Molecular mapping of genes conferring field resistance to South American Leaf Blight ( Microcyclus ulei) in rubber tree

Genetic analysis of agronomic and physiological traits associated with latex yield revealed complex genetic bases in Hevea brasiliensis

Hevea brasiliensis, a natural rubber producing species, is widely cultivated due to its high rubber yield potential. Natural rubber is synthesised in the rubber particles of laticifers. Latex diagnosis (LD) was established to characterise the physiological state of the laticiferous system by measuring its physiological parameters, i.e., sucrose, inorganic phosphorous (Pi), thiols and total solid content (TSC). Rubber clones are often classified in three groups i.e., quick starters, medium starters and slow starters. To better understand the genetic bases of latex yield, a biparental population was generated from a cross between the quick-starter clone PB 260 and the medium-starter clone SP 217. LD was performed during the peak latex production season and used to calculate sucrose loading. The agronomic and physiological parameters associated with latex yield led to the classification of genotypes according to the rubber clonal typology and to the identification of quantitative trait loci (QTL) using a high-density map. Inorganic phosphorous content was positively associated with yield during the first year of production thus enabling identification of quick-starter clones. In addition, the LD-based clonal typology led to determine the long-term yield potential and the use of appropriate ethephon stimulation. QTL analysis successfully identified several QTLs related to yield, sucrose, Pi and TSC. One QTL related to sucrose loading was identified in the same position as the QTL for sucrose on linkage group 1. To our knowledge, this is the first study to report QTL analysis for this trait. The use of a high-density map enables the identification of genes underlying QTLs. Several putative genes underlying QTLs related to yield, sucrose and TSC were identified.

Global Assessment of Climate-Driven Susceptibility to South American Leaf Blight of Rubber Using Emerging Hot Spot Analysis and Gridded Historical Daily Data

South American leaf blight (SALB) of Para rubber trees (Hevea brasiliensis Muell. Arg.) is a serious fungal disease that hinders rubber production in the Americas and raises concerns over the future of rubber cultivation in Asia and Africa. The existing evidence of the influence of weather conditions on SALB outbreaks in Brazil has motivated a number of assessment studies seeking to produce risk maps that illustrate this relationship. Subjects with dynamic and cyclical spatiotemporal features need to embody sufficiently fine spatial resolution and temporal granulation for both input data and outputs in order to be able to reveal the desired patterns. Here, we apply emerging hot spot analysis to three decades of gridded daily precipitation and surface relative humidity data to depict their temporal and geographical patterns in relation to the occurrence of weather conditions that may lead to the emergence of SALB. Inferential improvements through improved handling of the uncertainties and fine-scaled temporal breakdown of the analysis have been achieved in this study. We have overlaid maps of the potential distribution of rubber plantations with the resulting dynamic and static maps of the SALB hot spot analysis to highlight regions of distinctly high and low climatic susceptibility for the emergence of SALB. Our findings highlight the extent of low-risk areas that exist within the rubber growing areas outside of the 10° equatorial belt.

QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions

BACKGROUND

Rubber tree is cultivated in mainly Southeast Asia and is by far the most significant source of natural rubber production worldwide. However, the genetic architecture underlying the primary agronomic traits of this crop has not been widely characterized. This study aimed to identify quantitative trait loci (QTLs) associated with growth and latex production using a biparental population established in suboptimal growth conditions in Brazil.

RESULTS

A full-sib population composed of 251 individuals was developed from crossing two high-producing Asiatic rubber tree cultivars, PR 255 and PB 217. This mapping population was genotyped with microsatellite markers from enriched genomic libraries or transcriptome datasets and single-nucleotide polymorphism (SNP) markers, leading to construction of a saturated multipoint integrated genetic map containing 354 microsatellite and 151 SNP markers. Height and circumference measurements repeated over a six-year period and registration of cumulative latex production during six consecutive months on the same individuals allowed in-depth characterization of the genetic values of several growth traits and precocious latex production. Growth traits, circumference and height, were overall positively correlated, whereas latex production was not correlated or even negatively correlated with growth traits. A total of 86 distinct QTLs were identified, most of which were detected for only one trait. Among these QTLs, 15 were linked to more than one phenotypic trait (up to 4 traits simultaneously). Latex production and circumference increments during the last wintering period were associated with the highest numbers of identified QTLs (eleven and nine, respectively), jointly explaining the most significantly observed phenotypic variances (44.1% and 44.4%, respectively). The most important QTL for latex production, located on linkage group 16, had an additive effect of the male parent PB 217 and corresponded to a QTL at the same position detected in a previous study carried out in Thailand for the biparental population RRIM 600 x PB 217.

