Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution.

The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.

Testing intra-species variation in allocation to growth and defense in rubber tree (Hevea brasiliensis).

Background: Plants allocate resources to growth, defense, and stress resistance, and resource availability can affect the balance between these allocations. Allocation patterns are well-known to differ among species, but what controls possible intra-specific trade-offs and if variation in growth vs. defense potentially evolves in adaptation to resource availability. Methods: We measured growth and defense in a provenance trial of rubber trees (Hevea brasiliensis) with clones originating from the Amazon basin. To test hypotheses on the allocation to growth vs. defense, we relate biomass growth and latex production to wood and leaf traits, to climate and soil variables from the location of origin, and to the genetic relatedness of the Hevea clones. Results: Contrary to expectations, there was no trade-off between growth and defense, but latex yield and biomass growth were positively correlated, and both increased with tree size. The absence of a trade-off may be attributed to the high resource availability in a plantation, allowing trees to allocate resources to both growth and defense. Growth was weakly correlated with leaf traits, such as leaf mass per area, intrinsic water use efficiency, and leaf nitrogen content, but the relative investment in growth vs. defense was not associated with specific traits or environmental variables. Wood and leaf traits showed clinal correlations to the rainfall and soil variables of the places of origin. These traits exhibited strong phylogenetic signals, highlighting the role of genetic factors in trait variation and adaptation. The study provides insights into the interplay between resource allocation, environmental adaptations, and genetic factors in trees. However, the underlying drivers for the high variation of latex production in one of the commercially most important tree species remains unexplained.

Genetic diversity analysis and core germplasm bank construction in cold resistant germplasm of rubber trees (Hevea brasiliensis).

The rubber tree, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg., is the sole plant worldwide utilized for the commercial production of natural rubber. Following years of breeding, there exists a wide array of germplasm differentiation in rubber trees. The exploration of diversity and population structure within rubber tree germplasm resources, alongside the establishment of core germplasm resources, is instrumental in elucidating the genetic background and facilitating the effective utilization and management of these resources. By employing SNP molecular marker technology, 195 rubber tree resources were amplified, their genetic diversity analyzed, and a fingerprint map was subsequently constructed. Through this process, the cold-resistant core germplasm of rubber trees was identified. The results revealed that the PIC, He, and pi values ranged from 0.0905 to 0.3750, 0.095 to 0.5000, and 0.0953 to 0.5013, respectively. Both group structure analysis and cluster analysis delineated the accessions into two groups, signifying a simple group structure. A core germplasm bank was established with a sampling ratio of 10%, comprising 21 accessions divided into two populations. Population G1 consists of 20 accessions, while population G2 comprises 1 accession. The research findings have led to the creation of a molecular database that is anticipated to contribute to the management and subsequent breeding applications of rubber tree accessions.

Genome-Wide Identification and Expression Profile Analysis of the Phenylalanine Ammonia-Lyase Gene Family in Hevea brasiliensis.

The majority of the world's natural rubber comes from the rubber tree (Hevea brasiliensis). As a key enzyme for synthesizing phenylpropanoid compounds, phenylalanine ammonia-lyase (PAL) has a critical role in plant satisfactory growth and environmental adaptation. To clarify the characteristics of rubber tree PAL family genes, a genome-wide characterization of rubber tree PALs was conducted in this study. Eight PAL genes (HbPAL1-HbPAL8), which spread over chromosomes 3, 7, 8, 10, 12, 13, 14, 16, and 18, were found to be present in the genome of H. brasiliensis. Phylogenetic analysis classified HbPALs into groups I and II, and the group I HbPALs (HbPAL1-HbPAL6) displayed similar conserved motif compositions and gene architectures. Tissue expression patterns of HbPALs quantified by quantitative real-time PCR (qPCR) proved that distinct HbPALs exhibited varying tissue expression patterns. The HbPAL promoters contained a plethora of cis-acting elements that responded to hormones and stress, and the qPCR analysis demonstrated that abiotic stressors like cold, drought, salt, and H2O2-induced oxidative stress, as well as hormones like salicylic acid, abscisic acid, ethylene, and methyl jasmonate, controlled the expression of HbPALs. The majority of HbPALs were also regulated by powdery mildew, anthracnose, and Corynespora leaf fall disease infection. In addition, HbPAL1, HbPAL4, and HbPAL7 were significantly up-regulated in the bark of tapping panel dryness rubber trees relative to that of healthy trees. Our results provide a thorough comprehension of the characteristics of HbPAL genes and set the groundwork for further investigation of the biological functions of HbPALs in rubber trees.

