SegAnalysis is Mathematica
packages for mapping factors that cause deviation from expected
Mendelian segregation ratios in F2 progeny by a multiresponse
non-linear regression analysis.
SegAnalysis allows one to map reproductive barriers, inbreeding depression
genes, and hybrid vigor loci in a whole genome.
The genotype segregation of adjacent linked markers tends to be
similar, and hence when the frequencies of each allele in F
2 progeny are plotted along a linkage map, three continuous series
of allele frequencies are obtained for each chromosome, corresponding
to the genotypes of the heterozygote and the two homozygotes. In the
regression analysis, mathematical models are fitted to the observed
allele frequencies of markers on an entire chromosome. The influence
on genotype frequency of linked markers depends on whether the factor
acts in the gametophyte or zygote. In the models, a gametophytic factor
is described by two variables: the position, and the transmission rate
of one parent allele to the progeny. In contrast, a zygotic factor is
described by three variables: the position, the relative viabilities of
one homozygote and the heterozygote to the other homozygote. By comparing
results of several models, SegAnalysis can identify positions of factors,
distinguish gametophytic or zygotic factors, and determine their intensity
by characterizing the deviation from Mendelian segregation ratios in F
2 population. SegAnalysis can deal with following 18 mathematical
models:
Single: a single gametophytic factor.
OneOne: two gametophytic factors on the different gametophyte.
Two: two gametophytic factors on the same gametophyte.
TwoOne: two gametophytic factors on the same gametophyte and
another gametophytic factor on the different gametophyte.
Three: three gametophytic factors on the same gametophyte.
TwoTwo: two gametophytic factors on the same gametophyte and
the other two gametophytic factors on the different gametophyte.
ThreeOne: three gametophytic factors on the same gametophyte
and another gametophytic factor on the different gametophyte.
ThreeTwo: three gametophytic factors on the same gametophyte
and the other two gametophytic factors on the different gametophyte.
ThreeThree: three gametophytic factors on the same gametophyte
and the other three gametophytic factors on the different gametophyte.
ZOne: a single zygotic factor.
SingleZOne: a single gametophytic factor and a single zygotic
factor.
ZTwo: two zygotic factors.
OneOneZOne: two gametophytic factors on the different gametophyte
and a single zygotic factor.
TwoOneZOne: two gametophytic factors on the same gametophyte,
another gametophytic factor on the different gametophyte and a single
zygotic factor.
SingleZTwo: a single gametophytic factor and two zygotic factors.
OneOneZTwo: two gametophytic factors on the different gametophyte
and two zygotic factors.
TwoZTwo: two gametophytic factors on the same gametophyte and
two zygotic factors.
ZThree: three zygotic factors.
Installation Guide
Mathematica can run on Windows, Linux, Machintosh, UNIX platforms.
SegAnalysis consists of 394 items, which requires 30.7 Mb disk space
on a Macintosh computer. SegAnalysis will need at least 60 MB memory
for MathKernel in case of virtual memory off. Put SegAnalysis folder or
its alias on the path of Mathmatica ($Path). SegAnalysis folder was put
in the "Mathmatica 3.0 files:AddOns:Applications:" in our case. Our test
configuration is a Power Macintosh G3 266DT with 256 Mb memory and a 20
GB hard disk. We run MacOS 8.6 with 257 Mb virtual memory and Mathematica
3.0.1 PPC (memory of Front End and MathKernel were 30 and 70 Mb, respectively).
Preparing Data for SegAnalysis
Data files are three text files of lists of marker position and
each allele frequency, {position, frequency}. Marker positions are expressed
in Morgan of the Kosambi map function that should be calculated by other
programs (e.g. MAPMAKER
) using genotypes in the F2 population to be analyzed.
An example of a homozygote raw file follows:
{{0.040, 0.255319148936170}, {0.056, 0.223404255319149}, {0.177,
0.212765957446809}, {0.232, 0.234042553191489}, {0.305, 0.212765957446809},
{0.332, 0.202127659574468}, {0.435, 0.265957446808511}, {0.665, 0.276595744680851},
{0.681, 0.276595744680851}, {0.777, 0.287234042553192}, {0.788, 0.297872340425532},
{0.821, 0.255319148936170}, {0.964, 0.212765957446809}, {0.986, 0.212765957446809},
{0.997, 0.202127659574468}, {1.100, 0.244680851063830}, {1.144, 0.255319148936170},
{1.188, 0.244680851063830}, {1.249, 0.265957446808511}, {1.328, 0.287234042553192},
{1.361, 0.308510638297872}, {1.372, 0.308510638297872}, {1.450, 0.276595744680851},
{1.499, 0.287234042553192}, {1.510, 0.297872340425532}, {1.618, 0.297872340425532},
{1.740, 0.297872340425532}, {1.778, 0.287234042553192}, {1.794, 0.276595744680851},
{1.810, 0.276595744680851}, {1.958, 0.265957446808511}}