Rokimoto, several times you have made reference to projects you have, but you have never described to us what you are doing.
Of most interest to this group would be the feather color study. We are looking at feather color alleles that affect tissue pigmentation. From the old literature we know that alleles like dominant white, dominant sex-linked barring and, unexpectedly, dominant extended black are good alleles to have if you want to get rid of tissue pigmentation.
Rokimoto, How familiar are you with the research at Origen?Avigenics regarding the Fat, Juicy, Diseaseresistant, All eat and grow the same Super chicken? The way I read it they will all come from the DNA of 4 hens? The one picture I saw in a lab was of eggs in a holder, and the tops of the eggs were removed so you could see inside. Is this a way of growing the embryo,or just photo op dtuff? 4.7 million federal bucks should help to build a super chicken. It mostly seems so boring to me, but I readily admit, I dont have that scientific drive. But then, some friends and family are quite bored with my simple research. I love it.
Thank you for your interesting post, Rokimoto. I have seen some of your papers dealing with the mitochondrial DNA.
Robbpa:
Rokimoto, In regards to cloning and diversity.Bur wouldnt you clone many lines and also keep them in different areas on these small farms.and what about crossbreeding theae lines for hybrid vigor. I am all for research as I am a Reaganite, and I believe in the trickle down theory.
I'll bet the button quail are fun. The little "bumble bee" babies must be cute. Is there much genetic variation in button quail like there is in parakeets and finches?
Robbpa:
INFOMANIAC, Waste from a corn shelling combu\ine is to coarse., even with a waste chopper attatchment, also difficult to gather and bale. Small grains straw and chaff on the other hand could be excellent bedding. Especially if run thru. a shredder or a bale chopper. Alfalfa would be very good. High in protein , phosphorus and more, and the best for tilling under as green manure or bedding waste. You have an Allis All Crop combine. With proper screens you can harvest any grain or seed crop. They are real good on oats and oats are real good for chickens, gives them a good hard body.
Thank you, everyone,for participating. I am trying to understand the partitioning of the inbreeding effect into male and female contributions. If I can make it make sense to me, I'll write something about it on the genetics pages. This is what I understand from Rokimoto's post earlier in this thread:
The simple explanation for hybrid vigor is simple dominance over recessive detrimentals. Each line has it's own frequency of certain recessive detrimental alleles. If two lines do not share the same recessive detrimental alleles they will show hybrid vigor when you cross them. You can think of it as one line being AA bb CC DD EE ff and the other being aa BB CC dd EE FF so when you cross them you don't see the detrimental effects of bb ff or aa and dd in the hybrid (Aa Bb CC Dd EE Ff). This is why subsequent progeny from commercial hybrids are on average less productive than their hybrid parents. The recessives begin to segregate in the progeny. The increased genetic variance that you observe in the progeny of the hybrids is a measure of the non additive genetic effects (dominance and gene interactions). What you see is that the hybrids are much more uniform in egg weight and rate of lay than the progeny produced from these hybrids. You will get some good birds, but a lot more stinkers.
Thank you for your response, Rokimoto. I do appreciate your participation. I don't mean to be a pest, although I know I am ... it just comes naturally for me.
Info:
From a year or two ago, I know you are keeping Cornish Cross birds... Surely this is not the only line you maintain. Would you please tell us about the lines you are keeping?
P.S. Don't sell us short. We can understand if, for example, you maintain a line for mitochondrial DNA research. We're not entirely uninformed....
By Rokimoto on Friday, January 18, 2002 - 07:31 pm:
The tissue pigmentation that we are interested in is the pigment in the abdominal facia. It is a membrane between the abdominal skin and the fat pad. Severe cases can put melanocytes in both the skin and fat pad. This is a harmless pigment, but consumers do not like it. If the pigmentation gets into further processed products like chicken patties you see it as black flecks and consumers object to it.
The problem is that all broilers are white so we can't tell what feather color alleles they have (white masks most colors). Breeders can't select for the birds with the wrong feather color alleles. We are finding the genes and making molecular markers that industry can use to select for the alleles that they want to keep. By testing the DNA you don't need to even look at the bird to determine what color it should have been. We have developed molecular tests for most of the E locus alleles (e+, eb, eWh, ER, and E), and have determined that these can be effective DNA markers for selecting against tissue pigmentation. We are going after dominant white and sex-linked barring.
