Sugarcane - Bioenergy Crop Plants - page 531

understanding the balance between alleles. Sugarcane cultivars are known to be a hybrid resulting
from crosses between two polyploid genomes S. spontaneum ( x = 8; 2 n = 40-128) and S. officina-
rum ( x = 10; 2 n = 80). Modern cultivars are polyploid and aneuploid which renders allelic variation/
assortment a key aspect in breeding programs (D'Hont 2005; D'Hont et al. 1996).
Collectively, the Saccharum complex is diverse in genome content and organization. Sorghum ,
Miscanthus, and Erianthus are closely related species and represent genetic reservoirs for exploita-
tion of genetic diversity. Molecular phylogenetic studies within the Saccharinae group indicate that
Miscanthus sensu stricto and Saccharum are sister groups , while Sorghum and Erianthus share a
close relation. Monophyly supports Miscanthus and Saccharum relation, but a distinct clade named
Miscanthidium is identified (Hodkinson et al. 2002).
An International Genome Sequencing Initiative has recently been formed to produce a draft
sequence from several sugarcane cultivars so that tools are developed for understanding genome
ploidy variation, enabling gene discovery and generating a knowledge base molecular infrastructure
(http://bioenfapesp.org). Basic research will benefit not only from gene discovery but also from the
identification of regulatory sequences involved in sucrose metabolism, carbon partitioning in the
plant and responses to restrictive water supply. Breeding programs will have access to the devel-
opment of new molecular markers. The sugarcane monoploid genome is estimated to be about 1
Gb, comparable in scale to the human and maize genomes. The ground basis to tackle the sugar-
cane genome are available resources such as the EST collections (see below), array hybridization
profiles generated by SUCEST-FUN (described below), a collection of bacterial artificial chromo-
some (BAC) clones from R570 cultivar, and the recently released Sorghum genome (Paterson et al.
2009). Genetic maps are currently being improved by the inclusion of repetitive sequences such as
microsatellites and resistance gene analogs (RGAs) (Rossi et al. 2003) thus, increasing resolution.
Another class of repetitive sequences is transposable elements (TEs), which are composed in sugar-
cane by a heterogeneous universe of molecular entities previously described by Araujo et al. (2005).
TE selected BAC clones have been sequenced and specific insertion polymorphism studies provide
information concerning their association to genetic diversity. The ultimate goal in generating the
sugarcane genome sequence is to contribute with a large scientific community effort to improve
sugarcane breeding and develop a systems biology-based approach in sugarcane. Initially, shot-gun
sequencing and a draft assembly of 1000 BAC clones will provide resources for basic biological
processes including access to promoter regions and the possibility of comparative studies among
grasses and, specially, cultivars of interest. Furthermore, the sequencing initiative is expected to
provide tools for the identification of functional modules of gene variation.
The sugarcane directed genome sequence will provide valuable tools for understanding
genome polyploidy variation when compared to Sorghum and other Poaceae species ( Miscanthus ,
Erianthus, and Oryza ). Sugarcane is a domesticated crop that originated from New Guinea (Asia)
about 6000 AD. No more than a hundred years ago modern cultivars have been produced from the
cross of two closely related species and have progressively replaced the Noble clones spreading
in all of the sugarcane producing areas of the globe. Since then, breeding programs are devoted
to addressing the main questions that any crop under a heavy agricultural system is subjected to:
growth habit and harvest index; adaptation to photoperiod; resistance to diseases and abiotic stresses
(mainly water supply and temperature), flowering and genetic erosion (loss of variability to adapt).
Sugarcane varieties are basically maintained from vegetative propagation of selected clones. These
clones would in principle keep their agricultural traits. A sugarcane cultivar issued from a breeding
program is productive for approximately 15 consecutive years after which cultivar replacement is
needed because of loss of quality traits most probably because of genetic erosion and/or instability
or changes that occur in pest and disease agents to overcome plant resistance.
The genome of hybrids is highly polyploid and aneuploid (Grivet et al. 1996). Efforts on map-
ping genes and molecular markers to generate physical maps have been described but because of
the genetic complexity of sugarcane, its genome is poorly understood (Ming et al. 1998; Hoarau
et al. 2001; Lima et al. 2002; Pinto et al. 2004; Garcia et al. 2006; Raboin et al. 2008). Modern