Analysis of Genes for Stigma Coloration in Rice - IRRI books

marker. This can be a welcome alternative to breeders when the genes of interest are
difficult, time-consuming, or expensive to screen for directly. Examples of association
of RFLP markers with genes of economic importance in rice are presented by
McCouch et al (1991) and Yu et al (1991). Genes underlying quantitative traits can also
be “tagged” with RFLP markers and used for selection. avoiding time-consuming
progeny testing that would otherwise be required (Paterson et al 1988, Tanksley et al
1989).
Once a gene of interest has been located on an RFLP map, it becomes possible to
consider cloning that gene via chromosome walking using yeast artificial chromosome
libraries (Burke et al 1987). This can be an especially important contribution of RFLP
maps, since it opens the door to cloning genes of unknown gene product such as those
for resistance to or tolerance for diseases, insects, and environmental stresses (e.g.,
drought or salt tolerance).
In this paper, we discuss the strategies and current progress of a project at Cornell
University for constructing a high-density RFLP map for rice.
Map construction
Several factors contribute to the success of an RFLP mapping project. Considerations
regarding the type of plant population, source of clones, and selection of restriction
enzymes that have proven useful are presented here.
Population
choice
To construct a genetic map, one needs to obtain some type of segregating population
in which linkage can be detected and measured. There are many options for mapping
populations, including backcrosses, F 2 s, doubled haploids, and recombinant inbreds.
The ideal mapping population has two attributes:
• It is derived from two homozygous parents which, when compared with one
another, reveal polymorphism with every probe tested (using as few restriction
enzymes as possible).
• The progeny from this cross are homozygous so that they can be propagated in
perpetuity, thus allowing accumulation of large numbers of mapped markers by
many researchers.
In reality, it is seldom possible to find such an ideal population. In rice, we initially
made several compromises in population choice for the sake of expediency.
Indica/javanica F 2 population. The population from which we constructed our first
map was an F 2 derived from a cross between javanica cultivar Bulu Dalam and indica
breeding line IR34583-19-3-3. Using 11 restriction enzymes, it was possible to detect
more than 70% polymorphism with random Pst I genomic clones (McCouch et al
1988). Two hundred and thirty-five clones were thus mapped onto this population to
produce a rice RFLP map.
One of the first things we observed about the rice RFLP map derived from this
population was that there were more total map units than had previously been described
436 Tanksley et al