Overexpression of HbGRF4 or HbGRF4-HbGIF1 Chimera Improves the Efficiency of Somatic Embryogenesis in Hevea brasiliensis.

Transgenic technology is a crucial tool for gene functional analysis and targeted genetic modification in the para rubber tree (Hevea brasiliensis). However, low efficiency of plant regeneration via somatic embryogenesis remains a bottleneck of successful genetic transformation in H. brasiliensis. Enhancing expression of GROWTH-REGULATING FACTOR 4 (GRF4)-GRF-INTERACTING FACTOR 1 (GIF1) has been reported to significantly improve shoot and embryo regeneration in multiple crops. Here, we identified endogenous HbGRF4 and HbGIF1 from the rubber clone Reyan7-33-97, the expressions of which dramatically increased along with somatic embryo (SE) production. Intriguingly, overexpression of HbGRF4 or HbGRF4-HbGIF1 markedly enhanced the efficiency of embryogenesis in two H. brasiliensis callus lines with contrasting rates of SE production. Transcriptional profiling revealed that the genes involved in jasmonic acid response were up-regulated, whereas those in ethylene biosynthesis and response as well as the S-adenosylmethionine-dependent methyltransferase activity were down-regulated in HbGRF4- and HbGRF4-HbGIF1-overexpressing H. brasiliensis embryos. These findings open up a new avenue for improving SE production in rubber tree, and help to unravel the underlying mechanisms of HbGRF4-enhanced somatic embryogenesis.

Integrated physiology, transcriptome and proteome analyses highlight the potential roles of multiple hormone-mediated signaling pathways involved in tapping panel dryness in rubber tree.

Currently, one of the most serious threats to rubber tree is the tapping panel dryness (TPD) that greatly restricts natural rubber production. Over-tapping or excessive ethephon stimulation is regarded as the main cause of TPD occurrence. Although extensive studies have been carried out, the molecular mechanism underlying TPD remains puzzled. An attempt was made to compare the levels of endogenous hormones and the profiles of transcriptome and proteome between healthy and TPD trees. Results showed that most of endogenous hormones such as jasmonic acid (JA), 1-aminocyclopropanecarboxylic acid (ACC), indole-3-acetic acid (IAA), trans-zeatin (tZ) and salicylic acid (SA) in the barks were significantly altered in TPD-affected rubber trees. Accordingly, multiple hormone-mediated signaling pathways were changed. In total, 731 differentially expressed genes (DEGs) and 671 differentially expressed proteins (DEPs) were identified, of which 80 DEGs were identified as putative transcription factors (TFs). Further analysis revealed that 12 DEGs and five DEPs regulated plant hormone synthesis, and that 16 DEGs and six DEPs were involved in plant hormone signal transduction pathway. Nine DEGs and four DEPs participated in rubber biosynthesis and most DEGs and all the four DEPs were repressed in TPD trees. All these results highlight the potential roles of endogenous hormones, signaling pathways mediated by these hormones and rubber biosynthesis pathway in the defense response of rubber trees to TPD. The present study extends our understanding of the nature and mechanism underlying TPD and provides some candidate genes and proteins related to TPD for further research in the future.

Comprehensive Analysis of the Catalase (CAT) Gene Family and Expression Patterns in Rubber Tree (Hevea brasiliensis) under Various Abiotic Stresses and Multiple Hormone Treatments.

Catalase (CAT) is one of the key enzymes involved in antioxidant defense systems and mainly scavenges H2O2 and plays a vital role in plant growth, development, and various adverse stresses. To date, a systematic study of the CAT gene family in rubber tree has not been reported. In this study, five HbCAT gene family members were identified from the rubber tree genome, and these were mainly clustered into two subfamilies. Gene structure and motif analysis showed that exon-intron and motif patterns were conserved across different plant species. Sequence analysis revealed that HbCAT proteins contain one active catalytic site, one heme-ligand signature sequence, three conserved amino acid residues (His, Tyr, and Asn), and one peroxisome-targeting signal 1 (PTS1) sequence. Fragment duplication is a selection pressure for the evolution of the HbCAT family based on Ka/Ks values. Analysis of cis-acting elements in the promoters indicated that HbCAT gene expression might be regulated by abscisic acid (ABA), salicylic acid (SA), and MYB transcription factors; furthermore, these genes might be involved in plant growth, development, and abiotic stress responses. A tissue-specific expression analysis showed that HbCATs gradually increased with leaf development and were highly expressed in mature leaves. Gene expression profiling exhibited the differential expression of the HbCATs under cold, heat, drought, and NaCl stresses. Our results provide comprehensive information about the HbCAT gene family, laying the foundation for further research on its function in rubber tree.

