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Lecture 16, part 1 of 3
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November  7, 2017

MAPPING WITH MOLECULAR MARKERS



C. Segregation in a two-point cross

D. Calculating Linkage using molecular markers

Lander, E. S. et. al (1987) MAPMAKER: An Interactive Computer Package for Constructing Primary Genetic Linkage Maps of Experimantal and Natural Populations. Genomics 1:174-181.
Lander, E.S. and Green, P. (1987) Construction of multilocus linkage maps in humans. Proc. Natl. Acad. Sci. USA 84:2363-2387.

To get an idea about how molecular marker data can be used to build linkage maps, let's examine some molecular markers from TAIR - The Arabidopsis Information Resource (http://www.arabidopsis.org)  at Stanford University. One of the RFLP probes documented in AAtDB is the RFLP probe g4539, which can be examined by clicking here. (Note: In the current map, g4539 has been converted into a PCR marker.)

The Southern blot for this probe, shown at right, indicate two RFLP alleles, 2L and 1C, found in ecotypes Landsberg erecta and Columbia, respectively.  Note that while several bands are detected with this probe, only two are polymorphic between these two parents: 2L and 1C.
 

        ------------- segregating progeny ------------------->
marker/
map posn.
g6844   HHAAAAABHHBAAAHBHHHHABHHHABBAHHBHAHHBAAHHAHHBBHH­A­HHAHHBHHHAAAHHHBBHHHHAH­HBAAAAHHABHHHHBAHBABHBHAAHBHBHAHHBAHBAHHHAAHH­­­
g3843   HHAAAAABHHBAAAHBHHHHABHHHAHBAHHBHAHHBAABAAHHBBHHAAHHHAHHBHHBAAAHHHBBHAAHAHHHBAAAAAHABHHHHBAHBABHBHAAHBHBHAHHBHHBAHHBAA­­­­­
g2616   HHAAHHHBHHBAAAHBHHH­ABHHH­­­­­­­­­­­­­­­­­­­­­­­­­­­HHHHBBHBHHAHHHHHHHHHAH­HBHAAAAHABHHAABAHBABABHAAHHABHAHHBHABAHHBAHAH­­­
m210    HHAHHBHHHHHAAAHHBHHHAHHAHAHHHAABHHAHBHABAAA­AHBHAAHHHHAHBHHBBHAHHHAHHAHHBBHHBHHHHAHHBHHAHBAHHABHABAHBHAHHHH­HHABA­ABHH­­­­­
g6837   ­­­­­­­­­­­­­­­­­­­­­­­­­­HH­AABHHAHBHHBAAAH­HH­AA­H­­­­­­­­­­­­­­­­­­­­­­­HBHHHHAHHBHHAHBAHBABHABAHBHAHHHH­HHABA­­­HHAHHBA
g10086  ­­­­­­­­­­­­­­­­­­­­­­­­­AHHHAAHHHAHBHHBAHAHAHHH­A­H­­­­­­­­­­­­­­­­­­­­­­­HBHHHHAHHBHHAHBAHBABHABAHBHAHHHHAHH­­­­­BHHAH­­­
g4564­a           HAAHHBHHHHHAAAHHBHHHAHHAHAHHHAAHHHAHBHHBAHAHAHHHAAHHHHA         HBHHBBHAHHHAAHAHHBBHHBHHHHABHBHHAHBAHBABHABAHBHAHHHHAHHABAHABHH­­­­­
g3845                      HAHHHBHHHAHAAAAHBHH­AHBAHAHHHAAHHHAHBHHHAHAHAHAAHAHHHHAHBHHBBHAHHHAAHAHHBBHHHHBH­ABHBHHAHBABBHBHABAHBHAHHHHAHHABHHABHH­­­­­ 
g4539                      ­­­­­­­­­­­­­­­­­­­­­­­­­AHHHAAHHHAHBHHHAHAHAHAAHA­HHHAHBHHBBHAHHHAAHAHHBB­HHHBHHABHBHHAHBABBHHHABAHBHAHHHHAHHABHHABHHAH­­­ 
m557    HAHHHBHHHAHAAAAHBHHAAHBAHAHHHHAHHBAHBHHHAHAHAHAAHA­HHH AHBHHBBHAHAHAAHAHHBB­HHH BHHABHBBBAHHABBHHHABAHBHAHHHHAHHAHHHABHHAH­­­
g3883   HAHHHBHHHAHAAAAHBHHHAHBAHAHHHHAHHBAHBHHHAHAHAHAAHAHHHHAHBHHBBHAHAHAAHAHHBBHHHHBHHABHBBBAHHABBHBHABAHBHAHHHHAHHAHHHABHH­­­­­
g19833  HAHAHBHH­AHAAAAHBHH­AHBAH­HH­HAHHHA­BAHHAHAH­HA­HA­HHHAHBHHBBHAHAHAAHAHHBB­HHHBHHABHBBBAHBAB­HBHABAHBH­HHHH­HHAHH­ABHHAH­HA
g19838  ­­­­­­­­­­­­­­­­­­­­­­­­­­­­­HAHH­AHB­HHAHAHAHAA­A­HHHAHBHH­BHAHAHAAH­­HBBHHHHBHHABHBBBA­BAB­HBHABAHBHAHHHHA­­AHHH­BHH­H­­­
m272    HAHAHBHHHAH­­AAHBHA­HHBAA­HBHHAHHBAAHHHHABAHAAA­HA­HHAAHBHHHBHHHAHAAHAHHBB­HHBBHHABHHHHAHHHBBHBHABAHBHAHHHHHHHA­H­AHHHBBHHA
g4513   HAHAHBHHHAHAAAAHBHAHHHBAAAHBHHAHBBAAHHHHABAHAAAAHAAHHAAHBHHHBHHHAHAAHAHHBBHHHBBHHABHHHHAHHHBBHBHABAHBHAHHHHHHHAAHAAHHH­­­­­


A,B: homozygotes for alternative alleles H: heterozygote -: ambiguous result
Undisplayed Graphic

Figure 1. Example of multipoint linkage analysis using EM algorithm, showing convergence to maximum-likelihood genetic map for 16 RFLPs on human chromosome 7, studied in CEPH families (see text). The initial assumption of 5% recombination between consecutive RFLPscorresponded to a log10 likelihood -351.45. After 12 iterations, the recombination fractions converged to a map that was about 10
48 times more likely to have produced the observed data. The analysis used the first genetic reconstruction algorithm discussed in the text, involving only genotype-known data, and it required ~9 sec on an HP9000 minicomputer. Analysis of the full data set, using the hidden Markov-chain reconstruction algorithm, required ~4 min and did not alter the recombination fractions significantly.
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last  page PLNT3140 Introductory Cytogenetics
Lecture 16, part 1 of 3
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