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

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. 

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

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.

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

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.

Itsy bitsy Emily stories -

How Emily came to the neighborhood.

It was a clear day. Word had spread through the sparrows, of course. They were terribly good gossips. They had seen her coming through the front gate and they flew to spread the word to everyone. Sparrows are like that. They are very excitable. They had told Mama Mouse, who has quite nervous about the whole affair, and had decided to keep the children in that day. One of the children mentioned it to a cricket, who sung about it to the lizards, and it was a lizard who told Frog. It was he that had decided to do something about it.

What he had heard was that there was a something in the neighborhood that looked exactly like one of the big people that lived in the house, except she was only three and a half inches tall. According to the lizard it was definitely not an animal, but must have been some new minute variety of people. So frog went to investigate.

He watched as she came around by the flowers looking at each of the flowers looking at each one in turn as if she was some strange relative of the bees. He doubted that due to her lack of wings, long hair, and brightly colored clothes. Frog had never seen a bee wear clothes. Also she was walking rolling a penny with a stick and as she would roll she would hum a little tune and give the penny a little tap with the stick to keep it on track. Sometimes it would get off track and roll in a little circle flat on the ground. The itsy bitsy girl would get her knees and pry with all of her strength because the penny was nigh up to her waist. Well, not quite but it was still quite large for such an itsy bitsy girl. She also seemed quite young, which was contrary to one of the reports that he had heard that she was one of the big people, who were dangerous. She didn’t look at all dangerous to him rolling a penny down the road, humming a little tune and looking at flowers.

It was then that he decided and so with a leap and a ribbit he came out of his hiding place. The girl was so surprised that she gave her penny a huge tap and it rolled out of control into the jungle of grass, never to be seen again. As he landed, the little girl said, “ Oh, you startled me.”

Frog replied, “Ribbit.” Which is frog for hello, good bye, and many other things including “I love you.” It was a very useful phrase. The girl was startled, but introduced herself as Emily and explained that she was in need of help. She informed him that she was looking to move into the neighborhood. Her previous neighborhood had been destroyed due to landscaping. Frog shivered because he knew the dangers of landscaping. Landscaping was when the large people in the house decided to get busy with shovels, machines that whirred and made noise. This forced animals out of their homes and destroyed weedy sources of food. Luckily, the people in this house only landscaped sporadically. Being understanding of the problem, he told her he would help her find a new place to live and that she could call him “Frog.” Then he asked her what kind of place she would like.

She thought and then responded, “Maybe someplace warm with lots of flowers because I enjoy nectar to eat.”

“What else does something like you eat?” Frog asked.

“Sometimes nectar, sometimes seeds, sometimes vegetables or fruit.” Emily said

“Howbout flies?”

“Not usually flies.” she said.

Frog decided that due to her eating habits she would fit in best with the mice or maybe the bumblebees, although he was pretty sure that the bumblebees didn’t want a roommate.

So Emily and Frog ran to the mice’s burrow to see if they were willing to put up boarders. Papa mouse had left some time ago on an expedition and had not yet returned. This left Mama Mouse with a burrow full of young mice to care for by herself. Frog was pretty sure that Emily could help out around the house in exchange for a place to stay.

When they got to the entrance, Frog called out to them, “Hello in there,” and he gave a loud “Rribbbitt” to let them know who it was.

From inside he heard a tiny squeak that said “No one is home.”

Emily turned to frog and said “Did you hear that?”

Frog said, “I afraid of this. They are home; they are just timid. They are just worried about you.”

“Why would they be worried about me, I am just itsy bitsy.” Emily said. She thought that she heard very mouse-like giggles at that, but no matter what they did, even when they banged on the door and called out in loud voices, could they get anyone in the Mouse’s house to come out. Except, they did see the reflection of many young mice eyes and one young mouse was brave enough to peek out at them through the window of the door.

So they decided if some of the other animals in the neighborhood would be interested in an “extra help,” As Frog said. First, they went to the sparrows. They chitter-chattered that they didn’t have any room for a boarder. Then, they went to the robins, who told them that they were busy collecting stuff and they were about to have a brood of their own children and showed Emily and Frog their handsome blue eggs.

