Molecular Characterization and Evaluation of Special Sugarcane Varieties Suitable for Co-Generation of Power

Sugarcane is a major agro-industrial crop in India. The fibre content in sugarcane is gaining importance as fuel for co-generation of electricity. Hence, the present study was proposed to genetically characterize and identify suitable clones for co-generation with high yielding, optimum sucrose per cent, erect, non-lodging and good ratooning ability characters. Genetic analysis of 10 sugarcane hybrids was carried out using STMS primers. Out of 110 markers amplified, 77.27 % were polymorphic with an average of 8.5 polymorphic products per STMS primer. Similarity coefficient value of 0.79 and 0.48 was detected with closely and distantly related hybrids respectively. The average genetic similarity among the hybrids was ~78.6%. These results indicated the existence of moderate level of genetic diversity among these high biomass hybrids. Evaluation trial in replicated randomized block design including five early and five mid late clones was conducted at Regional Agricultural Research Station (RARS), Anakapalle during 2007 to 2010. Early clones viz., CoA 03081 (123.0 t/ha and 14.93 t/ha), CoA 02081 (122.0 t/ha and 14.78 t/ha) and CoA 07321 (118.7 t/ha and 14.10 t/ha) were significantly superior for cane and CCS yields than the best standard Co 7508 (104.0 t/ha and 13.34 t/ha). Midlate clones viz., CoA 07322 (137.0 t/ha and 17.12 t/ha) and CoA 02082 (132.0 t/ha and 17.00 t/ha) were significantly superior over the standard CoV 92102 (125.0 t/ha and 16.95 t/ha) for cane and CCS yields. The fibre content of the early and midlate clones ranged from 18.67 (CoA 02081) to 22.50 (CoA 03081) and 20.17 (CoA 07322) to 23.00 (CoA 03082), respectively. These elite clones recorded resistant reaction to red rot disease. The results revealed the potential of these clones suitable for co-generation of power with high yielding, high fibre content, optimum sucrose per cent and good ratooning ability.

Allele expression biases in mixed-ploid sugarcane accessions

Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, ASEGs were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.

Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.

Genome-Wide Characterization of NLRs in Saccharum spontaneum L. and Their Responses to Leaf Blight in Saccharum

Sugarcane is an important sugar and potential energy crop, and the complexity of its genome has led to stagnant progress in genome decipherment and hindered the genome-wide analysis of the nucleotide binding site leucine-rich repeat (NLR) receptor until the genome of Saccharum spontaneum was published. From the genome of S. spontaneum, 724 allelic and non-allelic NLRs were identified and classified into five types (N, NL, CN, CNL, and P) according to domain architectures and integrity and at least 35 genes encoded non-canonical domains. The phylogenetic analysis indicated NLRs containing the coiled-coil (CC) domain separated from those without CC in six Poaceae species, including S. spontaneum. The motif analysis determined the characteristics and potential functions of the 137 representative non-allelic NLRs, especially the core motifs contained in the NBS and LRR domains, which indicated that motifs were regularly distributed among clades. Through transcription factor binding site (TFBS) profiles, we predicted that the most important transcription regulator of NLRs in sugarcane were ERF, MIKC_MADS, and C2H2. In addition, based on three sets of transcriptome data from two sugarcane hybrids and one S. spontaneum clone infected by the necrotrophic fungal pathogen Stagonospora tainanensis causing sugarcane leaf blight (SLB), the expression dynamics of NLRs responding to the infection in three sugarcane clones were compared. The different genetic background led to the significant difference of NLRs response to SLB in different sugarcane clones, and we got an inference of the potential mechanism of SLB resistance. These results provided a basic reference and new insights to further study and utilize the NLRs.

