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Unveiling the genetic diversity of Rhizophora species from the western world and South Pacific using RAD-seq

Grant number: 18/02655-8
Support type:Scholarships abroad - Research Internship - Scientific Initiation
Effective date (Start): May 01, 2018
Effective date (End): July 25, 2018
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal researcher:Gustavo Maruyama Mori
Grantee:Andre Guilherme Madeira
Supervisor abroad: Yoshiaki Tsuda
Home Institution: Instituto de Biociências (IB-CLP). Universidade Estadual Paulista (UNESP). Campus Experimental do Litoral Paulista. São Vicente , SP, Brazil
Research place: University of Tsukuba, Japan  
Associated to the scholarship:17/12920-8 - Species delimitation within Rhizophora genus from Western Hemisphere and South Pacific, BP.IC

Abstract

The field of molecular ecology has greatly benefited with the development of next generation sequencing. Currently, it is possible to obtain a huge amount of genetic data faster and cheaper than ever before, allowing one to more readily access hundreds or thousands of single nucleotide polymorphism markers, SNPs, to answer evolutionary and ecological questions. Several methods were developed with this objective, each with different applications and limitations. Restriction site associated DNA sequencing, RAD-seq, is a widely used method, capable of generating up to thousands of markers but needing DNA in large quantities and with high purity. Multiplexed inter-simple sequence repeats genotyping by sequencing, MIG-seq, allows one to work with small quantities of DNA and lower quality but this method identifies lower quantities of SNPs. In our current undergraduate research project in Brazil, we use MIG-seq data to delimitate the species relationships inside the mangrove tree genus Rhizophora from the Western world and South Pacific. This species complex, composed by R. mangle, R. racemosa and the hybrid R. X harrisonii, presents a complex evolutionary history, with influences of geographic isolation, hybridization and introgression. Here, our goal is to complement our dataset based on MIG-seq with the analysis of RAD-seq data, increasing the quantity of genetic markers thus improving the robustness of downstream analyses. We will identify and genotype SNPs using two methods: PyRAD and STACKS. Using both programs will allow us to more broadly explore our data and still estimate population genetics summary statistics. (AU)

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