Molecular Breeding - Genetics, Genomics and Breeding of Crop Plants - page 233

genomic rearrangements, and other factors (Buckler and Thornsberry 2002).
Until recently, the extent of LD and the application of association mapping
in sunflower have not been studied in-depth. Recent reports by Liu and
Burke (2006), Kolkman et al. (2007) and Fusari et al. (2008) looking into the
patterns of nucleotide diversity in genic loci from wild and cultivated
sunflower, demonstrate that SNP frequencies and LD decay are sufficient in
wild populations (1 SNP/19.9 bp and LD decay within ~200 bp), exotic
germplasm accessions (1 SNP/38.8 bp and LD decay within ~1,100 bp),
and modern sunflower cultivars [1 SNP/45.7 bp and LD decay within ~5,500
bp according to Kolkman et al. (2007); 1 SNP/69 bp according to Fusari
et al. (2008)] for high-resolution association mapping in sunflower.
Naturally occurring allelic variation at specific candidate genes
underlying agronomically important traits is a new resource for the functional
analysis of plant genes, and facilitates the identification and selection of
new alleles and genes based directly on their DNA sequence. In sunflower,
numerous resistance gene candidates (RGCs) have been described as
underlying the Pl clusters conferring resistance to downy mildew located
on LG 8 (Gentzbittel et al. 1998; Gedil et al. 2001; Bouzidi et al. 2002; Slabaugh
et al. 2003), LG 13 (Radwan et al. 2003, 2004), and LG 1 ( Pl arg ; Radwan et al.
2008). These RGCs belong to different sub-classes of the resistance gene
products characterized by the presence of leucine-rich repeat (LRR) motifs
and a nucleotide binding site (NBS) N-terminal to the LRR domain. Slabaugh
et al. (2003) assessed genetic diversity at the LG 8 Pl cluster with specific
intron fragment length polymorphism (IFLP) designed from a RGC in this
cluster, and found an extraordinary level of diversity in this region in wild
sunflowers in comparison to domesticated germplasm. They concluded that
wild sunflowers represented a rich source of untapped resistance genes.
Radwan et al. (2008) have isolated and sequenced a collection of RGCs
(NBS-LRR homologs) from H. annuus , H. paradoxus , H. deserticola , H. tuberosus
and H. argophyllus . From these, 167 NBS-LRR loci were mapped in the
sunflower genetic map in 44 clusters or singletons, many of them co-
localizing to previously mapped downy mildew, rust, and broomrape
resistance genes. This process of sequencing and mapping RGC from diverse
germplasm will facilitate the discovery of novel resistance genes.
In addition to exploiting natural variation, breeders have also induced
novel genetic variation using both chemical and physical mutagens. A
relatively new method for identifying mutations in known genes called
TILLING (Targeting Induced Local Lesions In Genomes) has renewed the
interest in mutation breeding. TILLING is a powerful reverse genetics
approach that employs a mismatch-specific endonuclease to detect single
base pair (bp) allelic variation in a target gene using a high-throughput
assay (Till et al. 2003). This allows the identification of induced point
mutation in target genes within a mutagenized population, as well as the