Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

Intra-genotypic competition of Eucalyptus clones generated by environmental heterogeneity can optimize productivity in forest stands

The growth structure of Eucalyptus plantations is the result of site environment, genetic material, and different types of interaction between neighboring plants. It is well known that sites that are more homogeneous result in greater forest productivity. However, additional factors inherent in the micro- environment or the quality of cuttings can lead to heterogeneous clonal biomass at the end of the rotation cycle. This study of the growth patterns in commercial stands of Eucalyptus clones had two aims: (i) to determine whether environmental heterogeneity causes competition among genetically identical individuals and (ii) to validate the occurrence of intra-genotypic competition, revealing the potential relationship with forest productivity. The present study was developed based on two linear mixed models: a non-genetic model, which accounts for spatial autocorrelation and is used to estimate the effects of competition between neighboring trees into the single clone plots; and a genetic model to infer the nature of the clonal competition. Three hundred and six square plots containing one hundred plants from eight experiments using a randomized block design, with three replications, were evaluated. The experiments were positioned in different environmental conditions by combining two different plant spacings and two altitude elevations. Using the path analysis procedure, we verified that there were significant direct effects of competition according to the proximity of the trees in the plot. In addition, trees that were more distant caused indirect effects of competition through nearby trees. Stands with uniform growth conditions (measured by residual autocorrelation parameters) actually caused higher productivity. The results from the genetic correlations of intra-genotypic competition and productivity showed that the less competitive clones were always less productive, regardless of the experimental condition. The more competitively aggressive clones could optimize their productivity when planted in sites with high residual levels, reaching productivities similar to those of homogeneous stands. This suggests that the implementation of certain silviculture techniques, seeking to increase site uniformity, is less relevant to these clones. The selection and use of these clones might be useful for large companies, because they offer the opportunity to achieve high productivity, and for smaller producers who do not have access to the silvicultural quality used by large companies

Data from: Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model

We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as the percentage gain over the population average expected genetic value (EGV) for different proportions of genomically selected individuals, using a rigorous cross-validation (CV) scheme that removed relatedness between training and validation sets. Predictive abilities (PAs) were 0.40–0.57 for individual selection and 0.56–0.75 for family selection. PAs under an additive+dominance model improved predictions by 5 to 14% for growth depending on the selection target, but no improvement was seen for wood traits. The good performance of GS with no relatedness in CV suggested that our average SNP density (~25 kb) captured some short-range linkage disequilibrium. Truncation GS successfully selected individuals with an average EGV significantly higher than the population average. Response to GS on a per year basis was ~100% more efficient than by phenotypic selection and more so with higher selection intensities. These results contribute further experimental data supporting the positive prospects of GS in forest trees. Because generation times are long, traits are complex and costs of DNA genotyping are plummeting, genomic prediction has good perspectives of adoption in tree breeding practice

Phenotypic data for the 856 trees

Phenotypic data for the 856 trees of the experimental population. Data include information on the progeny trial (called landscape in the datafile), block,soil type, planting spacing, age at measurement in years, followed by the trait data, mean annual volume growth increment (MAI), basic wood density (BWD) and screened cellulose pulp yield (SPY). Please note that SNP data were available only for 768 trees of these 856 phenotyped trees as described in the pape

Pedigree data for the population

Expected pedigree data for the experimental population of full sib families based on the pedigree registered by the breeder. Individuals used in the study go from ID 11 to 856

SNP Data for 24,806 polymorphic SNPs

SNP Data for 24,806 polymorphic SNPs in 768 individuals of the 856 individuals used in the study. SNP data were generated using the EuCHIP60K. You will find detailed info on the SNP contained in this chip (genome location, target SNP, flanking sequence) in Silva-Junior et al. (2015). A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing 240 Eucalyptus tree genomes across 12 species. New Phytologist 206(4): 1527-1540. Please note that SNP data was available for 768 trees of the 856 trees phenotyped, as described in the pape