I have an Inbreeding depression project where we have backcrossed daughters to sires from a random bred population. We started with 10 sires, but produced enough daughters for the experimental design for only 7. All sires had hatchablities of less than 60% by the second backcross (F=0.375). Most of them less than 30% with two sires at around 11% hatchability. This isn't very good data for most of you trying to breed small populations and maintain production traits.
The last major project that we are working on is mitochondrial influence on production traits. Mitochondria are the powerhouses of the cell and produce about 90% of the energy that you use to live. You inherited your mitochondria from your mother. For some reason you never seem to get your fathers mitochondria even though some enters with the sperm. Chickens are the same way. Mitochondria have their own little DNA genomes and many maternally inherited genetic diseases are due to mutations in the mitochondrial DNA. We look at associating differences in mitochondrial DNA with production traits, and we are expanding to nuclear encoded mitochondrial genes in the latest grant that we got. Nuclear just means genes in the big genome in the cell. For humans and chickens most of the DNA in the cell is found in what we call the nucleus of the cell. Most of the genes that make up the functional mitochondria (thousands of genes) are encoded in the nuclear genome and only 13 protein genes are encoded in the mitochondrial DNA.
We also use mitochondrial DNA to study the evolution of gallanaceous birds. The various relationships between quail, chickens, pheasants, etc are difficult to determine using classical morphology. We think that we have a better idea using the genetic material to classify who is more closely related to whom. Classical designation has turkeys as the most distant group (turkeys, chickens, pheasants, partridges and old world quail) with pheasants and chickens most closely related. The DNA tells us that this is wrong and that turkeys seem to be more closely related to pheasants than chickens are. This may explain why chicken-turkey hybrids are possible, as are chicken and pheasant hybrids. Sort of strange, but turkeys are more closely related to pheasants than quail are.
We also have a small project looking at sex-linked late-feathering. It is used a lot to sex day old chicks. The late-feathering mutation reverts at a very high frequency (1 in a thousand) to early-feathering, so it is commercially relevant and a weird gene to look at. Usually mutant reversion is rare (about 1 in a billion), but late-feathering is associated with a structural difference in the Z chromosome that reverts at a high frequency.
I'll tell you something that you might be able to use to help you out. Murray McMurray Light Brown Leghorns, New Hampshire Reds, Production Rhode Island Reds, Ameraucanas and Black Australorps seem to be feather sexed. This just means that the males are almost always late-feathering and the females are almost always early-feathering. You can tell the males because late-feathering birds have shorter primary wing feathers. The coverts (feathers in the layer just above the primaries) are often as long or longer than the primary wing feathers of day old chicks. You should be able to sex the birds out of the box. Early-feathering birds have primary wing feathers much longer than the coverts. This typing is not 100% and some mistyping will occur. This is one reason why McMurray only guarantees 90% sexing accuracy (they usually do better than that).
If you don't know the difference between coverts and primaries you just have to pick up a chick and stretch out its wing. If you have the back of the chick toward you the coverts are the wing feathers that over lay the primaries. You can slip a piece of paper between the coverts and primaries and separate them into two layers. In most early-feathering breeds it is easy to tell the coverts and primaries because the primaries are always much longer than the coverts.
A more accurate typing can be made at 10 days of age: late-feathering birds will have sparse tail feathers usually less than 1 cm in length while early-feathering birds will have fuller tails and be longer than 1 cm in length.
You can generate your own feather sexing cross by crossing the late-feathering males to the early-feathering females, feather type the chicks and mark or band the birds. Save only the late feathering females (50% of the females) and the early-feather males (50% of the males). If you cross the early-feathering males to the late-feathering females you will generate the sex-linked cross, and you will be able to select the females and males at hatch. You will get early-feathering females and late-feathering males. So every other generation you can cull your birds at hatch and save on some feed.
By Robbpa on Friday, January 18, 2002 - 08:35 pm:
By Infomaniac on Friday, January 18, 2002 - 11:53 pm:
It's interesting that you associate the hatchability with the male. And I can just see those customers thinking that the black things in their chicken McNuggets are bug parts or dirt!
We had noticed the slow feathering gene in our Sil-Go-Links and postulated that it was coming to us from the RIR line. We have a "bald-back" gene now. The chicks have bald backs until about 6 months. Then they finally finish feathering. As best as we can tell, one of our Ameraucana sires has it and he has lav as well. We spent a lot of time making sure it wasn't due to picking, but we know it isn't. I've never seen this described in the literature and it seems to be a dominant trait, or at least incompletely dominant. The inheritance frequency is too high to support an hypothesis of a recessive gene. Long ago, I posted some pictures of our first bald-back chick. He eventually got his (very nice) feathers and wound up on the dinner table.
