Development of statistical models for QTL mapping in autopolyploids using SNPs, with applications in sugarcane

• Grant number: 13/12245-8
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: January 20, 2014
• End date: January 19, 2015
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Antonio Augusto Franco Garcia
• Grantee: Marcelo Mollinari
• Supervisor: Rebecca W. Doerge
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: Purdue University, United States
• Associated to the scholarship: 12/17009-8 - QTL mapping in autopolyploids using SNPs, with applications in sugarcane, BP.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). 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 the objective of developing new models for QTL mapping in species with high ploidy for subsequent implementation in an open-source software in R statistical environment. 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, specially in sugarcane studies. 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, used in this project) 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

(The scientific publications listed on this page originate from the Web of Science or SciELO databases. Their authors have cited FAPESP grant or fellowship project numbers awarded to Principal Investigators or Fellowship Recipients, whether or not they are among the authors. This information is collected automatically and retrieved directly from those bibliometric databases.)

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)