Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis)

Autor(es)

Mantello, Camila Campos ^{[1, 2, 3]} ; Boatwright, Lucas ^[2] ; da Silva, Carla Cristina ^[1] ; Scaloppi, Erivaldo Jose ^[4] ; Goncalves, Paulo de Souza ^[4] ; Barbazuk, W. Brad ^{[2, 5]} ; de Souza, Anete Pereira ^{[1, 6]}

Afiliação do(s) autor(es)

^[1] Univ Campinas UNICAMP, Mol Biol & Genet Engn Ctr CBMEG, Campinas, SP - Brazil

^[2] Univ Florida, Dept Biol, Gainesville, FL - USA

^[3] Natl Inst Agr Bot, John Bingham Lab, Cambridge - England

^[4] Agron Inst IAC, Rubber Res Adv Ctr CAPSA, Votuporanga, SP - Brazil

^[5] Univ Florida, Genet Inst, Gainesville, FL - USA

^[6] Univ Campinas UNICAMP, Biol Inst, Dept Plant Biol, Campinas, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: BMC Genomics; v. 20, JUN 4 2019.
• Citações Web of Science: 0

Resumo

BackgroundNatural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is native the Amazon rainforest, is the major producer of latex worldwide. Rubber tree breeding is time consuming, expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. In this work, transcriptome sequencing was used to identify a full set of transcripts and to evaluate the gene expression involved in the different cold-response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes.ResultsWe built a comprehensive transcriptome using multiple database sources, which resulted in 104,738 transcripts clustered in 49,304 genes. The RNA-seq data from the leaf tissues sampled at four different times for each genotype were used to perform a gene-level expression analysis. Differentially expressed genes (DEGs) were identified through pairwise comparisons between the two genotypes for each time series of cold treatments.DEG annotation revealed that RRIM600 and GT1 exhibit different chilling tolerance strategies. To cope with cold stress, the RRIM600 clone upregulates genes promoting stomata closure, photosynthesis inhibition and a more efficient reactive oxygen species (ROS) scavenging system. The transcriptome was also searched for putative molecular markers (single nucleotide polymorphisms (SNPs) and microsatellites) in each genotype. and a total of 27,111 microsatellites and 202,949 (GT1) and 156,395 (RRIM600) SNPs were identified in GT1 and RRIM600. Furthermore, a search for alternative splicing (AS) events identified a total of 20,279 events.ConclusionsThe elucidation of genes involved in different chilling tolerance strategies associated with molecular markers and information regarding AS events provides a powerful tool for further genetic and genomic analyses of rubber tree breeding. (AU)

• Processo FAPESP: 07/50392-1 - Mapa genético-molecular para Hevea brasiliensis e mapeamento de QTLs para características de importância econômica
• Beneficiário: Livia Moura de Souza
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 14/18755-0 - Análise do perfil de expressão por RNA-seq e identificação de genes envolvidos na resposta ao frio em seringueira
• Beneficiário: Camila Campos Mantello
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 15/24346-9 - Análise da variação alélica em genes de importância econômica entre regiões hom(e)ólogas do genoma de cana-de-açúcar (Saccharum spp.)
• Beneficiário: Carla Cristina da Silva
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 12/50491-8 - Avaliação da variabilidade alélica, estrutura populacional e desequilíbrio de ligação no germoplasma ex situ de seringueira (Hevea brasiliensis)
• Beneficiário: Anete Pereira de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Regular