Simulation of plant complex trait architectures using deep neural networks

• Grant number: 19/26858-8
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: October 01, 2021
• End date: September 30, 2022
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Anete Pereira de Souza
• Grantee: Alexandre Hild Aono
• Supervisor: Gregor Gorjanc
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: University of Edinburgh, Scotland
• Associated to the scholarship: 19/03232-6 - Genome wide selection in sugarcane using machine learning and complex networks for economically important traits, BP.DD

Abstract

Although the use of molecular markers SNPs (single nucleotide polymorphisms) hasmade a major contribution to genetic improvement programs, their application is still limited in the case of sugarcane, a species with high genomic complexity. Due to the lackof biocomputational tools compatible with this species uniqueness, specific methodologieshave to be used. As a result of sugarcane immeasurable importance to the biofuels andsugar manufacturing sectors, breeding of economically important cultivars makes a majorcontribution to the world economy. Genomic selection methodologies have proven to bean alternative to traditional marker-assisted approaches because of the polygenic nature ofquantitative phenotypic characteristics and the consequent complexity of applying methodsfor genotype-phenotype association. This research project proposes an innovative approach for sugarcane selection. Using a matrix of putative SNPs identified on Genotyping bySequencing data and softwares adapted to the species polyploidy and aneuploidy, an association modeling between these markers will be performed using complex networks. Throughcommunity detection methods in the built network, it is intended to perform data imputation, dimensionality reduction and identification of SNPs with related biological categories.To build the selection model, machine learning techniques will be used as nonlinear models,modelled to capture the specificity of the sugarcane genome. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

AONO, ALEXANDRE HILD; ULBRICHT FERREIRA, REBECCA CAROLINE; LIMA MORAES, ALINE DA COSTA; DE CASTRO LARA, LETICIA APARECIDA; GONZAGA PIMENTA, RICARDO JOSE; COSTA, ESTELA ARAUJO; PINTO, LUCIANA ROSSINI; DE ANDRADE LANDELL, MARCOS GUIMARAES; SANTOS, MATEUS FIGUEIREDO; JANK, LIANA; et al. A joint learning approach for genomic prediction in polyploid grasses. SCIENTIFIC REPORTS, v. 12, n. 1, p. 17-pg., 2022-07-21. (19/26858-8, 18/19219-6, 19/21682-9, 19/03232-6)

AONO, ALEXANDRE HILD; FRANCISCO, FELIPE ROBERTO; SOUZA, LIVIA MOURA; GONCALVES, PAULO DE SOUZA; SCALOPPI JUNIOR, ERIVALDO J.; LE GUEN, VINCENT; FRITSCHE-NETO, ROBERTO; GORJANC, GREGOR; QUILES, MARCOS GONCALVES; DE SOUZA, ANETE PEREIRA. A divide-and-conquer approach for genomic prediction in rubber tree using machine learning. SCIENTIFIC REPORTS, v. 12, n. 1, p. 14-pg., 2022-10-26. (19/26858-8, 18/18985-7, 19/03232-6)