Evaluation of the linkage desequilibrium and population structure in rubber tree ex situ germplasm (Hevea brasiliensis) using SNPs (Single Nucleotide Polymorphism)

• Grant number: 12/05473-1
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: November 01, 2012
• End date: February 29, 2016
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Anete Pereira de Souza
• Grantee: Livia Moura de Souza
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

The deforestation Amazon threatens the genetic resources of many native species in the region, among which is the genus Hevea, which is exclusively derived from the Amazon rainforest. The species Hevea brasiliensis is emblematic of this region because of its historic role in the economic development of the states that make up the Amazon, and also because it has become, in the early twentieth century, the base of the natural rubber industry in the world, which is developed mainly in Southeast Asian countries, where it employs millions of small farmers. However, due to the effect of restricting the genetic basis very strong, more than 95% of the area planted with rubber tree in the world, are planted with clones from only 5 to 10 primary trees. The genetic diversity of the species is still present in native populations in the area of natural distribution, but is endangered by the accelerated pace of deforestation.The objective of this project is to characterize the genetic diversity of populations of rubber by SNPs markers, which are detected from a database of ESTs (Expressed Sequence Tags) previously constructed and genotyped using sequencing technologies of new generation (NGS).The research activities are structured as follows: (1) collecting DNA samples from rubber trees in ex situ collections existent in Brazil. (2) Detection of SNPs in the genome and transcriptome of Hevea NGS technologies. (3) Characterization and genotyping of DNA samples with the selected SNP's. (4) Data analysis for comparison with other markers type and analysis genetic diversity.The results help to suggest forming public politics resolutions appropriate to optimize the conservation of genetic diversity of the rubber tree.Finally, all genomic resources (SNP's) generated by this project will be useful for genetic studies, the increase in rubber production, as well as a starting point to a future project to sequence the genome of the rubber.

Scientific publications

(6)

(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)

MUNYENGWA, NORMAN; GUEN, VINCENT LE; BILLE, HERMINE NGALLE; SOUZA, LIVIA M.; CLEMENT-DEMANGE, ANDRE; MOURNET, PIERRE; MASSON, AURELIEN; SOUMAHORO, MOUMAN; KOUASSI, DAOUDA; CROS, DAVID. Optimizing imputation of marker data from genotyping-by-sequencing (GBS) for genomic selection in non-model species: Rubber tree (Hevea brasiliensis) as a case study. Genomics, v. 113, n. 2, p. 655-668, MAR 2021. (12/05473-1, 12/50491-8)

CONSON, ANDRE R. O.; TANIGUTI, CRISTIANE H.; AMADEU, RODRIGO R.; ANDREOTTI, ISABELA A. A.; DE SOUZA, LIVIA M.; DOS SANTOS, LUCIANO H. B.; ROSA, JOAO R. B. F.; MANTELLO, CAMILA C.; DA SILVA, CARLA C.; SCALOPPI JUNIOR, ERIVALDO JOSE; et al. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE, v. 9, AUG 24 2018. (15/24346-9, 12/50491-8, 14/11807-5, 12/05473-1, 17/07908-9, 14/18755-0)

DE SOUZA, LIVIA MOURA; LE GUEN, VINCENT; MORENO CERQUEIRA-SILVA, CARLOS BERNARDO; SILVA, CARLA CRISTINA; MANTELLO, CAMILA CAMPOS; OLIVEIRA CONSON, ANDRE RICARDO; GOMES VIANNA, JOAO PAULO; ZUCCHI, MARIA IMACULADA; SCALOPPI JUNIOR, ERIVALDO JOSE; FIALHO, JOSEFINO DE FREITAS; et al. Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection. PLoS One, v. 10, n. 7, JUL 30 2015. (12/50491-8, 12/05473-1)

MANTELLO, CAMILA CAMPOS; CARDOSO-SILVA, CLAUDIO BENICIO; DA SILVA, CARLA CRISTINA; DE SOUZA, LIVIA MOURA; SCALOPPI JUNIOR, ERIVALDO JOSE; GONCALVES, PAULO DE SOUZA; VICENTINI, RENATO; DE SOUZA, ANETE PEREIRA. De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS One, v. 9, n. 7, JUL 21 2014. (07/50562-4, 12/50491-8, 12/11109-0, 12/05473-1)

DE SOUZA, LIVIA M.; DOS SANTOS, LUCIANO H. B.; ROSA, JOAO R. B. F.; DA SILVA, CARLA C.; MANTELLO, CAMILA C.; CONSON, ANDRE R. O.; SCALOPPI, JR., ERIVALDO J.; FIALHO, JOSEFINO DE F.; DE MORAES, MARIO LUIZ T.; GONCALVES, PAULO DE S.; et al. Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis). FRONTIERS IN PLANT SCIENCE, v. 9, JUL 3 2018. (12/50491-8, 14/11807-5, 17/07908-9, 14/18755-0, 12/05473-1)

SILVA, CARLA C.; MANTELLO, CAMILA C.; CAMPOS, TATIANA; SOUZA, LIVIA M.; GONCALVES, PAULO S.; SOUZA, ANETE P.. Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. MOLECULAR BREEDING, v. 34, n. 3, p. 1035-1053, OCT 2014. (07/50562-4, 12/50491-8, 12/05473-1)