Development of statistical models for genome wide association studies to identify genotype-environment interaction for water stress in sorghum

• Grant number: 12/13272-6
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): October 01, 2012
• Effective date (End): February 28, 2014
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Antonio Augusto Franco Garcia
• Grantee: Rodrigo Gazaffi
• Home Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

Water stress is one of the major factors responsible for reduction on sorghum production in the world, with significant impact on food security. The genetic basis for drought tolerance is still unknown, but it is possible to observe differential response through sorghum accessions. Association mapping studies can help to reveal the genetic control of quantitative traits by establishing statistical associations between molecular markers of single base polymorphism (SNP - Single Nucleotide Polymorphism) and the phenotype. However, statistical models that incorporates the interaction genotype by environment (G-E) in associative studies have not been developed, which restricts the practical use on plant breeding programs. G-E studies details the genetic basis of quantitative traits and also provide information about the best genotypes for each environmental conditions. Those information can be used on plant breeding programs through marker-assisted selection. In the present work, we propose to develop statistical model for association mapping, allowing the identification of interaction between SNP and environments. This model will be used to study genetic basis of drought tolerance in sorghum. The mapping population consists in a association panel composed by 377 accessions that were initially genotyped with SNP 1536 and are currently being genotyped by re-sequencing technology. The phenotypes were evaluated for drought tolerance in field conditions in two environments.

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)

GAZAFFI, RODRIGO; MARGARIDO, GABRIEL R. A.; PASTINA, MARIA MARTA; MOLLINARI, MARCELO; GARCIA, ANTONIO AUGUSTO F. A model for quantitative trait loci mapping, linkage phase, and segregation pattern estimation for a full-sib progeny. Tree Genetics & Genomes, v. 10, n. 4, p. 791-801, AUG 2014. Web of Science Citations: 12.

ROSARIO, M. F.; GAZAFFI, R.; MOURA, A. S. A. M. T.; LEDUR, M. C.; COUTINHO, L. L.; GARCIA, A. A. F. Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4. JOURNAL OF APPLIED GENETICS, v. 55, n. 1, p. 97-103, FEB 2014. Web of Science Citations: 0.