Erivaldo José Scaloppi Junior

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

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.

Genetic parameters and correlation in early measurement cycles in rubber trees

Knowledge of the traits present in plant populations of a species is essential to carry out selection and breeding. The objective of the present study was to estimate the genetic parameters and correlate genetically and phenotypically the variables rubber yield, annual trunk girth increase, number of latex vessel rings and bark thickness in early measurement cycles. A total of 22 rubber tree progenies (Hevea brasiliensis) were assessed in three locations during three early measurement cycles. The bark thickness variable correlated significantly for the three increase measurements made in the locations of Jaú, Pindorama and Votuporanga. The progeny mean based joint hereditability showed mean values greater than individual plants and within progeny plants of 0.848, 0.286 and 0.242, respectively. The variables annual trunk girth increase and bark thickness are genetically correlated variables. Rubber yield is correlated genetically with bark thickness that permits simultaneous selection for the two characteristics. The early measurement cycles were efficacious for finding genetic variability among the genotypes.

Correlações e análise de trilha em clones de seringueira

Correlations and path analysis in rubber tree clones Knowledge of genotype characteristics is very important during the processes of selection and breeding. The objective of this work was to study the relationship between agronomic and anatomical traits of the bark as well the direct and indirect effects on the rubber tree yield using the path coefficient analysis. Six rubber tree clones were evaluated in a randomized complete block design with four repetitions. The experiments were carried out in the Agribusiness Technological Development Cluster of the Center North /APTA located in Pindorama (SP), Brazil, during the year 2005. Significant positive correlation was found only between rubber tree yield and total number of latex vessel rings (r=0.88). The girth and the total number of latex vessel rings showed the highest direct effect on the rubber tree yield. On the other hand, the virgin bark thickness and the average diameter of latex vessels showed negative direct effect with high values. The indirect selection using the total number of latex vessel rings can provide gains during the selection in rubber tree breeding programs.

Ganho genético com base no tamanho efetivo populacional de progênies de seringueira

O objetivo deste trabalho foi estimar os ganhos geneticos de um teste de progenies de seringueira para a producao de borracha seca e, com base no maior tamanho efetivo populacional e maior ganho genetico, obter os melhores individuos. Foram utilizadas 30 progenies de meios-irmaos, provenientes de sementes de polinizacao mista - alogamia e autogamia - de testes clonais no Estado de Sao Paulo. Utilizou-se o delineamento experimental de blocos ao acaso, com 30 tratamentos (progenies), 3 repeticoes e parcelas lineares de 10 plantas, em um espacamento de 3x3 m, o que totalizou 900 plantas uteis. Aos tres anos, o perimetro, a 50 cm do solo (PA50), e a producao de borracha seca (PBS) foram avaliadas por meio do teste precoce de producao Hamaker Morris-Mann (HMM). As variaveis foram analisadas pelo metodo de modelo linear misto, via procedimento REML/BLUP, em progenies com sistema reprodutivo misto e taxa de autofecundacao de 22%. A identificacao dos 20 melhores individuos quanto a PBS e ao PA50 proporcionou ganho genetico de 67,96 e 16,48%, respectivamente, e um coeficiente de endogamia de aproximadamente 2,82%. O teste de progenies proporciona producao de sementes com melhor valor genetico, grande variabilidade e baixa endogamia

Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection.

The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

Genetic parameters and estimated genetic gains in young rubber tree progenies

The objective of this work was to assess the genetic parameters and to estimate genetic gains in young rubber tree progenies. The experiments were carried out during three years, in a randomized block design, with six replicates and ten plants per plot, in three representative Hevea crop regions of the state of Sao Paulo, Brazil. Twenty-two progenies were evaluated, from three to five years old, for rubber yield and annual girth growth. Genetic gain was estimated with the multi-effect index (MEI). Selection by progenies means provided greater estimated genetic gain than selection based on individuals, since heritability values of progeny means were greater than the ones of individual heritability, for both evaluated variables, in all the assessment years. The selection of the three best progenies for rubber yield provided a selection gain of 1.28 g per plant. The genetic gains estimated with MEI using data from early assessments (from 3 to 5-year-old) were generally high for annual girth growth and rubber yield. The high genetic gains for annual girth growth in the first year of assessment indicate that progenies can be selected at the beginning of the breeding program. Population effective size was consistent with the three progenies selected, showing that they were not related and that the population genetic variability is ensured. Early selection with the genetic gains estimated by MEI can be made on rubber tree progenies.

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

Rubber 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.