Mitochondrial DNA

[Glenn]

Thought it was getting crowded on the other thread so made a new thread. I found some more stuff from another site that I'll repost shortly. Welcome more information from our esteemed posters!

[Glenn]

Dr. Gene Freeman,an outstanding dairy cattle geneticist who has led research projects on mitochondria, expects to post information for us on the influence of mitochondria on butter fat content of milk within the next few days.
Since some may desire a background on what mitochondria are and what they do, I will post some background information ahead of Dr. Freeman to set the stage for his information. I'll start with the currently accepted theory about how they came about and then discuss how they function.

The currently accepted theory about the very first life forms is that they were very primitive one cell forms. They probably originated in the ancient oceans when the earth was about half as old as it is now. There is still confusion about which part of the ocean spawned these life forms but the regions of the sea bed where deep fissures occur that allow heat and chemicals from the sub mantel region to emerge is considered probable. At the time the first primitive life forms originated the was no oxygen in the atmosphere. The very first life forms did not use oxygen in their energy generating metabolism because there was no free oxygen available. They used what we now call anaerobic metabolism. One of the waste products given of by anaerobic metabolism is oxygen. Over a long period of time oxygen accumulated until there was enough that primitive single cell organisms developed that used this waste products that was accumulating at an ever faster rate because plants were now growing and incorporating the sun's energy into their anaerobic metabolism and giving off oxygen.
The very early anaerobic single cell organism enclosed their primitive genetic blue prints (genes) in a spherical structure (nucleus) and probably resembled some of todays protozoa, while the aerobic organism protected their genetic material by forming it into circles. Some of the early anaerobic organism consumed some types of the aerobic organisms by engulfing them through the cell wall and then digesting them in the cytoplasm the same way some present day protozoa do.
There is one very important bottom line difference in the energy generation efficiencies of aerobic and anaerobic metabolism. Aerobic metabolism is about 7 times more efficient a method of generating free (useable) energy. This gives cells with aerobic metabolism a great energy advantage.
It is believed that some types of the primitive aerobic bacteria were resistant to digestion by the cytoplasm of the primitive protozoa like organism and indeed were able to live and even multiply in the cytoplasm of the anaerobic host. They gave a more efficient energy supply to the cell cytoplasm of the host cell that had attempted to consume them. These better powered twin energy (anaerobic and aerobic) source cells were able to evolve into multicellular organism. Over time many of the genes of the original primitive bacteria like organism have become incorporated into the nuclear genes of the cell but the aerobic energy generating enzymes are still contained in the mitochondria. These conserved genes number in the 20s and most produce enzymes involved in aerobic metabolism. The interior structure of the mitochondria resemble primitive battery plates in the way they inter digitize. Some of the present day primitive soil organisms have a structure that closely resembles that of the mitochondria. The mitochondria have a 2 layer cell wall like bacteria and circular genes like bacteria. Mitochondria are structures found only in the cytoplasm. They are not involves in nuclear chromosome division. They multiply about 10 fold in number prior to cell division but the allocation of them is a chance matter of what ever is included in the portion of cytoplasm that is pinched off into each of the newly formed daughter cells.
About 15% of the total DNA of the cell is located in the mitochondria. It is contributed to the calf exclusively by the dam. It may well be the basis for athlete recruiters desire to visit with the prospects mother to be able to better judge the energy level of an individual. Mitochondria have a mutation rate about lke the bacteria i.e. about 100 times faster than nuclear genes.
This theory of mitochondria is sometimes referred to as "The lucky Gulp Theory". It has become well accepted at the present time.
In the next post we can briefly consider what happens to the mitochondria from the male. Let me know if you think background posts are helpful.
Regards
Bill