Primer reporte de susceptibilidad del clon de caucho natural FX-3864 a Microcyclus ulei en la altillanura colombiana / First report of susceptibility of natural rubber clone FX-3864 a Microcyclus ulei en la altillanuera colombiana

El mal suramericano de las hojas (SALB), enfermedad endémica del caucho (Hevea brasiliensis), es causado por Microcyclus ulei (forma imperfecta Fusicladium macrosporum) y constituye el principal limitante del cultivo en América, área donde el microorganismo patógeno es endémico. En forma semejante al de otros cultivos agrícolas, el manejo de esta enfermedad está condicionado a la disponibilidad de resistencia genética en el hospedero. En razón de su productividad y condición de resistencia genética, el clon FX 3864 ha sido ampliamente plantado en zonas con diferente potencialidad epidémica a la incidencia del SALB en Colombia, particularmente las denominadas de “no escape” a la enfermedad. Durante el 2010, plantaciones con el clon FX 3864 en fase productiva presentaron síntomas de SALB en zonas de escape ubicadas en la altillanura colombiana (departamento del Meta). En parcelas trampa ubicadas en áreas aledañas a los cultivos se estableció que la severidad promedio de la enfermedad alcanzó niveles de 5,78% en este clon. Verificada la causalidad de la enfermedad mediante observaciones al microscopio se procedió a confirmar el origen del material sobre el cual se desarrollaban las lesiones, utilizando marcadores moleculares (4 microsatélites específicos). Los resultados de la prueba permitieron confirmar la susceptibilidad del hasta hace poco resistente clon FX 3864 al SALB en Colombia. Se sugiere tomar en consideración la nueva condición de este clon y, en concordancia, reorientar los programas de fomento del cultivo advirtiendo a los agricultores sobre los riesgos potenciales de ocurrencia de la enfermedad en las nuevas áreas programadas.

South American Leaf Blight (SALB), caused by Microcyclus ulei (anamorph Fusicladium macrosporum), is an endemic major disease of the rubber tree (Hevea brasiliensis) in America. As well as in other crop systems, its management on rubber plantations relies on plant genetic resistance availability, among other means. FX 3864 is a rubber tree clone widely planted in Colombia due to its production capability and disease resistance. During 2010 SALB symptoms developed in commercial crops at the Meta region of Colombia. Crop traps located nearby the plantations showed mean disease severity levels of 5.78%. Once the causal organism was microscopically confirmed as responsible for the diseased tissue, their origin was characterized by molecular means using 4 microsatellites specific to the rubber tree. The procedure confirmed that FX 3864 was the clone of origin of the leaf tissue. SALB occurring over FX 3864 implies the need to redirect crop disease management measures to be followed on the new development areas of rubber cultivation, warning growers about potential hazards of disease incidence.

Analysis of genetic variation in clones of rubber (Hevea brasiliensis) from Asian, South and Central American origin using RAPDs markers

El caucho natural (Hevea brasiliensis) representa a especies potenciales para reforestación y programas de explotación comercial en ciudades tropicales como Colombia. La variabilidad genética de una colección de caucho que se encuentra en la Estación experimental de Paraguaycito en Buenavista, departamento del Quindío en Colombia fue estudiada para aumentar el conocimiento en cuanto a las especies y realizar un mejor uso de los árboles disponibles. Un total de 25 clones, seis de Sur América, 17 de Asia y 2 de América Central fueron seleccionados y analizados usando RAPDs. Las muestras aisladas de ADN de los árboles fueron con 102 primers, 23 de los cuales mostraron polimorfismos. Aunque se encontró un alto grado de similaridad, los análisis grupales de datos llevaron a diferenciar los árboles de de caucho en términos de su origen geográfico. Por lo tanto, las relaciones genéticas que se encontraron entre los clones podrían ayudar a seleccionar parentales para uso en programas de reproducción y diseño de estrategias para la conservación de los clones que tengan características agronómicas deseables.

