scholarly journals Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

2018 ◽  
Author(s):  
Camila Campos Mantello ◽  
Lucas Boatwright ◽  
Carla Cristina da Silva ◽  
Erivaldo Jose Scaloppi ◽  
Paulo de Souza Gonçalves ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Hevea Brasiliensis ◽  
Amazon Basin ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Snp Markers ◽  
Large Field ◽  
New Variety ◽  
Cold Response ◽  
Cold Temperatures

AbstractNatural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

scholarly journals High-resolution genetic map and QTL analysis of growth-related traits of Hevea brasiliensis cultivated under suboptimal temperature and humidity conditions

2018 ◽  
Author(s):  
André Ricardo Oliveira Conson ◽  
Cristiane Hayumi Taniguti ◽  
Rodrigo Rampazo Amadeu ◽  
Isabela Aparecida Araújo Andreotti ◽  
Livia Moura de Souza ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Tree Height ◽  
Interval Mapping ◽  
Mapping Method ◽  
Snp Markers ◽  
Genetic Maps ◽  
Stem Diameter ◽  
Breeding Cycle ◽  
Phenotypic Traits

AbstractRubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67% to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.

scholarly journals De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e102665 ◽  
Author(s):  
Camila Campos Mantello ◽  
Claudio Benicio Cardoso-Silva ◽  
Carla Cristina da Silva ◽  
Livia Moura de Souza ◽  
Erivaldo José Scaloppi Junior ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Hevea Brasiliensis ◽  
De Novo Assembly ◽  
De Novo ◽  
Rubber Tree ◽  
Snp Markers ◽  
Rubber Biosynthesis

scholarly journals Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

2020 ◽  
Author(s):  
Ying Wang ◽  
Hui-Liang Li ◽  
Yong-Kai Zhou ◽  
Dong Guo ◽  
Jia-Hong Zhu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Hevea Brasiliensis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Molecular Regulation ◽  
Auxin Signaling ◽  
Abnormal Embryo ◽  
Regulation Mechanisms

Abstract Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes had been identified and the molecular regulation mechanisms of late SE still not well understood. Results In this study, the transcriptomes of embryogenic calluses (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, more than 85.92% of the clean reads were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs mainly involved in phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcript factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

scholarly journals Novel insights into the cold resistance of Hevea brasiliensis through coexpression networks

2021 ◽  
Author(s):  
Carla Cristina Silva ◽  
Stephanie Karenina Bajay ◽  
Alexandre Hild Aono ◽  
Felipe Roberto Francisco ◽  
Ramir Bavaresco Junior ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cold Stress ◽  
Cold Exposure ◽  
Stress Responses ◽  
Hevea Brasiliensis ◽  
Large Scale ◽  
Gene Expression Regulation ◽  
Rubber Tree ◽  
Early Years ◽  
Cold Response

Hevea brasiliensis, a tropical tree species from the Amazon rainforest, is the main source of natural rubber worldwide. Due to the high pressure of fungal diseases in hot, humid regions, rubber plantations have been moved to escape areas, which are dryer and have lower temperatures during the winter. Here, we combined gene expression data of a primary (GT1) and a secondary (RRIM600) young rubber tree clones, which present different cold tolerance strategies, to analyze rubber tree gene expression regulation during 24 h of cold exposure (10 degrees Celsius). Together with traditional differential expression approaches, a RNA sequencing (RNA-seq) gene coexpression network (GCN) comprising 27,220 genes was established in which the genes were grouped into 832 clusters. In the GCN, most of the rubber tree molecular responses to cold stress were grouped in 26 clusters, which were divided into three GCN modules: a downregulated group comprising 12 clusters and two upregulated groups comprising eleven and three clusters. Considering the three modules identified, the general Hevea response to short-term cold exposure involved downregulation of gibberellin (GA) signaling, complex regulation of jasmonic acid (JA) stress responses and programmed cell death (PCD) and upregulation of ethylene responsive genes. The hub genes of the cold-responsive modules were subsequently identified and analyzed. As a result of the GCN strategy applied in this study, we could not only access individual DEGs related to the Hevea cold response, but also provide insights into a deeper cascade of associated mechanisms involved in the response to cold stress in young rubber trees. Our results may represent the genetic stress responses of the species, developed during its evolution, since the varieties chosen for this work are genotypes that were selected during the early years of rubber tree domestication. The understanding of H. brasiliensis cold response mechanisms can greatly improve the breeding strategies for this crop, which has a narrow genetic base, is impacted by climate change and is the only source for large-scale rubber production.

scholarly journals Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

2021 ◽  
Author(s):  
Ying Wang ◽  
Hui-Liang Li ◽  
Yong-Kai Zhou ◽  
Dong Guo ◽  
Jia-Hong Zhu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Hevea Brasiliensis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Molecular Regulation ◽  
Auxin Signaling ◽  
Abnormal Embryo ◽  
Regulation Mechanisms

Abstract Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.

scholarly journals Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ying Wang ◽  
Hui-Liang Li ◽  
Yong-Kai Zhou ◽  
Dong Guo ◽  
Jia-Hong Zhu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Hevea Brasiliensis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Molecular Regulation ◽  
Auxin Signaling ◽  
Abnormal Embryo ◽  
Regulation Mechanisms

Abstract Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. Results In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

scholarly journals Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1440
Author(s):  
Gunlayarat Bhusudsawang ◽  
Ratchanee Rattanawong ◽  
Thitaporn Phumichai ◽  
Wirulda Pootakham ◽  
Sithichoke Tangphatsornruang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Single Molecule ◽  
Plant Cell Wall ◽  
Rubber Tree ◽  
Cost Effective ◽  
Tree Breeding ◽  
Snp Markers ◽  
Intron Length Polymorphism ◽  
Breeding Lines ◽  
Gene Based Markers

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

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

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Camila Campos Mantello ◽  
Lucas Boatwright ◽  
Carla Cristina da Silva ◽  
Erivaldo Jose Scaloppi ◽  
Paulo de Souza Goncalves ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Cold Response ◽  
Response Strategies

scholarly journals Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis

2020 ◽  
Author(s):  
Ying Wang ◽  
Hui-Liang Li ◽  
Yong-Kai Zhou ◽  
Dong Guo ◽  
Jia-Hong Zhu ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Hevea Brasiliensis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Molecular Regulation ◽  
Auxin Signaling ◽  
Abnormal Embryo ◽  
Regulation Mechanisms

Abstract Background: Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE were still not well understood. Results: In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions: This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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