Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
Sugarcane cultivars derive from interspecific hybrids obtained by crossing Saccharum officinarum and Saccharum spontaneum and provide feedstock used worldwide for sugar and biofuel production. The importance of sugarcane as a bioenergy feedstock has increased interest in the generation of new cultivars optimised for energy production. Cultivar improvement has relied largely on traditional breeding methods, which may be limited by the complexity of inheritance in interspecific polyploid hybrids, and the time-consuming process of selection of plants with desired agronomic traits. In this sense, molecular genetics can assist in the process of developing improved cultivars by generating molecular markers that can be used in the breeding process or by introducing new genes into the sugarcane genome. For meeting each of these, and additional goals, biotechnologists would benefit from a Communicated by Paul Moore
We have isolated two complete genomic clones, Glav1 and Glav3, encoding 11S globulins (legumins) in oat. The structure of Glav1 deviates from that of the typical legumin gene. This clone possesses an extra intron and an extra exon that is composed entirely of repeats of sequences found elsewhere in the clone. If this exon is functional, the protein encoded by Glav1 will contain novel octapeptide and hendecapeptide repeats. The two Glav clones show stronger and more extensive homology with one another than with the two previously published genomic clones, OG1-E1 and ASglob5. This result suggests that the oat globulin gene family may be divided into distinct subfamilies or that there may be significant cultivar-specific differences among members of this gene family.
Over the past 15 years, recombinant DNA and in vitro culture technologies have been used in concert at the South African Sugarcane Research Institute (SASRI) to genetically engineer sugarcane. The purpose of such research has been two-fold, viz. to establish proof-of-principle regarding the delivery of novel input and resistance traits to sugarcane and to investigate the genetic basis of sucrose accumulation. Underpinning these goals has been the in-house development of essential genetic resources, including the isolation of appropriate transgenes and gene promoter elements, and the optimisation of transformation and tissue culture technologies. With regard to the latter, emphasis has been placed on the development of tissue culture strategies that minimise the potential for somaclonal variation, while maximising the efficiency of germplasm transformation, selection, regeneration and acclimation. The isolation of promoters to drive high-level and targeted transgene expression, as well as the identification of DNA sequences with the potential to deliver the desired phenotype, have been strongly driven by advances in gene discovery and expression technologies. Early approaches relied on the analysis of Expressed Sequence Tag libraries constructed from sugarcane tissues at different developmental stages or challenged with selected abiotic and biotic stress agents. Subsequent improvements in DNA subtractive hybridisation technologies (e.g. suppression subtractive hybridisation) and gene expression analysis (e.g. Affymetrix ® Sugarcane Genome GeneChip) provided new and powerful means for gene and promoter discovery. Reviewed here are the advances in in vitro culture, gene discovery and transgene expression research, which have formed the foundation of the genetic engineering program at SASRI. Also discussed are the opportunities and challenges in these areas of research that are presented by the availability of ultra-high throughput DNA sequencing (e.g. the 454 Sequencing System) for transcriptome analysis and technologies for rapid and accurate profiling of the sugarcane metabolomes.
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