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present in any recipient lines increases the prob-
ability that each SNP will be useful in multiple
mapping populations, particularly if data from
diverse recipient (and donor) lines are available.
Once this procedure is in place, it is a simple mat-
ter to inspect the QTL region and choose between
10 and 20 robust SNPs for marker design, with a
view to producing a fine linkage map of the QTL
region. These SNP markers can then be geno-
typed on larger populations using low-cost SNP
genotyping platforms for fine-mapping and sub-
sequent deployment of these markers in a breed-
ing program for marker-assisted selection.
populations will considerably speed the process
of QTL cloning and marker development as out-
lined above.
References
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for saline-resistant varieties of rice I. Variability for salt
tolerance among some rice varieties.
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QTLs using backcross lines derived from
Oryza sativa
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Conclusions
As these examples illustrate, the availability of
cheap high-throughput sequencing technologies,
combined with some lateral thinking in analy-
sis techniques, stands to revolutionize the way
the genetics of quantitative traits are analyzed,
such as the case with salt tolerance. These tech-
nologies should provide a level of precision that
has never yet been matched in terms of marker
density. As data from significant numbers of
genotypes become available, association map-
ping will finally free QTL discovery from the
expense and restrictive nature of mapping pop-
ulations, and resequencing information should
allow the rapid identification of genes under-
lying association or traditional QTLs. The low
cost of these technologies should allow even
modest-sized research groups to make signifi-
cant advances. Thus, the genetics of quantitative
traits may be expected to mature rapidly, and
the emphasis will shift back to deriving accu-
rate and detailed phenotype information, both
as information to feed into association mapping
and to validate identified candidate genes. The
applications of NGS (next-generation sequenc-
ing) will be of particular importance for complex
traits for which QTLs of relatively large effects
could be identified, and where several donors of
novel QTLs are available, as is the case with
salinity tolerance in rice. Resequencing tolerant
donors and few sensitive lines used in mapping
Sanchez,
G.,
Iglesias,
D.
J.,
Lopez-Climent,
M. F., Gomez-Cadenas,
A., and Talon,
M. 2009.
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