William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Mitochondria in bulls.
Remember,information is built just like a brick wall. One fact on top of another.
Bulls have mitochondria in the cytoplasm of their cells the same as cows do. The bull's mitochondria are derived exclusively from the cytoplasm of the dam's egg that forms the bull. The sire makes no contribution to the mitochondria of his offspring. But the sire's mitochondria are an indispensable part of the fertilization of the egg. They contribute the power that gives the sperm the fantastic motility necessary to reach the egg to fertilize it. The sperm consists of 3 regions. The head, the mid piece and the tail. The head is mainly composed of packed chromosomes and has an enzyme patch on the top front portion of its outer surface that is covered with a transparent membrane to preserve the enzyme until the sperm is close to the egg wall which it must digest to form a tunnel for the passage of the head of the sperm into the egg. The mid piece is the power plant of the sperm. The mid piece consists of the filaments of the tail as they attach to the head of the sperm surrounded by a chain of mitochondria joined like little sausages and wrapped 2 or 3 layers deep around the tail filaments next to the head. They generate the energy that imparts the motion to the tail that imparts motility to the sperm.
The wall of the egg is a very thick dense membrane that is rather tough. You may have seen pictures of the contents of an egg being aspirated through a very fine pipet and noted how thick and tough it appeared. That is the structure the enzyme patch on the sperm head must digest a path through. On the inside of that tough cell wall which is called the zona pellucida, is another tightly stretched very thin membrane that separates the egg cytoplasm from the tough zona pellucida. This thin inner membrane is call the vitteline membrane. When the enzyme digests a hole in the vitteline membrane the membrane snaps like a tiny balloon popping. This breaks the head of the sperm from the mid piece and the tail and allows only the head to enter the egg's cytoplasm. The change in the composition of the zona pellucida caused by the action of the digestive enzyme on the sperm and by the rupture of the vitteline membrane makes the zona pellucida refractive to addition digestion by other sperm when they reach it and is usually effective in restricting fertilization to a single sperm.
There is one more recently discovered aspect of sperm formation that reveals another aspect of natures intricate blueprint. The cells that divide several times to form the large number of sperm are called spermatogonia cells. They contain an unusually abundant supply of a selenium rich enzyme. The level of this enzyme was considered to be far in excess of what was needed. It turned out that nature has a unique use for this enzyme after the sperm pieces are formed. This enzyme then polymerizes to forms a flexible coating of the back portion of the sperm head, the mitochondria of the mid piece and a little bit of the base of the tail of the sperm. A flexible super glue that holds the parts of the sperm together. We still need to find out if we can improve the quality of sperm through supplemental selenium.
The number of mitochondria in the cells of various tissues is quite variable. The tissue that has one of the most abundant supplies of mitochondria is the heart tissue. Sections of heart muscle consist of about as great a volume of mitochondria as muscle tissue,the mitochondria are so densely packed in the muscle tissue.
With this brief over view of mitochondria we should be able to gain considerable information from Dr. Freeman's posts.
Hope you find this interesting
Regards
Bill


William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

A freshly collected semen sample is a whitish fluid that contains million of sperm in each cc. of seminal fluids. The sperm and the seminal fluids together constitute semen. The mitochondria furnish the energy to cause the sperm tail filaments to beat in a thrashing manner to propel the individual sperm through the seminal fluids in its search for the egg cell wall. When the enzyme in the sperm head surface patch is exposed by loss of the thin membrane that had covered it (to protect the enzyme from becoming diluted and spent while the sperm traveled in search of the egg cell), contacts the egg cell wall the enzyme in the sperm head patch starts the egg cell wall digestion process. The mitochondria are not involved in this egg cell wall digestion except to have supplied the energy to propel the sperm through the seminal fluids in search of the egg.
The energy generated by the mitochondria comes from the aerobic metabolism of substrate to convert ADP to ATP. The ATP releases energy to molecular motors attached to each tail filament near the inner surface of the membrane covering the head of the sperm and becomes reduced back to ADP. The ADP is then recharged to ATP in the rudimentary battery plate like membrane folds inside the mitochondria. These membrane folds are called Christie. It is interesting to note that with the aid of a very powerful scanning electron microscope the ATP molecules can be visualized as a little mushroom shaped structure emerging from the surface of the Christie of the mitochondria. This enzyme facilitated process is completely different from the digestion of the egg cell wall that is accomplished by a digestive type of enzyme.
A common design of motility generating filamentous structures in nature is two central filaments surrounded by a circle of nine single filaments. The tail of the sperm has this design. As an aside I had to smile when a few years ago a tire company introduced a new tire cord that their research had developed that had improved flexibility and strength. You guessed it. It was two central filaments surrounded by nine individual filaments.
Hope this helps clarify points that may have been confusing. If not ask again and I'll try again.
Regards
Bill

