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Comparative QTL mapping and genomic synteny between sweet sorghum and sugarcane

Grant number: 12/25236-4
Support type:Scholarships in Brazil - Doctorate
Effective date (Start): May 01, 2013
Effective date (End): February 28, 2015
Field of knowledge:Agronomical Sciences - Agronomy
Principal Investigator:Antonio Augusto Franco Garcia
Grantee:Guilherme da Silva Pereira
Home Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

Sweet sorghum and sugarcane are two important grasses for bioenergy purposes. However, despite their known evolutionary relationship, the genomes of these species differ in complexity and size. Sorghum bicolor is a diploid species, with basic chromosome number equal to ten, which has about 740 Mb completely sequenced, whereas Saccharum x officinarum has a autopolyploid genome with frequent aneuploidy, and the monoploid size is estimated at 1 Gb. Therefore, genetic studies and breeding in sugarcane is challenging. In this context, the possibility of integrating mapping studies between sorghum and sugarcane becomes feasible given the employment of appropriate methodologies. In this work, we propose to map and to compare QTLs for agronomic traits in both species. We will use two mapping populations. The population of sorghum consists of 272 RILs densely genotyped by SNP markers, which are physically mapped against the genome of the species. The population of sugarcane is an F1 segregating progeny with 154 individuals, being genotyped by SSR and SNP markers. SNP markers in sugarcane allow estimation of alleles dosages as well as the construction of informative genetic maps through methodologies being developed by our research group. The populations, already established in experimental areas, are being evaluated for agronomic and disease resistance phenotypes. Adjusted means for individuals in each population will be obtained by using a mixed models approach. QTL mapping in sorghum population involves the use of multiple interval mapping model, and in sugarcane population we will use multiple QTL mapping model extended to maps based on multiple dosages. Comparison of the genomes will be based on the original marker sequences from sugarcane, which will be aligned against the complete genome of sorghum. The putative QTL associated with syntenic regions will allow inferences about the evolutionary conserved control of traits between the species. Furthermore, the discovery of markers significantly linked to QTLs may suggest applications in gene cloning and marker assisted selection.

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)
PEREIRA, GUILHERME S.; GARCIA, ANTONIO AUGUSTO F.; MARGARIDO, GABRIEL R. A. A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. BMC Bioinformatics, v. 19, NOV 1 2018. Web of Science Citations: 4.
ALMEIDA BALSALOBRE, THIAGO WILLIAN; PEREIRA, GUILHERME DA SILVA; ALVES MARGARIDO, GABRIEL RODRIGUES; GAZAFFI, RODRIGO; BARRETO, FERNANDA ZATTI; ANONI, CARINA OLIVEIRA; CARDOSO-SILVA, CLAUDIO BENICIO; COSTA, ESTELA ARAUJO; MANCINI, MELINA CRISTINA; HOFFMANN, HERMANN PAULO; DE SOUZA, ANETE PEREIRA; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO, MONALISA SAMPAIO. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics, v. 18, JAN 11 2017. Web of Science Citations: 22.
BALSALOBRE, THIAGO W. A.; MANCINI, MELINA C.; PEREIRA, GUILHERME DA S.; ANONI, CARINA O.; BARRETO, FERNANDA Z.; HOFFMANN, HERMANN P.; DE SOUZA, ANETE P.; GARCIA, ANTONIO A. F.; CARNEIRO, MONALISA S. Mixed Modeling of Yield Components and Brown Rust Resistance in Sugarcane Families. AGRONOMY JOURNAL, v. 108, n. 5, p. 1824-1837, SEP-OCT 2016. Web of Science Citations: 5.
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
PEREIRA, Guilherme da Silva. Comparative QTL mapping between sweet sorghum and sugarcane for bioenergy traits. 2015. Doctoral Thesis - Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz Piracicaba.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.