Mapping of genomic regions and identification of putative candidate genes associated with common bean response to root-knot nematode (Meloidogine incognita)

• Grant number: 18/09069-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: August 01, 2018
• End date: September 07, 2020
• Field of knowledge: Agronomical Sciences - Agronomy - Plant Health
• Principal Investigator: Maria Lúcia Carneiro Vieira
• Grantee: Willian Giordani
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

Phytonematodes are among the major phytosanitary problems on common bean (Phaseolus vulgaris), especially the root-knot nematodes (Meloidogyne spp.), perhaps the most widespread agricultural pest, and particularly the specie M. incognita, one of the most economically damaging pathogens. The control of these nematodes involves unfeasible agronomic practices, emphasizing the need for the development of resistant/tolerant cultivars, which are scarce for beans. Despite the availability of powerful genetic and molecular techniques, little was done to improve the understanding of the mechanisms involved in the common bean response to root-knot nematodes. In this context, the present project aims to detect, through genome-wide associative studies (GWAS), genomic regions associated with the common bean response to M. incognita, as well as identify candidate genes in RNA-Seq libraries (SANTINI, 2015) and by qRT-PCR. For the GWAS, a panel composed of 180 genotypes derived from a core collection of the IAC germplasm will be used. This panel was previously genotyped by the GBS approach, which allowed the identification of 82,680 SNPs (DINIZ, 2016). Once we map the associated genomic regions, RNA-Seq libraries obtained at four and 10 days after inoculation (SANTINI et al., 2015) will be used to verify the expression and select putative candidate genes. The expression of these genes will be confirmed by qRT-PCR, in genotypes presenting extreme responses. We expect to discover SNPs for genotype discrimination according to the response to M. incognita, contributing to selection process in common bean breeding programs, as well as identify putative candidate genes that may be validated in functional analyzes and eventually used for genome editing.

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)

GIORDANI, WILLIAN; GAMA, HENRIQUE CASTRO; CHIORATO, ALISSON FERNANDO; RODRIGUES MARQUES, JOAO PAULO; HUO, HEQIANG; BENCHIMOL-REIS, LUCIANA LASRY; ARANHA CAMARGO, LUIS EDUARDO; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO VIEIRA, MARIA LUCIA. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. PLANT GENOME, NOV 2021. (20/02755-2, 18/09069-7)

GIORDANI, WILLIAN; GAMA, HENRIQUE CASTRO; CHIORATO, ALISSON FERNANDO; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO VIEIRA, MARIA LUCIA. Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean. G3-GENES, GENOMES, GENETICS, v. 12, n. 4, p. 16-pg., 2022-02-26. (18/09069-7, 20/02755-2, 14/06647-9)

CHAVARRIA-PEREZ, LOURDES MARIA; GIORDANI, WILLIAN; GRACAS DIAS, KAIO OLIMPIO; COSTA, ZIRLANE PORTUGAL; MASSENA RIBEIRO, CAROLINA ALBUQUERQUE; BENEDETTI, ANDERSON ROBERTO; CAUZ-SANTOS, LUIZ AUGUSTO; PEREIRA, GUILHERME SILVA; BACHEGA FEIJO ROSA, JOAO RICARDO; FRANCO GARCIA, ANTONIO AUGUSTO; et al. Improving yield and fruit quality traits in sweet passion fruit: Evidence for genotype by environment interaction and selection of promising genotypes. PLoS One, v. 15, n. 5, MAY 14 2020. (12/09100-5, 16/12977-7, 10/06702-9, 18/09069-7, 17/04216-9)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

GIORDANI, Willian. Dissecting the genetic architecture of quantitative traits in common bean (Phaseolus vulgaris L.): response to root-knot nematode infection and seed morphology. 2021. Doctoral Thesis - Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC) Piracicaba.