Rokimoto, do you have any projects just for fun?
This is a really dumb, basic biology question ... the organelles in the cytoplasm, like mitrochondria ... when the cells multiply, how are the organelles reproduced? Are they synthesized from information contained in genes in the nucleus? or do they somehow reproduce themselves?
By Rokimoto on Saturday, January 19, 2002 - 12:04 pm:
Chicken companies like Avigenics are trying to use the modern technology to do something with chickens. Some of them are trying to make transgenic chickens (chickens with foreign DNA in their genomes) for industrial or pharmacological purposes. A lot of the egg is protein and if you could make the bird produce a useful protein it could be valuable. Biological medicines would be possible as well as producing enzymes for industrial purposes (like waste management where enzymes would be used to biodegrade the waste). I'd like to think that this could revitalize the small farm. At the moment small farmers cannot make enough money to make a go of it. Not very many people could compete against the million hen egg facilities that they have now. But if you raised a small flock that produced eggs with that were used to produce a vital protein for heart disease you could raise a small flock and still make money. For biosecurity reasons small flocks at separate locations would be the best means of raising transgenic birds and other animals.
These companies are also working on "cloning" chickens to develop superior genetic lines. Every generation you have some exceptional birds that are well above the mean for the population. If you could clone these birds and produce a lot of them you could more rapidly improve your line. The problem is genetic diversity would be decreased in the line. Genetic diversity is the stuff that makes selection and improvement possible. If you decrease your genetic diversity you decrease your selection progress, so you are cutting your own throat. There is also the problem of making all the bird the same. If these birds are susceptable to some disease you could wipe out the industry. The corn seed industry found this out the hard way when they switched to male sterile germ plasm to produce hybrid seeds. A huge percent of the maize crop was lost because of a disease that ravaged the male sterile lines. The new technologies have benefit, but we will have to carefully think about application.
Infomaniac:
The feather color project is a pretty fun project, but it is a lot of work. I have some button quail at home that do not have anything to do with my research. I just like watching things hatch and grow up. I have some button eggs that will start hatching Sunday. I am thinking of button quail projects. The hens do not live long and longevity research is getting funding and button quail do not cost a lot to feed and they are cheaper to raise than mice. I've had buttons for a year and a half and I'm still on my second 50 lb bag of gamebird breeder. In that time I've raised about 50 to adults and given away most of them so they really do not eat very much, but I also bought around four 20 lb bags of wild finch seed from Walmart. We've spent more to feed the wild birds in our backyard. The bedding is the most expensive material that you have to buy. I use corn cobs and the bedding is up to 3 times the price of the same weight in feed. I don't know how they figure that a waste material is worth more than the stuff you feed your animals, but that's the way things are at the pet store. Right now I have 9 adults in RubberMaid containers that I put wire windows and doors in. They stack on an end table in the living room and you raise them like parakeets or any other caged bird.
Siegel et al. 1957. Some Phenotypic Differences Among Homozygous, Heterozygous, and Hemizygous Late Feathering Chicks. Poultry Sci. 36:232-239. May answer your question about bare backs. There are phenotypes associated with sex-linked late-feathering like bare back. I don't know the genetics because some late-feathering lines do not have it, but show Barred Rocks and show Rhode Island Red lines are prone to the late-feathering with naked backs. We also segregated the bare back phenotype in our broiler pigmentation cross. We know that sex-linked late-feathering was segregating in this cross.
We also find tardy feathering in multiple lines. The tardy feathering allele "retarded" mimics sex-linked late-feathering, but it is an autosomal recessive.
We know in our inbreeding study that the hatchability difference is due to the males because we breed some of each males inbred daughters to the other males in the study as control crosses and there is a small decrease in hatchability due to the inbreeding of the hen, but quite a lot more if you breed a daughter to her father. Hatchability of a poor sires daughters might be 60% with other males, but only 11% with her sire. As you inbreed the inbred hens do get reproductively weaker, but one outcross can pretty much remove that weakness. I have an inbred line that hatchability is 30% within line crosses, but outcross matings have a hatchability of over 80% with the same hens.