Origins, History and Molecular Characterization of Creole Cane

Since it was first introduced to Europe in 711 CE and planted in the Americas in 1506, a single type of cane dominated sugar production for 1100 years, until it was finally ousted by Tahitian cane c. 1790. This cane became known as ‘CreoleâĂŹ and is present in the ancestry of many sugarcane hybrids, even today. Whether there was only a single variety of Creole cane or multiple varieties has been a matter of debate for decades. Creole cane remains relevant today, as a Creole cane from Jamaica is the currently chosen lecotype for Saccharum officinarum. In this study we identify 18 historical images of Creole cane, many not previously published. We employ image analyses to characterize the internodes and demonstrate evidence for only a single type of Creole in the new world. Chloroplasts and 45s ribosomal RNA sequences from the cultivar BH10/12 (known to have a Creole female parent) were determined that Java ribbon cane is the historical New World sugarcane known as Creole. We demonstrate that Creole cane is an hybrid and not a single species. Thus S. officinarum has no type specimen. We also sequence a ribbon cane (also known as Guinguam) that appeared in the Caribbean between 1790 and 1810 and demonstrate that this cane was a Sinense type from Java that links back to the work of Rumphinus (1660s).

Irrigation Water Use Efficiency and Water Productivity of Commercial Sugarcane Hybrids under Water-Limited Conditions

HighlightsSugarcane hybrids with improved IWUE have greater scope in sugarcane agriculture as irrigation water is getting scarce.Among sugarcane hybrids, Co 8371 registered high mean water productivity of 4.18 kg m-3, followed by Co 85019 (3.92 kg m-3), while in I2, six hybrids had significantly higher water productivity (Co 85019, Co 0212, Co 86249, Co 10026, Co 0218 and Co V92102) above 4 kg m-3.Deficit irrigation scheduling (irrigation at recommended interval, with 50% crop evapotranspiration replacement) appears to be far more useful than reducing frequency as well as quantity of irrigation water alone. Hybrid mean water productivity was 3.2, 2.7, and 2.1 kg m-3 in I0, I1, and I2, respectively.ABSTRACT. The escalating deficit rainfall scenario in India indicates that drought is a recurrent phenomenon associated with tropical sugarcane farming, and the availability of irrigation water for sugarcane cultivation will be much less in coming years. To meet the challenge of limited and costly water supply, tropical sugarcane growers will have to find ways of increasing the efficiency of irrigation to maintain high cane yields. More efficient irrigation systems, accurate irrigation scheduling, and the right choice of sugarcane hybrids are potential means of increasing irrigation water use efficiency (IWUE), water productivity (WP), and global water security. With the objective of optimizing irrigation water use, a field experiment evaluating the physiological efficiency of commercial sugarcane hybrids for WP in a sandy clay soil under water-limited conditions was conducted during 2016-2017 at the ICAR-Sugarcane Breeding Institute in Coimbatore, India. The replicated field experiment was laid out in split-plot design with three irrigation levels as the main plot and 33 sugarcane hybrids as subplots. The prevailing climatic conditions during the experiment represented a tropical wet and dry climate, with the wet season lasting from October to December due to the northeast monsoon. The results showed that full irrigation at recommended intervals with 100% crop evapotranspiration (ET) replacement (I0) produced significantly higher cane yield than deficit irrigation at recommended intervals with 50% crop ET replacement (I1) and skipping alternate irrigations with 50% crop ET replacement (I2). The deficit irrigation treatments (I1 and I2) had declines in cane yield of 41.2% and 56.4%, respectively. IWUE was similar in I0 and I1, while I2 had reduced IWUE by 23%. WP was significantly influenced by irrigation level; reduction in irrigation water reduced WP by 17.5% and 36.3% in I1 and I2 compared to I0. Among sugarcane hybrids, Co 85019, Co 13006, Co 10026, Co 99004, CoLk 8102, Co 86249, Co 8371, Co 94008, and Co 95020 yielded higher than the genotypic mean under both deficit irrigation treatments, suggesting their usefulness in deficit irrigation strategies. Sugarcane hybrids with high WP can play a pivotal role in sustaining sugarcane productivity and can reduce the large volumes of irrigation water consumed in water-scarce tropical India. Thus, considering water security, the implications of the results are of paramount importance in promoting the coordinated development and management of water, land, and related resources to maximize economic benefits and social welfare in an equitable manner without compromising the sustainability of vital ecosystems at local as well as national levels. Keywords: Cane yield, Global water security, Sugarcane, Water-limited condition.