Genetic variation in growth traits and yield of rubber trees (Hevea brasiliensis) growing in the Brazilian state of São Paulo

Analysis of variance and covariance was preformed on growth traits (stem girth, bark thickness, total height gain and rubber yield) of 22 open-pollinated progenies of the rubber tree Hevea brasiliensis from an Asian Hevea collection introduced to Agronomic Institute (Instituto Agronômico, Campinas, São Paulo, Brazil; IAC) in 1952. This progeny trial was replicated at three sites in São Paulo state and it was found that at three years from sowing there was statistically significant variation for girth, bark thickness, height and rubber yield. An individual test sites, values of individual plant heritability for girth ranged from h= 0.36 to h= 0.89 whereas values for heritability for progeny means ranged from h= 0.77 to h= 0.87. These moderate and high heritabilities suggest that a combination of progeny and within-progeny selection would be effective at increasing girth in this population at individual sites. Across sites, values of individual-plant heritability for girth ranged from h= 0.36 to h= 0.47, whereas values for heritability of progeny means girth ranged from h= 0.77 to h= 0.87. There were high positive genetic correlations between increased girth and bark thickness suggesting that breeding aimed at increasing girth would also increase bark thickness and possibly height

Age-age correlation for early selection of rubber tree genotypes in São Paulo State, Brazil

In a field trial involving 68 rubber tree (Hevea spp.) clones calculation of genotypic correlation coefficients revealed significant age-age correlation from age 1 to 6 (immature period) for girth A and for age 7 to 12 (mature period) for girth B and for age 7 to 12 (production of latex) for yield. Rank correlation coefficients between all immature ages of girth (girth A), all ages of mature girth (girth B) and all annual rubber production (yield) were significant for the three traits, with the coefficients decreasing with increasing age. Selection of the sets of best 30, 15, 10 and 5 clones from the available 68 clones at a given age was generally accompanied by a descending order of percentage success. It was suggested: (a) to have the best 30 clones of age 6, select the set of best 36 clones at age 2, (b) to have the best 15 clones of age 6, select the set of best 20 clones at age 3, (c) to have the best 5 clones of age 6, select the set of best 8 clones at age 4, and (d) to have the best 3 clones of age 6, select the set of best 3 clones at age 5. More than 80% of the targeted clones on girth A or girth B basis and more than 76.7% clones on yield basis were found to get selected at steps (a) through (d). For achieving early multiplication of the most productive clone for deployment, multiplication should be started with the best 36 (i.e. 60%) clones selected at age 2.

Genetic variability and selection for laticiferous system characters in Hevea brasiliensis

Six laticiferous system characters were investigated in 22 three-year-old, half-sib rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell.-Arg.] progenies, evaluated at three sites (Votuporanga, Pindorama and Jaú, all in the São Paulo State, Brazil). The traits examined were: average rubber yield (Pp), average bark thickness (Bt), number of latex vessel rings (Lv), average distance between consecutive latex vessel rings (Dc), density of latex vessels per 5 mm per ring averaged over all rings (Dd) and the diameter of the latex vessels (Di). The joint analysis showed that site effect and progeny x sites interaction were significant for all traits, except Lv. Estimates of individual heritabilities across the three sites were high for Bt; moderate for Lv, Pp and Dc; low for Dd and very low for Di. Genetic correlations in the joint analysis showed high positive correlations between Pp and the other traits. Selecting the best five progenies would result in genetic gains of 24.91 percent for Pp while selecting best two plants within a progeny would result in a Pp genetic gain of 30.98 percent.

Estimation of variance components and prediction of breeding values in rubber tree breeding using the REML/BLUP procedure

The present paper deals with estimation of variance components, prediction of breeding values and selection in a population of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell.-Arg.] from Rio Branco, State of Acre, Brazil. The REML/BLUP (restricted maximum likelihood/best linear unbiased prediction) procedure was applied. For this purpose, 37 rubber tree families were obtained and assessed in a randomized complete block design, with three unbalanced replications. The field trial was carried out at the Experimental Station of UNESP, located in Selvíria, State of Mato Grosso do Sul, Brazil. The quantitative traits evaluated were: girth (G), bark thickness (BT), number of latex vessel rings (NR), and plant height (PH). Given the unbalanced condition of the progeny test, the REML/BLUP procedure was used for estimation. The narrow-sense individual heritability estimates were 0.43 for G, 0.18 for BT, 0.01 for NR, and 0.51 for PH. Two selection strategies were adopted: one short-term (ST - selection intensity of 8.85 percent) and the other long-term (LT - selection intensity of 26.56 percent). For G, the estimated genetic gains in relation to the population average were 26.80 percent and 17.94 percent, respectively, according to the ST and LT strategies. The effective population sizes were 22.35 and 46.03, respectively. The LT and ST strategies maintained 45.80 percent and 28.24 percent, respectively, of the original genetic diversity represented in the progeny test. So, it can be inferred that this population has potential for both breeding and ex situ genetic conservation as a supplier of genetic material for advanced rubber tree breeding programs.