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Print Friendly Recombinant inbred intercross (RIX) mapping is a powerful new gene
mapping method that greatly extends the utility and power of existing sets
of recombinant inbred strains. An RIX is a large diallele cross made by
systematically crossing one or more sets of RI strains. Here we
demonstrate the potential of RIX mapping using the set of 13 CXB lines
established by Don Bailey and colleagues ~30 years at the Jackson
Laboratory. The CXB RI strains can be intercrossed to generate as many as
156 unique F1 genotypes. Our mapping panel consists of C57BL/6ByJ, BALB/cByJ,
all 13 CXB parental strains (~36 cases/strain), and most of the 78
nonreciprocal F1 RIX hybrids (~12 cases/F1). The set of RIX strains has a
genotype distribution pattern that resembles an F2 intercross with close
to a 1:2:1 ratio of CC, CB, and BB genotypes at most loci. Unlike an RI
set, RIXs can therefore be used to estimate dominance deviation. Unlike an
F2, large numbers of animals with predetermined genotypes can be
phenotyped to gain highly reliable trait statistics. The increase in
numbers of genotypes and phenotypes greatly boosts the power to detect
QTLs and does so without the expense of genotyping. There is also an
appreciable gain in positional precision. Like RI sets, and unlike
standard intercrosses, RIX data are cumulative, allowing correlative
physiological, anatomical, pharmacological, and behavioral studies over a
long period of time. A total of more than 10,000 RIX lines with precisely
known genotypes and recombination breakpoints can now be easily generated
using over 100 well characterized RI lines (Williams et al.,
2001; AXB/BXA, BXD, BXH, and CXB). RIX lines can also be generated
selectively with breakpoints in candidate intervals to test and refine
positions of existing or putative QTLs. To study the genetics of myopia and eye growth, we used the CXB RIX set
to map QTLs that modulate eye size. Eyes were taken from anesthetized
adult mice (50 to 60 days) and weighed immediately. Eyes of the CXB
strains weigh 19.8 ± 2.0 (SD) mg; those of RIX progeny weigh 20.6 ± 0.8 mg
(SD). Heterosis is therefore mild. We corrected for differences in age,
sex, body weight, and brain weight by multiple linear regression. The
adjusted data—the weight residuals—range from –1.2 to +1.2 mg. A dense map
of the CXB strains (900 MIT markers) was produced and imported into Map
Manager QT. Using the 13 parental strains we could only detect weak
linkage on Chr 8 and Chr 12, with LODs under 3. Pursuit of these putative
QTLs would normally have entailed the arduous construction of reciprocal
congenics or the production and genotyping of a large intercross. In
marked contrast, the analysis of RIX lines was extremely rapid and
involved no additional genotyping. Strong linkage (LOD > 4) was detected
on chromosomes 3, 6, 12, and 13. The LOD on Chr 13 peaks at 6.3 near
D13Mit20. The approximate confidence band extends from 20 to 40 cM. A new
eye weight QTL in this interval accounts for as much as 40% of the genetic
variance among RIX F1s, and alleles have a linear effect on eye weight
(residuals for the three genotypes: BB = –0.77, CB = –0.14, and CC = 0.33
mg). An important difference between mapping trait variance with an F2 and
an RIX panel is that non-syntenic linkage can produce spurious linkage in
the RIX. For example, among the CXB inbred strains, genotypes at D12Mit147
and D13Mit20 are almost perfectly concordant despite their complete
physical separation on Chr 12 and Chr 13. Naturally these two markers are
also "linked" in the RIX panel. Only the eye weight locus on Chr 13
remains compelling after examining a matrix of correlations of non-syntenic
markers and comparing these to group means. To protect against this
problem of non-syntenic linkage, we have generated full-genome correlation
matrices for four of the major RI sets (AXB/BXA, BXD, BXH, and CXB), in
each case by using genotypes of ~900 MIT markers. These matrices can be
inspected to reveal and protect against non-syntenic linkage in both RI
and RIX sets. In conclusion, this study is a practical verification of the
improved statistical power of RIX mapping and highlights a complication
introduced by the fixation of particular combinations of genotypes (non-syntenic
linkage disequilibrium) in parental RI sets. Supported by NINDS R01 NS35485, R01EY13070, EY12991, and an NIH/NSF-sponsored
Neuroinformatics grant P20 MH62009. Since 3 August 2000
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Neurogenetics at University of Tennessee Health Science Center
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