Breeding of Sugarcane - Industrial Crops: Breeding for BioEnergy and Bioproducts - page 37

to tackle the challenging task of sequencing the sugarcane genome [ 25 ]. Other
efforts that are underway include BAC-by-BAC and whole genome shotgun
sequencing (WGS). Sequencing of R570 using the BAC library is being pursued
by groups in Australia, France, South Africa, USA, and Brazil ( http://
sugarcanegenome.org ) . Furthermore, there is an ongoing sequencing effort for
SP80-3280, the Brazilian cultivar that contributed most of the available ESTs [ 17 ].
In sugarcane improvement, the choice of parents for crossing requires careful
characterization and evaluation of the germplasm as well as good knowledge and
breeding skills to make the right decisions. Molecular markers can be a tool to help
guide this route. This technology has been used in genetic diversity studies, cultivar
identification, and genetic mapping. In addition, it is also used in molecular
diagnostic tests to detect various sugarcane pathogens in different laboratories
worldwide.
Several types of molecular markers have been used in genetic studies sugarcane,
e.g., restriction fragment length polymorphisms (RFLPs), amplified fragment
length polymorphisms (AFLPs), and target region amplification polymorphism
(TRAP). With transcriptome studies, the abundance of microsatellite sequence
ESTs allowed the emergence of EST-derived SSRs (EST-SSRs). New techniques
using a high-throughput microarray platform, like DART (Diversity Arrays Tech-
nology), were implemented in sugarcane and can generate a final array comprising
5,000-7,000 polymorphic markers [ 28 ]. More recently, next-generation sequencing
(NGS) technologies have been used for whole-genome sequencing to discover large
numbers of single nucleotide polymorphisms (SNPs). The markers in sugarcane
SNPs may be useful for genome saturation, estimates of allelic dosages, and
genome-wide association studies (GWAS).
Investigation of genetic diversity within sugarcane cultivars has shown that
modern sugarcane cultivars are highly heterozygous with many distinct alleles at
a locus. Some authors also investigated the association between genetic similarity
(AFLP data) and pedigree data from improved genotypes and species [ 29 ]. More-
over, molecular profiles of sugarcane varieties can also be used as additional
information in Plant Breeding Rights applications.
Genetic mapping is a basic tool of genomic research. Molecular linkage maps
provide information about the organization of the genome and may be used for
genetic studies and breeding applications. Unfortunately, genetic linkage maps are
inherently difficult to construct in sugarcane for several reasons: (a) elevated ploidy
levels (presence of simplex and multiplex alleles), (b) irregular chromosome
numbers in various homo(eo)logy groups, and (c) a wide array of genotypes is
expected in segregating population (due to heterozygosis and ploidy) [ 30 ]. Over the
past two decades of early studies of sugarcane genetic maps, there have been
19 linkage maps constructed from 13 pedigrees. Although there are huge efforts
of researchers to incorporation molecular markers in genetic maps of sugarcane,
they are still incomplete [ 17 ]. Currently, the genetic maps are constructed from
1,500 to 2,500 markers, and there are no saturated genetic maps covering all
sugarcane chromosomes [ 31 ]. In addition, current mapping methods are restricted
to the use of single-dose markers (1:1 and 3:1). Thus, the use of few dosages