No one in the neighborhood seemed to have room. Frog took her over to the lizards to talk to them. They didn’t have room either. They went by the ants. Fire ants don’t tend to be very talkative sorts. As one of their mottos stated, they usually stung first and asked questions later. Frog didn’t think there was much of a chance, he just wanted to be thorough. This particular day was an important day in the fire ant community because they had a new queen and the hive was ready to split into two. When an ant hive was to divide, all of the followers of the new queen swarm to the top of the nest accompanied by the new queen and her consorts, the winged ants. They fly or swarm to a new nest. This is one of the only times that the queen ever leaves the nest. The rest of the time she is deep inside the ant nest laying eggs and reproducing, taking care of the hive. The only ones that go out are the worker ants or the army ants. They tend to be very authoritarian-type figures and rather unsociable, if you ask anyone that knows them. At least, anyone who has stuck a shovel through their nest and has been bit and stung dozens of times.

And on this particular day, just as Frog and Emily were passing by, was when the new queen first emerged from her hole. As they were identifying themselves to the sentries and trying to maintain a safe distance, the queen called out. “ Hello there, come talk to me why don’t you,.”

Emily and frog were both surprised to find that the queen ant was not only amicable, but also very interested in hearing about their dilemma. She even offered to let Emily stay with them in the new hive. But since the new hive was a few feet underground and Emily would have to find an entrance big enough to fit herself in, Emily was pretty sure that she would have a hard time convincing the sentry ants that she was part of the hive. She declined but thanked the queen for the offer. The queen was disappointed because she was often lonely inside the hive. She longed to go outside and see the world. She wanted to have friends that were not ants and told Emily and Frog so.

Frog and Emily sat on a pebble with their head in their hands because they had not found anywhere for Emily to live. They were a bit discouraged. Now Frog had not yet offered to let her stay at his house, and he did have a wonderful little house. He had a spare bedroom that was high up and had a good view of the flowers that he was pretty sure she would like. He didn’t know exactly how to offer such a thing. He had never had a roommate or a child before, but Emily seemed like she would be a good person to stay with. She maybe could be a very good friend. He was not sure she would like to live with a frog like himself. Some people in the neighborhood thought him a bit stodgy since he read so much and his house was filled with papers and books from one end to the other.

The house was quite nice, especially for a frog. And so what he decided to do was invite her back to his house to look at a map of the surrounding neighborhoods to see whom they could come and discuss possible living arrangements for Emily. So Emily went to Frog’s house.

As soon as Emily came in he told her, “wait here, make yourself at home.”

She sat down, looking out the window at the flower bed. The house was situated just on the edge of the porch where it had light in the morning, and also where it was protected from the rain and from dangerous animals to frogs like dogs and cats and people that wished to pick him up.

When frog returned with the map there was Emily looking out the window. Now Emily, feeling very brave, needing somewhere to live, said “Frog, couldn’t I stay here with you.”

For looking down at his feet Frog said. “At least for now, I guess.”

And so it was decided that Emily would stay with Frog at least for the rest of the season, until Frog went down for his winter nap. That gave frog plenty of time to find her somewhere else to stay in the winter time. So that was how itsy bitsy Emily came to live with her friend Frog.

They were inseparable after that. Frog even let Emily ride on his back around the neighborhood. No one that thought they knew Frog could believe he would let a tiny person ride on his back as if he was a horse or something. Riding on a frog is great fun and if you ever get the chance you should take it. Some notable authors have compared it to flying, but it is much more bouncy that that, but still very enjoyable. This was the beginning of many adventures together.

Serenity

The BEST TV Show that ever has been on TV was cancelled after 13 episodes. Those of you who have seen the show will surely agree. It is now a movie (and we hope returning to TV). Here is a link to the trailer.

My brother Rich climbing at the Boise State Climbing Gym.  

Corn, its a wierd one mister grinch.

