Firstly, I would like to take this opportunity to thank Prof. Broman for r/QTL and all the accompanying resources you so freely provide.
Secondly, apologies for the long-winded question you are about to read.
I am constructing a map using markers with known positions. To investigate what markers might be switched I generated new linkage groups using "formLinkageGroups()". This resulted in some chromosomes being split into two or three linkage groups.
For example. Chromosome 5 was split into three linkage groups, LG 9, 22 and 23, each of which had the following order (marker names are based on the order they occur on the physical chromosome):
Linkage group 22:
Sc5_16, Sc5_17, Sc5_18, Sc5_19, Sc5_20, Sc5_23, Sc5_24, Sc5_26, Sc5_30, Sc5_31, Sc5_32, Sc5_33, Sc5_34, Sc5_35, Sc5_36, Sc5_37, Sc5_39, Sc5_40, Sc5_41, Sc5_42, Sc5_43, Sc5_44, Sc5_46, Sc5_53, Sc5_133, Sc5_134, Sc5_135, Sc5_136, Sc5_137, Sc5_138, Sc5_139
Linkage group 9:
Sc5_52, Sc5_54, Sc5_55, Sc5_56, Sc5_57, Sc5_59, Sc5_63, Sc5_64, Sc5_67, Sc5_68, Sc5_69, Sc5_70, Sc5_71, Sc5_72, Sc5_73, Sc5_74, Sc5_75, Sc5_80, Sc5_82, Sc5_83, Sc5_84, Sc5_86, Sc5_87, Sc5_88, Sc5_91, Sc5_92, Sc5_93, Sc5_98, Sc5_100, Sc5_101, Sc5_102, Sc5_103, Sc5_105, Sc5_106, Sc5_107, Sc5_109, Sc5_110, Sc5_111, Sc5_112, Sc5_116, Sc5_117, Sc5_120, Sc5_122, Sc5_123, Sc5_124, Sc5_126, Sc5_127, Sc5_128, Sc5_129, Sc5_130, Sc5_131, Sc5_149, Sc5_150, Sc5_151, Sc5_157, Sc5_158, Sc5_159, Sc5_160, Sc5_161, Sc5_162, Sc5_164, Sc5_165, Sc5_166, Sc5_167, Sc5_168, Sc5_170, Sc5_171, Sc5_172, Sc5_178, Sc5_182, Sc5_183, Sc5_184, Sc5_185, Sc5_187, Sc5_192, Sc5_193, Sc5_194, Sc5_195, Sc5_196, Sc5_197, Sc5_201, Sc5_202, Sc5_203, Sc5_204, Sc5_206, Sc5_218, Sc5_223, Sc5_229, Sc5_231, Sc5_232, Sc5_234, Sc5_239, Sc5_240, Sc5_244, Sc5_245, Sc5_251, Sc5_252, Sc5_253, Sc5_254, Sc5_256, Sc5_270, Sc5_276, Sc5_280, Sc5_281, Sc5_283, Sc5_284, Sc5_285, Sc5_286, Sc5_287, Sc5_288, Sc5_289, Sc5_291, Sc5_292, Sc5_293, Sc5_294, Sc5_295, Sc5_296, Sc5_297, Sc5_298, Sc5_299, Sc5_301, Sc5_302, Sc5_303, Sc5_304, Sc5_307, Sc5_308, Sc5_309, Sc5_310, Sc5_311, Sc5_312, Sc5_313, Sc5_314, Sc5_317, Sc5_318, Sc5_319, Sc5_320, Sc5_321, Sc5_322,
Sc5_330, Sc5_331, Sc5_333, Sc5_334, Sc5_336, Sc5_337, Sc5_338, Sc5_339, Sc5_343, Sc5_347, Sc5_350, Sc5_351, Sc5_352, Sc5_353, Sc5_354, Sc5_355, Sc5_356, Sc5_357, Sc5_360, Sc5_361, Sc5_363, Sc5_364, Sc5_365, Sc5_367, Sc5_369, Sc5_370, Sc5_371, Sc5_372, Sc5_373, Sc5_376, Sc5_377, Sc5_378, Sc5_381, Sc5_386, Sc5_389, Sc5_393, Sc5_394, Sc5_395, Sc5_397, Sc5_398, Sc5_399, Sc5_402, Sc5_403, Sc5_404, Sc5_406, Sc5_407, Sc5_408, Sc5_409, Sc5_410, Sc5_411
Linkage group 23:
Sc5_414, Sc5_415, Sc5_416, Sc5_417, Sc5_418, Sc5_419, Sc5_420, Sc5_421, Sc5_422, Sc5_423, Sc5_424, Sc5_425, Sc5_426, Sc5_427, Sc5_428, Sc5_429, Sc5_430, Sc5_431, Sc5_432, Sc5_434, Sc5_435, Sc5_439, Sc5_440, Sc5_442, Sc5_443, Sc5_447, Sc5_449, Sc5_450, Sc5_451, Sc5_452
I have attached the recombination frequency/LOD heat-map of these linkage groups and an individual plot of recombination frequency/LOD for an individual marker that is representative of what I see for any marker in linkage group 22 and 23.
It is clear from above that the groups are formed of markers that are at either end of the chromosome (LG-22 and LG-23) and the core of the chromosome (LG-9). I have also colour coded the location in the core linkage group (LG-9) where these other markers should belong.
When I look at the two-locus genotype tables (using "
geno.crosstab()"). For markers in each group they obviously satisfy each other but appear "switched" when compared to LG-9.
My question is what to do here. Because the heat-map indicates to switch these markers. But is it not likely that these are potentially indicating recombination hot-spots or that the chromosome is long enough to be considered as three separate chromosomes? I have encountered this sort of thing before and often I just remove the alleles that appear to be switched. But here this is quite a few markers and would mean eliminating whole regions of the chromosome in question from my map.
Even focusing on the markers I highlighted in red. These may appear great candidates to switch but they do not look so when compared within themselves. I think maybe I have gotten confused somewhere but I do not want to make a blunder in my map making here so have come to the group for help.
Any comments, thoughts or suggestions would be greatly appreciated.