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

Camila Campos Mantello,Carla Cristina Da Silva,Erivaldo Jose Scaloppi,W Brad Barbazuk,Anete Pereira De Souza,Paulo De Souza Goncalves,Lucas Boatwright

doi:10.1186/s12864-019-5852-5

Abstract

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.

Highlights

Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry
Sequencing and transcriptome assembly In the present study, we sequenced leaf tissue RNA from the RRIM600 and GT1 genotypes, which resulted in a total of 529,339,330 paired-end (PE) reads for the RRIM600
When we summarized the total HQ PE reads from both genotypes, we obtained 933,614,104 reads, which were employed to construct the reference transcriptome

Summary

Introduction

An indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. Rubber tree breeding is time consuming, expensive and requires large field areas. Genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Cold stress prevents plants from achieving their full genetic potential, inhibiting metabolic reactions, reducing the photosynthetic capacity and altering membrane permeability [1, 3]. Temperate plants can generally achieve cold acclimation and acquire tolerance to extracellular ice formation in their vegetative tissues. Tropical crops such as maize and rice lack the cold acclimation ability and are sensitive to chilling [1]. Determining gene expression profiles under cold stress could help to elucidate the mechanisms of cold acclimation in plants and can be an effective method for selecting candidate genes. Candidate genes can be targeted to identify genetic variation and develop molecular markers

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Results

Conclusion