QTL mapping in autopolyploids using SNPs, with applications in sugarcane

• Grant number: 12/17009-8
• Support Opportunities: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): November 01, 2012
• Effective date (End): November 18, 2015
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Antonio Augusto Franco Garcia
• Grantee: Marcelo Mollinari
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated scholarship(s): 13/12245-8 - Development of statistical models for QTL mapping in autopolyploids using SNPs, with applications in sugarcane, BE.EP.PD

Abstract

Sugarcane is among the most important crops in the world, specially in developing countries. However, the complex polyploid structure of its genome is not well understood. In the recent years, many research groups have been making tremendous efforts to identify loci that control genotypic variation in quantitative traits (QTLs). Despite all advances in the development of models for QTL mapping in tetraploids, the vast majority of the models used for QTL mapping in species with high ploidy level, such as sugarcane, are approximations of those used in diploid organisms. In this context, this project has three scientifically relevant objectives: i) develop new models for QTL mapping in species with high ploidy levels; ii) implement these models in an open-source software in R statistical environment; iii) use the new models to map QTLs for agronomically important traits in sugarcane, using SNP markers. Thus, it is expected to be able to study the effects of allelic dosage precisely, as well as dominance and epistatic effects. Furthermore, it is expected that the inclusion of such effects in the mapping model, will provide more accurate and realistic estimates of QTLs than previously reported in literature. In order to perform the analyzes, the SNPs will be classified using a Bayesian approach with the software SuperMASSA, of which the applicant is co-author. A genetic map will be constructed using the model based on hidden Markov chains, as proposed by the applicant in his doctoral thesis. The models that are proposed in this project will be based models for QTL mapping in polyploids available in literature, however many theoretical developments are needed before such models contemplate co-dominant markers (such as SNPs) and high ploidy levels. The results of this project should provide important information for understanding the genetic architecture of species with higher ploidy levels, such as sugarcane.

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)

MOLLINARI, MARCELO; FRANCO GARCIA, ANTONIO AUGUSTO. Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3-GENES, GENOMES, GENETICS, v. 9, n. 10, p. 3297-3314, OCT 2019. (08/52197-4, 13/12245-8, 12/17009-8)