How many genes?

Alright, so today is the day that I tell you all about my first scientific publication. I hope to explain it in a manner that you can understand with a basic knowledge of biology. Hopefully this post will put me in a good enough mood to work on writing my second paper, which I’m supposed to be doing this week.

Alright, so the goal of my first paper was to answer one question “How many genes causes differences in pigmentation traits?”. I am specifically interested in male pigmentation because 1) Males are more colorful than females when it comes to cichlids and 2) Because male color is thought to be important when it comes to females choosing mates.

To answer this question, I first created a hybrid cross between two different species of fishthat differ in their male pigment patterns. The fish on the left with orange fins is Metriaclima mbenjii and the fish on the right is Metriaclima zebra. I hope you will agree in that they are different when it comes to their pigment patterns. The pictures below each fish are close up picture of their fins. For the first two pictures, those are their dorsal and tail fins. You can see a big difference in color. M. mbenjii fins are orange while M. zebra fins are more blue. In the last picture you are looking at the pelvic fin. This is the fin underneath the body closer to the head. One difference you can see is that the M. zebra has more little black dots on that fin than M. mbenjii.

So, now would be a good time to talk briefly about pigment cells. Humans (and all mammals) have only one type of pigment cell, melanocytes. These cells can either  produce brown-red pigment or black pigment. Fish on the other hand have at least three main pigment cell types, with other minor pigment cell types also described. So, those little black dots on the fins, those are melanophores (what we call melanocytes in humans). In the M. mbenjii the orange in the fins is caused by a pigment cell called a xanthophore. These can be anywhere from yellow to orange. In the M. zebra, that blue color is caused by light reflecting pigment cells called iridophores.

Ok, so back to the hybrid cross. I crossed female M. zebra with a single male M. mbenjii. The resulting offspring are what we call the F1 generation. I’ve included a picture of an F1 male. As you can see, he looks in between the two parent species. The next thing I did was cross an F1 family. As horrible as this sounds, you mate a family of siblings together. This is because it helps when it comes to keeping track of the genetic markers later. So, when we breed the F1 together, the resulting offspring are called the F2 generation. And we made a lot of F2 babies from this F1 family, over 200.

Alright, so now that I have all of these fish, how do I go about figuring out how many genes causes the red fins versus blue fins? Well, I have to quantify our pigment traits, get some sort of actual numbers that we can compare. So, I counted those black pigment cells after taking pictures of the finds, scales, and face of the fish. I also used image analysis to quantify the orange cells. These cells don’t contract to where you can count them, so image analysis detecting the number of yellow pixels was the best I could do. So, I counted all of the cells and measured color in 20 M. zebra males, 20 M. mbenjii males, 20 F1 males, and 100 F2 males. It was a lot of work, and thankfully I had an amazing undergraduate student who worked with me on all of this.

After we did all of those counts we calculated the mean and variance for each set of individuals for each trait. I then used what is know as the Castle-Wright equation. This equation examines the means and variances of the parents, and the variances of the F1 and F2 generations. You plug all of your numbers in and the resulting number is the number of genes thought to underlie your trait. So, I’ll only give you few of the estimates as not to bore you, but for the dorsal fin, we estimated one gene causes differences in the red versus blue fin, for the tail fin, it was about 3 genes that control differences in color, and for the pelvic fin pigmentation differences are also thought to be controlled by 3 genes.

I won’t bore you with the nitty-gritty details of the rest of the paper because quite frankly you probably don’t care. But I thought I would share the basics of how you can go about estimating the number of genes controlling a quantitative trait. My current work is focused on determining where in the genome the genes that control the pigmentation traits are located.

This article was published in the May 2012 issue of the Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. If you have any question, I’m happy to answer them!

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