CONCLUSIONS

Our results identified a set of significant QTLs for rubber tree, showing that the performance of modern Asiatic cultivars can still be improved and paving the way for further marker-assisted selection, which could accelerate breeding programs.

A Review of a Century of Studies on South American Leaf Blight of the Rubber Tree

In the past, South American leaf blight (SALB) of the rubber tree has been responsible for very severe damage in rubber plantations in South America. It is still the main obstacle holding back the development of rubber cultivation on the American continent and is a major risk for Asia and Africa, which are still exempt from this scourge. However, knowledge about the disease and about rubber tree resistance factors has progressed over the last decade, suggesting some solutions, notably for varietal improvement. This article is an overview of knowledge on this subject, particularly the most recent achievements.

Genetic Determinism of Sensitivity to Corynespora cassiicola Exudates in Rubber Tree (Hevea brasiliensis)

An indirect phenotyping method was developed in order to estimate the susceptibility of rubber tree clonal varieties to Corynespora Leaf Fall (CLF) disease caused by the ascomycete Corynespora cassiicola. This method consists in quantifying the impact of fungal exudates on detached leaves by measuring the induced electrolyte leakage (EL%). The tested exudates were either crude culture filtrates from diverse C. cassiicola isolates or the purified cassiicolin (Cas1), a small secreted effector protein produced by the aggressive isolate CCP. The test was found to be quantitative, with the EL% response proportional to toxin concentration. For eight clones tested with two aggressive isolates, the EL% response to the filtrates positively correlated to the response induced by conidial inoculation. The toxicity test applied to 18 clones using 13 toxinic treatments evidenced an important variability among clones and treatments, with a significant additional clone x treatment interaction effect. A genetic linkage map was built using 306 microsatellite markers, from the F1 population of the PB260 x RRIM600 family. Phenotyping of the population for sensitivity to the purified Cas1 effector and to culture filtrates from seven C. cassiicola isolates revealed a polygenic determinism, with six QTL detected on five chromosomes and percentages of explained phenotypic variance varying from 11 to 17%. Two common QTL were identified for the CCP filtrate and the purified cassiicolin, suggesting that Cas1 may be the main effector of CCP filtrate toxicity. The CCP filtrate clearly contrasted with all other filtrates. The toxicity test based on Electrolyte Leakage Measurement offers the opportunity to assess the sensitivity of rubber genotypes to C. cassiicola exudates or purified effectors for genetic investigations and early selection, without risk of spreading the fungus in plantations. However, the power of this test for predicting field susceptibility of rubber clones to CLF will have to be further investigated.

Population Genetics of the Rubber-Producing Russian Dandelion (Taraxacum kok-saghyz)

The Russian dandelion, Taraxacum kok-saghyz (TKS), is a perennial species native to Central Asia that produces high quality, natural rubber. Despite its potential to help maintain a stable worldwide rubber supply, little is known about genetic variation in this species. To facilitate future germplasm improvement efforts, we developed simple-sequence repeat (SSR) markers from available expressed-sequence tag (EST) data and used them to investigate patterns of population genetic diversity in this nascent crop species. We identified numerous SSRs (1,510 total) in 1,248 unigenes from a larger set of 6,960 unigenes (derived from 16,441 ESTs) and designed PCR primers targeting 767 of these loci. Screening of a subset of 192 of these primer pairs resulted in the identification of 48 pairs that appeared to produce single-locus polymorphisms. We then used the most reliable 17 of these primer pairs to genotype 176 individuals from 17 natural TKS populations. We observed an average of 4.8 alleles per locus with population-level expected heterozygosities ranging from 0.28 to 0.50. An average pairwise F_ST of 0.11 indicated moderate but statistically significant levels of genetic differentiation, though there was no clear geographic patterning to this differentiation. We also tested these 17 primer pairs in the widespread common dandelion, T. officinale, and a majority successfully produced apparently single-locus amplicons. This result demonstrates the potential utility of these markers for genetic analyses in other species in the genus.

SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome

Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.

QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate

The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions.

Microsatellite marker development for the rubber tree (Hevea brasiliensis): characterization and cross-amplification in wild Hevea species

Background

The rubber tree (Hevea brasiliensis) is native to the Amazon region and it is the major source of natural rubber in the world. Rubber tree breeding is time-consuming and expensive. However, molecular markers such as microsatellites can reduce the time required for these programs. This study reports new genomic microsatellite markers developed and characterized in H. brasiliensis and the evaluation of their transferability to other Hevea species.

Findings

We constructed di- and trinucleotide-enriched libraries. From these two libraries, 153 primer pairs were designed and initially evaluated using 9 genotypes of H. brasiliensis. A total of 119 primer pairs had a good amplification product, 90 of which were polymorphic. We chose 46 of the polymorphic markers and characterized them in 36 genotypes of H. brasiliensis. The expected and observed heterozygosities ranged from 0.1387 to 0.8629 and 0.0909 to 0.9167, respectively. The polymorphism information content (PIC) values ranged from 0.097 to 0.8339, and the mean number of alleles was 6.4 (2–17). These 46 microsatellites were also tested in 6 other Hevea species. The percentage of transferability ranged from 82% to 87%. Locus duplication was found in H. brasiliensis and also in 5 of other species in which transferability was tested.

Conclusions

This study reports new microsatellite markers for H. brasiliensis that can be used for genetic linkage mapping, quantitative trait loci identification and marker- assisted selection. The high percentage of transferability may be useful in the evaluations of genetic variability and to monitor introgression of genetic variability from different Hevea species into breeding programs.

Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ∼4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection.

Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis)

Genomic simple sequence repeat (SSR) markers are particularly valuable in studies of genetic diversity, evolution, genetic linkage map construction, quantitative trait loci tagging, and marker-assisted selection because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance, and extensive genome coverage. The traditional methods of SSR marker development, such as genomic-SSR hybrid screening and microsatellite enrichment, have the disadvantages of high cost and complex operation. The selectively amplified microsatellite method is less costly and highly efficient as well as being simple and convenient. In this study, 252 sequences with SSRs were cloned from the rubber tree (Hevea brasiliensis) genome from which 258 SSR loci were obtained. The average repeat number was six. There were only 10 (3.9%) mononucleotide, trinucleotide, and pentanucleotide repeats, whereas the remaining 248 (96.1%) were dinucleotide repeats, including 128 (49.6%) GT/CA repeats, 118 (45.7%) GA/CT repeats, and 2 (0.8%) AT/TA repeats. A total of 126 primer pairs (see ESM) were successfully designed of which 36 primer pairs generated polymorphic products from 12 accessions of the cultivated species, 4 related species, and 3 species of the family Euphorbiaceae. In addition, investigations based on four genomic SSRs (GAR4, ACR22, CTR25, and GTR28) by cloning and sequencing provided evidence for cross-species/genera applicability, and homologous sequences were obtained from the rubber tree and Euphorbiaceae. Further analysis about the variation of the flanking regions of the four markers was carried out.

[Construction of genetic linkage map for rubber tree (Hevea brasiliensis) based on SSR markers.]

Out of 260 polymorphic loci screened from a total of 441 pairs of EST-SSR and genomic-SSR primers, 176 were used for constructing the genetic map of rubber tree (Hevea brasiliensis) by an F1 segregating population including 94 progenies from the cross Reyan 88-13xIAN873. Chi-square test carried out on the polymorphic loci used in constructing the map showed that 147 loci followed a segregation ratio of 1:1 and 12 loci followed a ratio of 1:2:1 and 17 loci followed a ratio of 1:1:1:1. Only 13 (7.38%) loci were distorted from the Mendelian ratio. The genetic linkage map consisted of 91 marker loci in 18 linkage groups and covered 1 937.06 cM with an average genetic distance of 21.29 cM between adjacent markers. The largest linkage group consisted of 16 marker loci, while the smallest one contained only 2 marker loci.