So in Josh's plant breeding web page he has links to two papers that show that corn hybrid vigor may be due to inconsistent sequences. In some cases the genes themselves are hemizygous. In others the retrotransposon insertions are different, affecting gene expression due to changes in upstream promoters. O what we don't know else is going on.

I have too much to do. I will explain later. Right now I have to write it up for Cotton inc. They pay the bills.

Feeling better

I am feeling better. I don't know why, nothing has changed. I still have to plant way too much, but it is coming along.

Links:
Plantbreeding web page

Food blog

Emily painted this for us yesterday. She says she learned Chinese characters from Sagwa, a cartoon about chinese cats that write with their tales. I didn't believe her, but my Chinese math teacher says that they are just about right for the characters for rain. Just like she said 

My daughter Emily and I out in my cotton field. This is the end of my season last year. Theis is a F1 plant, next to us is the F2s. 

No motivation

I am not really depressed. I am not really happy. I am not really sad.

I am just monotone today. It is like a constant F flat in my head. There are moments where it fades and I feel ? ? ?

I don't know quite how now. That F flat is playing today.

Do you listen to Philip Glass? There are a number of his songs that are repetitive to a point where you would think that the performers would throw down their instruments and scream out an aria in C sharp major just to mix it up a little. That is how I feel with my life. I just haven't got up the courage to throw down my fiddle and start screaming.

I went to BYU to resolve things with my professors there. It is like none of it ever happened. It is like a dream that felt like a lifetime and then you wake up to find that it is almost the same time as when you fell asleep. Before I left, I sent an email with a tentative itinerary, outlining what I wanted to do. I asked for comments and for suggestions. In return, nothing. silence. ambivalence. when I got there, I proceded to start doing what I said on my itinerary. Response: "Ok, sounds good." "Where have you been eating for the past three days." "Oh, were you here till midnight working again? " Nothing. silence. ambivalence.

I went through all of the sequences and found all possible ligation points, restriction digestion sites, and vector contamination. Then I annotated them and sorted them by primer design and problem. Then I tested all the primers for ones without problems to see if the size was the same. Results: 95% that amplified were OK. 5% were not. This is error rate in sequencing so might have missed ligation site. Response: OK. Nothing. silence. ambivalence. Then I tested ones designed from other species and a subset of possibly messed up ones. Response OK, give us the good ones.

Then I did GISH. In one day. This is not that short of a protocol. I didn't finish. Response: Oh OK. Did they read my report? No. Did the look over the lab notebook with raw data? NO. Did they look over the sequencing data? NO. Did they have any questions. No. and NO.

Since then,
Nothing. SILENCE. AMBIVALENCE.

When I got back. I asked what they thought about my field plans here. Response: whatever you think is best.

Nothing. Silence. Ambivalence.

What a sweet melody of advice from my advisors on my graduate committees.

Food blog

I have never been as hungry as reading about food on this blog:

http://orangette.blogspot.com/

Good recipes. Great writing.

I am late and procrastinating getting on my bike and going home.

Planting has begun and so my fingers and back ache from standing pressing seeds into peat pellets all day. Nilesh's experiment is all planted and tomorrow we will plant mine and Waynes. Total: 12,000. Not bad. My experiments for the bottoms are almost ready. After planting tomorrow I need to pull seed for check rows and then decide how I want to randomize. I wanted to just plant it out in order, without randomization, because it was for selection only. Stelly now has changed his mind and wants to put it out randomized. I refuse to collect data on all 4 acres of cotton. It is just too much.

Leila gives Christian the evil eye as Emily tries to eat a giant raw oyster 

Emily, Leila and Aleah on Valentines Day 2005. My three favorite girls. 

Glass engine

This is the best website I have seen. I know I am behind the times, but This is the BEST interface I have ever seen. Give it a try. I wish our library had something like this, except with a fine and gross control.

http://www.philipglass.com/glassengine

Emily, my oldest daughter, drew this picture of a rainy night time.  

Boxplots of field data from 2003. Notice 0 yield in species, F1, F2 and pretty much the BC1F2. The good news was the BC3F1 generation. Good yields, better fiber than cultivated parent.