William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Ribosomes are minute compact masses of protein that are abundantly distributed throughout the cytoplasm. They process the protein assembly instructions carried to them by messenger RNA that has passed through nuclear pores and received the configuration instructions for the new protein molecule by reading the configuration of a portion of a nuclear gene, passed back out of the nucleus into the cytoplasm and contacted a ribosome with the specifications of the protein to be assembled. Ribosomes are not energy generators. They are users. The ATP generated by the mitochondria is probably the source of much of the energy they use. The traffic of molecules from the cytoplasm through the nuclear membrane is rather rigorously controlled. It has been commonly accepted that all the ribosomes were located in the cytoplasm and none were in the nucleus. Resent research indicates that there is a small population of ribosomes in the nucleus. The function of these has not been established but it is possible that some proteins are required for normal maintenance of the nucleus and that they are best built inside the nucleus. One of the major molecules that transports "cargo" from the cytoplasm both into and out of the nucleus through the nuclear pores has recently been identified. It is a 19 revolution coil of protein that has two small short chop stick like projections that are believed to physically grasp the protein component to be imported into the nucleus and mechanically carry it through a nuclear membrane pore and release it into the nucleoplasm.
Diagrams of the molecule remind me of a 19 coil soft spring or a short toy slinky.
Hope this is of interest.
Regards
Bill

William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Dr. Gene Freeman is working on a post on mitochondria for us. I hope we will have it available in a few days. That will give more information about the differences that each parent contributes to the offspring besides the nuclear genes. I consider that both the mitochondria contribution as well as possible epigenetic factor contribution play a role in the characteristics that may be expressed in the offspring.It is becoming well accepted that certain male contributed genes are silenced by epigenetic factors during periods of the development of the early embryo. It is well established that certain breeds of swine contribute more favorably as dams of the offspring than as sire. The same is undoubtedly true of cattle. I wonder if some one can supply information on this point. I don't have the facts in mind. Where the favorable influences originate is still based on both fact and speculation as far as I know. It is my speculation that the dam may make a greater contribution to the epigenetic factors than the sire.
Regards
Bill

William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

There is a research paper in the Jan. 9, 2004 issue of Science that gives a brief glimpse in mice of where 2 (perhaps out of several) of the genetic control points may be located that determine two important production traits of cattle. This research was done in mice but much of the genetic blueprint of mammals is fairly similar. Most of the genetic imprinting goes on in the pre implantation and the germ line development stages of the embryo. Most of the imprinted genes are on alleles of maternal origin but a few imprinted genes are on male origin alleles. The research reported in this paper focused on the mechanism that caused the imprinting of a specific gene on a maternal allele of a pair of genes. An epigenetic origin protein binds to a conserved site upstream of the active gene. When the protein takes on methyl molecules its electron conductivity is enhanced and the activity of the gene is increased.
This maternal gene is only a short distance from the insulin like growth factor gene and that gene is imprinted by a similar mechanism but on the parental (male) allele.
It was reported that the families of mice bred to have a deficiency in the gene on the maternal allele being studied had reduced fertility but the development of the offspring that were produced was normal.
There seems to me be three important concepts that emerge from this early research work that bear keeping in mind when we are selecting seed stock animals.
1) The maternal (dams) alleles contains the majority of the imprint marks (sites). This would indicate that when the offspring isn't a reasonably close blend of both parents it's more likely to favor its dam over its sire except in a few traits where just the opposite will be true.
2) The insulin like growth harmone is marked on the parental allele. This suggests we should expect the sire to have a greater influence in some aspects of growth.
3) There may be some epigenetic factors that influence fertility that we should continue to work to select.
Wish I could present a list of what traits are more likely to resemble the sire or the dam but that information is not yet known. We will have to wait. I know that some will read this and think "what a bunch of useless information". But if only a few read it and think "I want to know more about that" and start looking critically at the "living laboratories" grazing in their pastures, plans of action can occur.
Remember we only see what we know to look for.
Regards
Bill



