Molecular Breeding - Genetics, Genomics and Breeding of Crop Plants - page 239

regulatory variation in genes determining complex traits. These studies,
when combined with QTL mapping, permit the identification of positional
candidate genes for a phenotype of interest whose expression varies
between the parental lines (Wayne and McIntyre 2002). A number of
microarray studies have been carried out in sunflower, which are
unraveling genes involved in complex traits such as quantitative resistance
to Phoma macdonaldii (Alignan et al. 2006), early sunflower seed
development (Hewezi et al. 2006a), chilling sensitivity (Hewezi et al.
2006b), chilling and salt stresses (Fernández et al. 2008), and drought
tolerance (Roche et al. 2007). In addition, microarray analyses combined
with QTL mapping is being used to determine the potential adaptive value
of differentially expressed genes in the sunflower species Helianthus
deserticola (Lai et al. 2006). The use of other profiling techniques such as
proteomic approaches that are more suitable for determining changes in
protein expression, rather than predicting them from transcript expression
data, are also being used in sunflower to identify gene products underlying
complex traits. For example, Hajduch et al. (2007) reported 77 protein
spots differentially expressed in the high oil line RHA801 versus the low
oil line RHA280. Identification of 44 of these proteins indicated that the
two main processes affecting low or high oil concentration in these lines
were glycolysis and amino acid metabolism. However, the use of such
profiling technologies for applied aspects in plant breeding is still rare
due to a limited correlation with QTL studies. Jansen and Nap (2001) have
proposed the use of gene expression data in QTL analyses by evaluating
the expression levels of genes within a segregating population,
identification of the so-called expression QTL (eQTL), and co-localization
of eQTL and trait QTL in the same population. This approach has
demonstrated its utility in understanding complex traits in an increasing
number of crops (Dwivedi et al. 2007), and it is also a potential source for
the development of “perfect markers”.
Finally, if QTLs are mapped accurately to a relatively small region of a
chromosome, another approach to determining their underlying genes
consists of cloning the QTLs using a map-based cloning strategy. To our
knowledge, there are no examples of QTL cloning in sunflower. However,
there have been major advances in recent years, such as the development of
both bacterial artificial chromosome (BAC) and binary-bacterial artificial
chromosome (BIBAC) libraries (Gentzbittel et al. 2002; Özdemir et al. 2004;
Feng et al. 2006; Tang et al. 2007), which provide the necessary tools for
making such an approach feasible. Additionally, association mapping could
be used for higher-throughput QTL cloning by identifying correlations
between candidate gene sequence variation and phenotypic variation in
breeding lines, without requiring the development of special mapping