Hermann Paulo Hoffmann

Sugarcane improvement: how far can we go?

In recent years, efforts to improve sugarcane have focused on the development of biotechnology for this crop. It has become clear that sugarcane lacks tools for the biotechnological route of improvement and that the initial efforts in sequencing ESTs had limited impact for breeding. Until recently, the models used by breeders in statistical genetics approaches have been developed for diploid organisms, which are not ideal for a polyploid genome such as that of sugarcane. Breeding programs are dealing with decreasing yield gains. The contribution of multiple alleles to complex traits such as yield is a basic question underlining the breeding efforts that could only be addressed by the development of specific tools for this grass. However, functional genomics has progressed and gene expression profiling is leading to the definition of gene networks. The sequencing of the sugarcane genome, which is underway, will greatly contribute to numerous aspects of research on grasses. We expect that both the transgenic and the marker-assisted route for sugarcane improvement will contribute to increased sugar, stress tolerance, and higher yield and that the industry for years to come will be able to rely on sugarcane as the most productive energy crop.

Repetibilidade e número de colheitas para seleção de clones de cana-de-açúcar

This work aimed at the establishment of the repeatability coefficients (r), determination of the predictability degree (R2) and the needed measurement numbers for tons of cane per hectare, percentage of pol (sucrose) in the juice of cane and tons of pol in the juice of cane per hectare in sugarcane genotypes. A randomized block experimental design, with three replicates in four experiments and four replicates in the other experiments was used. The repeatability estimates were obtained by the statistical methods: anova; main components based on correlation matrix; and structural analysis (correlation, average r). The estimates of the repeatability coefficients showed values with very similar magnitude. The general average repeatability for those three traits was above 0.60, therefore showing regularity in the genotype performance at several measurements (cuts) and reliability in the genotype discrimination that was higher than 87%. The results showed that for those three traits there is a need for the use of, at least, three cuts so that the selection can be accomplished with predictability of a real value above 80% for the genotype.

GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

BackgroundSugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes.ResultsWe used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes.ConclusionsThis study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.

Reaction of sugarcane varieties to orange rust (Puccinia kuehnii) and methods for rapid identification of resistant genotypes

Sugarcane orange rust was recently introduced into Brazil and its control is based on the use of resistant varieties. This study aimed to determine the reaction of Brazilian sugarcane varieties to the disease in the field and to compare artificial inoculation methods. Rust severity was assessed in 17 varieties at a 15-day interval. The maximum disease severity (MS%) and the area under the disease progress curve (AUDPC) were determined for each genotype. The artificial inoculation methods tested were: spraying of a spore suspension on 60-day-old plants in the greenhouse, or placing the spore suspension into the leaf whorl of 5-month-old field-grown plants. Nine out of the 17 varieties studied were resistant to the disease, including the most widely grown in new plantings, RB867515 and RB966928. Varieties RB72454, SP89-1115 and SP79-2233 were susceptible, while RB925211 and SP81-3250 were moderately susceptible. Varieties RB855156, RB92579 and SP83-2847 showed an intermediate reaction. Both inoculation methods correlated well with field results. Spray inoculation discriminates better the responses of the varieties and enables the evaluation of more disease variables. Leaf whorl inoculation allows the use of field-grown plants and generates results in a shorter time.

RB965902 and RB965917 Early/medium maturing sugarcane varieties

The varieties RB965902 and RB965917 were developed for harvesting at the beginning to the middle of the sucrose extraction period (early/medium maturity) and released for the South-Central region of Brazil. In specific environments, the tons of Pol per area (sucrose yield) of these varieties is higher than of the commercial standard RB855453 and they are resistant to the main diseases of the crop.

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

Background Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. Results The hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes. Conclusion All these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars

Metabolic composition is known to exert influence on several important agronomic traits, and metabolomics, which represents the chemical composition in a cell, has long been recognized as a powerful tool for bridging phenotype–genotype interactions. In this work, sixteen truly representative sugarcane Brazilian varieties were selected to explore the metabolic networks in buds and culms, the tissues involved in the vegetative propagation of this species. Due to the fact that bud sprouting is a key trait determining crop establishment in the field, the sprouting potential among the genotypes was evaluated. The use of partial least square discriminant analysis indicated only mild differences on bud outgrowth potential under controlled environmental conditions. However, primary metabolite profiling provided information on the variability of metabolic features even under a narrow genetic background, typical for modern sugarcane cultivars. Metabolite–metabolite correlations within and between tissues revealed more complex patterns for culms in relation to buds, and enabled the recognition of key metabolites (e.g., sucrose, putrescine, glutamate, serine, and myo-inositol) affecting sprouting ability. Finally, those results were associated with the genetic background of each cultivar, showing that metabolites can be potentially used as indicators for the genetic background.

Validação de marcadores moleculares associados à resistência à ferrugem marrom em cana-de-açúcar

ABSTRACT Brown rust caused by the fungus Puccinia melanocephala is an important disease affecting sugarcane ( Saccharum spp.) and is present in almost all growing areas. A major effect gene, Bru 1, was described as a durable resistance source in sugarcane against isolates of P. melanocephala . The aim of this study was to evaluate the efficiency of two molecular markers strongly associated with Bru 1 gene, R12H16 and 9O20-F4-RsaI, for prediction of genetic resistance to brown rust in sugarcane varieties. Thus, this study included 14 RB varieties, developed by RIDESA (Interuniversity Network for the Development of the Sugarcane Industry), which were among the 10 most cultivated varieties in the central-south region of Brazil in the period of 1974-2015. To evaluate the disease in the field an experiment was conducted in randomized blocks with four replicates. The severity of Barreto, F.Z.; Balsalobre, T.W.A. Chapola, R.G.; Hoffmann, H.P.; Carneiro, M.S. Validation of molecular markers associated with brown rust resistance in sugarcane.

Método rápido para extração de DNA de Puccinia kuehnii

An efficient, rapid and low-cost DNA extraction method was developed for Puccinia kuehnii, the causal pathogen of orange rust in sugarcane, an emerging disease in the western hemisphere. The extraction protocol was tested for recently collected spores, as well as for spores stored at -80oC for 7 months. An initial amount of 15 mg of spores led to average DNA concentrations ranging from 880.8 mg/mL to 1115.9 mg/mL. Amplification of the extracted DNA was positive for the evaluated samples.