By Robbpa on Saturday, January 19, 2002 - 07:52 pm:
By Infomaniac on Sunday, January 20, 2002 - 01:54 pm:
You've given me an idea. We use hay for bedding in our layer houses because we grow it ourselves so it costs us only what the production costs are. I'll bet the waste from a combine (combining corn) would be a good source for poultry bedding. We have a man close-by who sells sawdust for animal bedding, but a lot of it comes from that green-treated wood, and chickens eat so much of their bedding material that we are afraid to use it.
By Rokimoto on Sunday, January 20, 2002 - 05:48 pm:
The final product would likely be hybrids between clones, but the genetic diversity would still be very limited. To keep disease susceptablility in check you need to mix clone groups so that the disease does not spread through the population very rapidly. This defeats the purpose of having uniform birds for processing and production.
Info:
I use wood shavings and we do not have a problem. I used to use alfalfa hay because people told me not to use barley straw because the birds ate it and it gets stuck in their crops. I do not know if this is true, I never tested it.
I forgot to answer your queation about mitochondrial replication. Mitochondria have multiple copies of their genomes and seem to divide by simple division some genomes go into each new daughter mitochondrion by chance. When the cell divides some mitochondria go into each cell, there are usually hundreds of mitochondria per cell. Egg cells have thousands of mitochondria, so they don't have to replicate as fast as the cells in the embryo, they just get partioned into each cell as they divide.
By Robbpa on Sunday, January 20, 2002 - 10:18 pm:
By Infomaniac on Monday, January 21, 2002 - 09:50 am:
Given: Inbred males and inbred females. Control (non-inbred) males and non-inbred females.
Step 1: Breed the inbred females to non-inbred males and observe hatchability of eggs. Let the hatchability (percent of eggs that develop live embryos and actually do hatch) be represented by the symbol, H1.
Step 2: Breed the inbred females to their fathers and observe the hatchability of the eggs produced. Let this hatchability be represented by the symbol H2. Rokimoto points out that H1 >> H2.
But, H1 >> H2 could just be the hybrid vigor vs. inbreeding factor. It seems to me that there isn't enough information yet to assign the inbreeding depression to either sex.
If you would then breed the inbred cock to non-inbred females to get a third hatchability, H3, AND, if H1 from above is about the same as H3 (H1 and H3 both being low values of hatchability), that would be strong evidence supporting the claim that the male is responsible for most of the inbreeding depression as judged by hatchability studies.
By Rokimoto on Monday, January 21, 2002 - 11:04 am:
The alternative explanation is overdominance, but genetic tests indicate that overdominance may have a minor effect in hybrid vigor, and that most of the effect can be partitioned as the result of simple dominance. Overdominance is when the heterozygote Aa is superior to the homozygotes aa or AA. This seems to be relatively rare.
Outcrosses are less likely to produce the homozygous recessive detrimentals and 1/4 of the inbred progeny of any sire would be expected to be recessive homozygotes for any detrimental allele that he carried. Any one chicken carries a lot of recessive detrimentals. Each human carries an average of 5.
Most of this can be found in the Drosophila literature where they were looking into the genetics of fly populations.
By Infomaniac on Monday, January 21, 2002 - 12:14 pm:
Either I mis-understand you or you didn't address my question! LOL!
I understand how the detrimental recessives collect in inbred individuals. My problem is that one can't assign inbreeding effects to either sex based on just hatchabilities judged from the same females (bred to their fathers then to unrelated males). My point was that one also needs the hatchabilities from the inbred males bred to their daughters and ALSO bred to unrelated females. If the hatchability of the eggs obtained from the inbred male is constant regardless of the female, then I agree that he is responsible a significant part of the inbreeding depression of hatchability.
By Rokimoto on Monday, January 28, 2002 - 01:29 pm:
You are right about the inbred males and female testing. The males in our study were not inbred, but only their daughter were, so we measured the decrease between sire and daughter and the daughters with other relatively unrelated sires. Some sires were low with control hens, but not as low as they were when they were crossed to their daughters.
Inbreeding does affect the males, but we had inbreeding data for the females. We were not working with inbred males. We have an inbred line that the male fertility is not very good mainly because we have trouble getting semen from these males. They are all consistently bad. I put one male in a pen with unrelated females to see if natural mating might be better, but I hardly got any fertile eggs. This wasn't a good experiment, but the males are consistently poor semen producers. Part of being inbred is that you are pretty uniform, all the hens look about the same and so do all the males. I've let this line lapse, but when we had them caged together it was like looking at a line of clones. The line is 99.99% inbred and was developed using full sib matings and is kept inbred by mostly cousin matings.