Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range “Chicago” technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree’s 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.

Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.

<p style="text-align: justify;">Selection for drought-tolerant clones has become a major challenge in rubber breeding programs undertaken to ensure the sustainability of natural rubber production, as rubber plantations are expanding in drought-prone areas. Xylem vulnerability to cavitation is a trait related to drought-induced mortality. It can be rapidly evaluated without subjecting plant materials to drought stress, making it useful in large-scale screening for drought tolerance in the near future. We first compared the most widely used techniques for measuring vulnerability to cavitation (air pressurization and Cavitron) on this species, and the effect of sample conditions (size, age and sunlight exposure), in order to ensure reliable analysis. Secondly, ten rubber clones were compared for their xylem vulnerability to cavitation in branches and petioles, and for other traits related to drought response, including stomatal response and leaf shedding occurring during a simulated drought. We also tested the plasticity of vulnerability to cavitation on two clones grown in three locations with contrasting precipitation regimes. We found no clonal variability and a small phenotypic plasticity for xylem vulnerability to cavitation in branches. However, clonal differences in xylem vulnerability to cavitation were found in petioles, and clones also showed differences in stomatal response and in leaf shedding behavior in response to a simulated drought. Our study suggests a genetic canalization for vulnerability to cavitation in organs critical for survival, such as branches, whereas there are clonal differences for traits related to drought avoidance: vulnerability to cavitation of petioles, leaf shedding behavior and stomatal response. The insights gained in this study for screening rubber tree clones for drought tolerance is also discussed. </p>

Drought shapes the distribution and survival of trees even in tropical wet forests, and the wood and leaf trait spectra are used to understand drought adaptations. However, trait variation may result from ontogenetic adjustment or be related to tree size and not reflect evolutionary adaptations. Intraspecific variation in adaptations to drought can be an important factor in a species’ distribution and response to climate change, but excluding potentially confounding factors and proving adaptive evolution are challenging. Provenance trials can identify hereditary variability. We analysed wood and leaf traits in rubber (Hevea brasiliensis) tree clones from 15 locations in the Amazon basin that were planted in northern Thailand, controlled for tree size, tested for genetic relatedness and the phylogenetic signal in traits and compared trait variations with the climate at the location of origin. Correlations between traits and tree size were low. Intraspecific trait variation was similar to relationships in published among‐species comparisons, and correlations among wood traits and correlations among leaf traits were stronger than between wood and leaf traits. Genotype explained 30%–70% of the trait variation, and traits differed in how much of this variation was controlled by location or the relatedness among clones. There was no correlation with mean temperature or total annual rainfall. However, rainfall in the driest quarter (19–199 mm) was strongly related to leaf mass per area, carbon isotopic composition and area‐based nitrogen content (r2 = 0.54–0.70) and weaker to wood traits (vessel density and vessel lumen fraction). Trees from locations with a stronger dry season also had higher growth rates in Thailand. All traits correlating with climate showed a significant phylogenetic signal. We found no evidence of increased drought tolerance, but the trait spectrum and higher growth in trees from drier locations suggest that deciduous rubber trees have adapted via drought avoidance rather than tolerance. Our study also underlines the importance of looking at a suite of traits rather than individual ones to understand adaptive strategies. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13203/suppinfo is available for this article.

This experiment aimed to evaluate the leaf chlorophyll fluorescence and gas exchange response to drought conditions of young rubber plants with different scions. Buds from four genotypes of a progeny derived from crossed clones of RRIM600 x RRII105 from Nongkhai Rubber Research Center, T187, T186, T149 and T172, were grafted to RRIM 600 rootstocks. Eight-month old plants with two flushes were used in this study. Two levels of water treatment were used, drought condition (W1) and well-watered as control (W0). Leaf chlorophyll fluorescence, stomatal conductance (gs) and net photosynthesis rate (Pn) were investigated in three phases: before drought, during drought and after re-watering. Leaf gas exchange parameters were measured using Li-6400 (LiCor Inc.). Leaf chlorophyll fluorescence was measured using FluorPen FP 100 (Photon Systems Instruments). Before drought, genotype T186 had the greatest net photosynthesis rates followed by T172, T187 and T149; there was no difference in maximum quantum yield of photosystem II (Fv/Fm) and performance index on absorption basis (PIABS). Drought conditions caused reduction in stomatal conductance, net photosynthesis rates, and leaf chlorophyll fluorescence in all genotypes. In re-watering conditions, genotype T186 and T172 experienced quick recovery while the others showed partial recovery but the values of all parameters did not reach previous levels before treatment.