Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
Highlights
Sugarcane was one of the earliest inspirations for use of technology by humans, but the crop has been given less attention in the area of scientific research
Most of the technical difficulties associated with sugar and bioenergy/biomaterial production from sugarcane can be addressed by genetic approaches (Hotta et al, 2010; Furtado et al, 2014), for instance, using genomic assisted breeding programs will allow for input responsive genotype development (Scortecci et al, 2012), and understanding the sub-genomic origins of the important traits like fiber or sugar will help in designing breeding strategies for the end product specific sugarcane genotypes
We outline the developments in characterizing the sugarcane genome and sub-genome structures, sequencing strategies and comparative genomics to provide a review of progress made in recent years in meeting the challenges of describing and translating the complex sugarcane genome
Summary
Edited by: Sean Mayes, Crops for the Future, Malaysia and University of Nottingham, United Kingdom. Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system.
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