Wednesday, June 22, 2005

The most evil weed of them all, except morning glory. Smell melon. Posted by Hello

Saturday, June 18, 2005

Song et al. Figure of the comparative map. The black linkage group is from BC1F1 the right is from haploid/doubled haploid. Note inversion of markers bsd1122, jspr297,bsd1604 and lower larger inversion. Interesting that there are three groups, almost like three separate linkage groups in haploid line. Posted by Hello

Cotton mapping article

I am going to try and post an article a day that I have read and reviewed briefly here. Most will have to do with my work.

This article looked at two maps: BC1F1 TM-1(G. hirsutum) x [TM-1 x Hai7124 (G. barbadense)], and Vsg (G. barbadense) x [TM-1 x Hai7124]. Vsg is a virescent, a pale yellow-green, semigamous barbadense line. Semigamy is a mutation where the sperm and the egg nucleus do not fuse at fertilization and so depending on orientation of the spindles can produce progeny that are haploid, diploid, or with sectors of both. Haploids may be maternal or paternal. Sectors may be haploid or diploid. Diploid sectors are most vigorous and may overcome haploid regions.

The authors claim the maps are highly collinear. Discrepancies are noted as minor statistical errors or difficulty in ordering markers due to high number of double cross overs. I disagree with this claim. The differences are significant. I am posting an example linkage group. This may be due to using semigamous line or for comparing BC1s with different recurrent species. Was DNA extracted from whole plants? All lines tested in semigamous cross were haploid/doubled. How many were truly doubled? How many paternal/maternal haploids were produced? Maternal haploids would have no linkage information. Only paternally derived haploids would be beneficial since F1 was paternal. Were they chimaeric?

Maybe we should all do like in the Quadmap paper and bootstrap each linkage group to get a sense of how reliable the associations are.

Xianliang Song, Kai Wang, Wangzhen Guo, Jun Zhang, and Tianzhen Zhang. 2005. A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. and Gossypium barbadense L. Genome 48: 378–390

Thursday, June 16, 2005

Cinnamon is dead

When I got up this morning, Cinnamon, our beta, was lying on the kitchen table. Fish don't do well lying on the table. Last night I changed is water, he didn't seem to happy about it, but he was swimming around fine when I went to bed. When I woke up he was dead. Can fish committ suicide? Or should this be ruled and accidental death? Could I be charged with aquatic negligent homicide by doing something wrong changing the water?

I wonder what Emily is going to say.

Wednesday, June 15, 2005

Crossing season is COMING. Cotton flower, Ms4 dominant male sterile line.  Posted by Hello

Been offline a bit

Between my home connection failing due to server upgrades that reset my passwords and the end of classes and beginning of chopping in the field, I have not been posting. Well, hopefully that is going to change.

The cotton is now knee high. The first blooms are appearing. The F&B field will be ready for crossing in a week or two. The books are printed. The summer is fully here. When i am out chopping in the field. Chopping is our PC way of saying hoeing. Saying "I am going hoeing" or "I am a hoeer" or "I am going to find a hoe out in the field. " Hoe sounds too much like Ho. short for whore in case that little bit of Americana hadn't been up your way.

The only really troubling thing is my random-mating population for the mustelinum looks an awful lot like tomentosum. I am concerned that somehow it got mixed up between packaging the seed and planting. I hope not. If so i will have to random mate it by hand out at the bottoms where I have backup populations. I am glad that I do, just in case. I hate it when I make these kind of big mistakes, because then I have to admit it to Wayne, our technician, who already thinks I am incompetent.