Sucrose importation into laticifers of Hevea brasiliensis, in relation to ethylene stimulation of latex production

BACKGROUND AND AIMS

The major economic product of Hevea brasiliensis is a rubber-containing cytoplasm (latex), which flows out of laticifers (latex cells) when the bark is tapped. The latex yield is stimulated by ethylene. Sucrose, the unique precursor of rubber synthesis, must cross the plasma membrane through specific sucrose transporters before being metabolized in the laticifers. The relative importance of sucrose transporters in determining latex yield is unknown. Here, the effects of ethylene (by application of Ethrel on sucrose transporter gene expression in the inner bark tissues and latex cells of H. brasiliensis are described.

METHODS

Experiments, including cloning sucrose transporters, real time RT-PCR and in situ hybridization, were carried out on virgin (untapped) trees, treated or untreated with the latex yield stimulant Ethrel.

KEY RESULTS

Seven putative full-length cDNAs of sucrose transporters were cloned from a latex-specific cDNA library. These transporters belong to all SUT (sucrose transporter) groups and differ by their basal gene expression in latex and inner soft bark, with a predominance of HbSUT1A and HbSUT1B. Of these sucrose transporters, only HbSUT1A and HbSUT2A were distinctly increased by ethylene. Moreover, this increase was shown to be specific to laticifers and to ethylene application.

CONCLUSION

The data and all previous information on sucrose transport show that HbSUT1A and HbSUT2A are related to the increase in sucrose import into laticifers, required for the stimulation of latex yield by ethylene in virgin trees.

Guayule and Russian dandelion as alternative sources of natural rubber

Natural rubber, obtained almost exclusively from the Para rubber tree (Hevea brasiliensis), is a unique biopolymer of strategic importance that, in many of its most significant applications, cannot be replaced by synthetic rubber alternatives. Several pressing motives lead to the search for alternative sources of natural rubber. These include increased evidence of allergenic reactions to Hevea rubber, the danger that the fungal pathogen Microcyclus ulei, causative agent of South American Leaf Blight (SALB), might spread to Southeast Asia, which would severely disrupt rubber production, potential shortages of supply due to increasing demand and changes in land use, and a general trend towards the replacement of petroleum-derived chemicals with renewables. Two plant species have received considerable attention as potential alternative sources of natural rubber: the Mexican shrub Guayule (Parthenium argentatum Gray) and the Russian dandelion (Taraxacum koksaghyz). This review will summarize the current production methods and applications of natural rubber (dry rubber and latex), the threats to the production of natural rubber from the rubber tree, and describe the current knowledge of the production of natural rubber from guayule and Russian dandelion.

Prospects for biopolymer production in plants

It is likely that during this century polymers based on renewable materials will gradually replace industrial polymers based on petrochemicals. This chapter gives an overview of the current status of research on plant biopolymers that are used as a material in non-food applications. We cover technical and scientific bottlenecks in the production of novel or improved materials, and the potential of using transgenic or alternative crops in overcoming these bottlenecks. Four classes of biopolymers will be discussed: starch, proteins, natural rubber, and poly-beta-hydroxyalkanoates. Renewable polymers produced by chemical polymerization of monomers derived from sugars, vegetable oil, or proteins, are not considered here.

Bypassing of a polygenic Microcyclus ulei resistance in rubber tree, analyzed by QTL detection

Genetic resistance components of the Hevea brasiliensis x H. benthamiana RO 38 cultivar to Microcyclus ulei disease were investigated by inoculating isolates which succeeded in partially or completely infecting genotypes of a mapping population. Progeny of a cross between RO 38 and a susceptible cultivar was inoculated under controlled conditions with three isolates and scored for two resistance traits. Interval mapping and a nonparametric test were used to detect resistance quantitative trait loci (QTLs). Eight significant QTLs were detected, all of them inherited from the interspecific parent. Among these QTLs, only one contributed to the partial resistance against a highly pathogenic isolate, and no QTL was detected for resistance against the most pathogenic isolate. As an unexpected result, a single isolate can thus completely bypass this polygenic resistance. This complex situation, where no clear relationship can be established between number of resistance factors and qualitative vs quantitative or partial vs complete resistance, is discussed and suggestions as to the detection of new and sustainable resistance sources are proposed.