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In silico selection of sugarcane introns to aid in genome editing

Grant number: 22/10264-4
Support Opportunities:Scholarships in Brazil - Scientific Initiation
Effective date (Start): October 01, 2022
Effective date (End): September 30, 2023
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Diego Mauricio Riano Pachon
Grantee:Beatriz Rodrigues Estevam
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Host Company:Universidade de São Paulo (USP). Escola Politécnica (EP)
Associated research grant:20/15230-5 - Research Centre for Greenhouse Gas Innovation - RCG2I, AP.PCPE
Associated scholarship(s):23/02452-8 - Selection of sugarcane introns with low propensity to form stable secondary structures, BE.EP.IC


Applying crop breeding technologies with the aim of improving traits of economical or societal interest is common. Recently, the CRISPR/Cas technologies started to be applied in plants with high specificity, and it being adopted in diverse breeding programs in Brasil. Sugarcane (Saccharum spp.) as a crop is of great economic importance in Brasil, because of its uses as source of food and energy, however, due to the complexity of its genome and high ploidy, genome edition in this crop is not easy. There are several factors that affect the introduction of mutation sin an effective way using CRISPR/Cas. The factor with the greatest individual weight is the introduction of introns of the target species in the Cas9 construct. Based on this, during this project our goal is to identify computationally a set of introns from the from the publicly available sugarcane genome drafts that have the potential to be used in future constructs of Cas9, and thus improve the efficiency of genome editing in this crop.

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