-scale genotyping data (ddRAD-seq) in Agave plants, an emerging energy crop.

Grant number: 22/15603-1
Support Opportunities:Scholarships in Brazil - Scientific Initiation
Effective date (Start): February 01, 2023
Effective date (End): January 31, 2024
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Marcelo Falsarella Carazzolle
Grantee:João Vitor Rodrigues Mio
Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil


Due to the demand for the reduction of greenhouse gas emissions, it is necessary to search for new energy alternatives. Some species of plants of the genus Agave are used for the production of sisal fiber in semi-arid areas and Brazil is the largest producer of this fiber in the world. The production is concentrated in the hinterlands of the Northeast region and this crop has great importance in the local economy, being the main source of income for the population. Moreover, agaves are drought resistant plants with high productivity even without irrigation, having great potential in the generation of biofuels in semi-arid regions. However, the lack of molecular markers to identify interesting genotypes and guarantee the quality of the plants is something that slows down the growth of this crop. The Laboratory of Genomics and Bioenergy (LGE) has a germplasm bank with more than 80 agave accessions with different phenotypes that need to be genotyped. A type of molecular marker still widely used to genotype plant species are microsatellite markers, but their in vitro validation is difficult. The development of a methodology for in silico validation of these markers could accelerate their application in the field and save resources in primer validation. Thus, in order to generate markers capable of differentiating individuals of Agave sisalana and hybrid 11648, a bioinformatics methodology for in silico validation of microsatellites will be developed. Primers for amplification of microsatellite loci will be generated using genomic data available in the LGE database. These primers will be validated in silico through alignments against reads from a genotyping experiment of 95 individuals of A. sisalana and hybrid 11648 collected in the semi-arid region of Bahia. Polymorphic markers between individuals will be selected for further testing, decreasing the amount of time and resources needed. The method will facilitate the validation of microsatellite markers and will provide markers that can be used in the field to select more productive genotypes with higher quality.

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