Developing new genetic markers for Agave, an emerging energy crop in Brazil.

• Grant number: 24/06624-0
• Support Opportunities: Scholarships abroad - Research Internship - Scientific Initiation
• Start date: August 31, 2024
• End date: November 29, 2024
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Marcelo Falsarella Carazzolle
• Grantee: João Vitor Rodrigues Mio
• Supervisor: Martin Mascher
• Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: Leibniz Institute Of Plant Genetics And Crop Plant Research, Gatersleben, Germany
• Associated to the scholarship: 22/15603-1 - In silico validation of microsatellite markers using large-scale genotyping data (ddRAD-seq) in Agave plants, an emerging energy crop., BP.IC

Abstract

Some species of plants from the genus Agave are used for sisal fiber production in semi-arid areas, and Brazil is the world's largest producer of this fiber. Production is concentrated in the Northeast region in an area called "sertão", composed of 80 million hectares of semi-arid underutilized land. This crop is one of the only income sources for the local population. Additionally, agaves are drought-resistant and have high productivity even without irrigation, possessing great potential for biofuel generation in dry climates. However, the lack of molecular markers to identify genotypes of interest and ensure plant quality slows down the growth of this crop in the region. Our laboratory at Unicamp has a germplasm bank with more than 80 accessions of agave with different phenotypes that need to be genotyped. One type of molecular marker used to genotype plant species is microsatellites (SSRs), but their in vitro validation is laborious. We developed a method for in silico validation of SSRs to accelerate their application in the field and save resources in their standardization. We applied the pipeline in Agave sisalana and hybrid 11648 individuals, using a combination of ddRAD-seq sequences of populations with SSR prediction from draft genome sequences. We obtained around 900 regions with polymorphisms and selected the ones that would better differentiate individuals, generating, for each cultivar, 5 primer pairs that will be tested in the wet lab. Another type of marker widely used to genotype plants are the ones based on single nucleotide polymorphisms (SNPs). They can also be obtained from the same ddRAD-seq dataset, by aligning the reads to a reference genome. Therefore, this would be another important source of molecular markers for agave. During the proposed internship, plant genome assembly and SNP calling will be the objective. These techniques will be applied in barley (Hordeum vulgare), an important species with a good genome assembly and standardized pipelines. After successfully applying the pipeline in barley, the same procedure will be performed in hybrid 11648. This will provide a good basis for the development of SNP markers in addition to the SSR markers already developed in agave.