Biology Reference
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massively parallel genotyping, linkage mapping,
and gene expression analysis (Stoffel et al. 2012).
Recently, the whole genome of cv. Salinas has
been sequenced and assembled into scaffolds
(Reynes-Chin-Wo et al. 2012). Approximately
45,000 gene models have been predicted in scaf-
folds (Michelmore et al. 2010; Reynes-Chin-
Wo et al. 2012) that are being assigned to
the reference molecular map using genotyping-
by-sequencing (GBS) (Elshire et al. 2011) of
RILs from the mapping population. The let-
tuce genome sequence was released publically
in 2012. The most comprehensive and recent
information regarding the lettuce genome project
is available at the Compositae Genome Project
(CGP) website ( http://cgpdb.ucdavis.edu). The
Salinas 88
sary to estimate the extent of LD in the lettuce
genome. Analysis of the Tvr1 genomic region
indicates extensive LD (Simko et al. 2009). How-
ever, this genomic region may not be represen-
tative of the overall LD in the lettuce genome,
because considerable variation in the extent of
LD exists within an individual genome (Tenail-
lon et al. 2001). Moreover, the extent of LD is
highly dependent on the population in which
it is measured (Rafalski and Morgante 2004).
In cultivated lettuce, the population structure is
profound and generally in good agreement with
horticultural types (Simko and Hu 2008; Simko
2009). It was observed that the decay of LD
within crisphead cultivars is slower than the LD
decay within a group of romaine cultivars (Simko
et al. 2009).
MAS is used in both public and private
lettuce-breeding sectors for selecting material
with a desirable combination of resistance genes.
Although MAS has been used for only four dis-
eases (downy mildew, corky root, LMV, and
dieback), current progress in the analysis of
the lettuce genome indicates that development
of assays for MAS will accelerate in the near
future. Besides using MAS for disease resis-
tance, assays already exist or are in develop-
ment for selecting material with resistance to
lettuce aphid ( Nasonovia ribisnigri Mosley), late
bolting, male sterility, and slow deterioration of
minimally processed salad. Use of MAS for
polygenic traits remains problematic. To cap-
ture the effects of polygenic traits, a selection
based on a large number of molecular mark-
ers distributed throughout the whole genome
was proposed. This selection method was termed
genomic selection (GS) (Meuwissen et al. 2001).
Simulation (Bernardo and Yu 2007) and empir-
ical (Heffner et al. 2011a) studies revealed that
accuracies of the prediction of phenotypes using
GS were significantly greater than with MAS.
The accuracy of the GS was tested in both multi-
family prediction models (Heffner et al. 2011b)
and bi-parental plant populations (Lorenzana and
Bernardo 2009). Use of GS in lettuce breeding
has not yet been reported.
La Brillante mapping population
was recently used to test the sequence-based
genotyping (SBG) approach, a technology for
simultaneous marker discovery and co-dominant
scoring (Truong et al. 2012). More than 1,000
SNP markers for lettuce were developed with
SBG and used to construct a de novo linkage
map.
Association mapping technique allows the
linking of plant resistance phenotypes to geno-
types through analysis of biodiversity in a wide
gene pool (Simko 2004). In lettuce, only the Tvr1
gene was mapped through association mapping
(Simko et al. 2009, Simko et al. 2010b). How-
ever, the test of association in this study was lim-
ited to only a few molecular markers from the
specific genomic region. The availability of an
ultrahigh-density molecular linkage map com-
bined with high-throughput genotyping will have
a substantial effect on mapping and tagging let-
tuce resistance genes. It will allow genome-wide
association studies (GWAS) (Atwell et al. 2010)
to detect genetic variations associated with a par-
ticular disease. The sequenced, assembled, and
mapped transcriptome of lettuce will be used
to dissect the signaling pathways controlling
the plant-pathogen interaction. Because GWAS
requires a genomic map with marker density
higher than is the extent of linkage disequilib-
rium (LD) (Brachi et al. 2011), it will be neces-
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