William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

It is a pleasure to post this summary of mitochrondia research prepared for us by Dr. Don Beitz and Dr. Gene Freeman both of whom are Distinguished Professors at ISU. I know there will be questions as we all have different levels of preparation in this area. When you have questions let me know and I'll try to answer them. If I can't I'll forward them to Gene or Don. This is a long post but may be of considerable interest to many.
Regards
Bill


Mitochondria – Molecular Differences and Phenotypic Expression
A. E. Freeman and Don Beitz
Department of Animal Science
Iowa State University


Mitochondria are tiny organelles found in the cytoplasm of cells and are essential in the events that generate more than 92% of the energy (ATP) production in mammals. They are about 1-2 microns long and about 0.5 micron wide and are mostly oval in shape. As a reminder, a micron is one millionth of a meter. The energy sources for mitochondria of cattle are volatile fatty acids from ruminal fermentation and long-chain fatty acids, amino acids, and glucose from digestion of fats, protein, and starch. Even though the mitochondria are very small, they are essential for life and the productivity of our livestock.

Perhaps a little review of DNA, the storehouse of genetic information in animal cells would be useful. The structure of DNA can be likened to a spiral staircase. Each step on the staircase is composed of two nucleotides attached to each other. There are four different nucleotides: Adenine and thymine, which form one-step by pairing together and cytosine and guanine, which pair together to form another step. Most cellular DNA is located in the nucleus, but some, enough to code for 13 different proteins, is located in the mitochondria. If this pairing of nucleotides is changed by a mutation, the coding for the population of proteins, for example, in the mitochondria will be different and may affect mitochondrial function and hence animal productivity. By using Holstein cows at the Iowa State University Breeding Farm, we looked for this type of mutation to associate mitochondrial mutations with economic traits of milk production and of reproduction. The nuclear DNA is packaged as chromosomes and is linear in nature, whereas the mitochondrial DNA (mtDNA) is circular. The order of the nucleotides in the DNA determines hereditary nature of plants and animals. Therefore, DNA, together with the management an animal receives, determines the traits of production that we observe.

Genetics of mitochondria

Mitochondria are maternally inherited. That is, mitochondria are transmitted from females to both male and female offspring; males do not transmit mitochondria to their offspring. There has been only one reported exception where mtDNA from the sire got into an embryo, but this occurred after 26 generations of backcrossing in mice. Thus, mitochondria allow for a possible genetic basis for maternal inheritance and a possible genetic basis of why some cow families are better milk producers than are other families.

Mitochondria have a separate set of DNA from the nuclear DNA. The mtDNA is much smaller, being about 16,300 bases (nucleotides). Nuclear DNA of humans contains an estimated 3 billion bases per nucleus. The mtDNA codes for proteins by the same cellular mechanisms as the nuclear DNA. MtDNA consists of only 13 protein-coding regions, 12 of which are essential for electron transport and ATP production; 22 transfer ribonucleic acid genes; and 2 ribosome genes. mtDNA contains a displacement loop (D- loop) of 910 base pairs ( steps on the spiral staircase) that is a control region for replication of the mtDNA and is known to be more variable in nucleotide order than the remainder of the mtDNA. Mitochondria do not have enough DNA to code for all of their own proteins. Nuclear genes code at least 48 proteins that are part of the respiratory chain that produces ATP, which, upon degradation to ADP, releases energy to drive chemical reactions that support life and that result in growth, milk production, and reproduction. The coding of some mitochondrial enzymes (proteins) by both mtDNA and nuclear DNA allows for possible maternal line-by-sire interactions. These interactions may explain why some producers think that some dairy sires “work better” on some cow families than on others.

Variation in Mitochondrial DNA found in the Iowa State Dairy Herd

We have used two experimental approaches to relate mtDNA to traits of economic importance in the dairy industry. Our first approach was to sequence the nucleotides in the mtDNA, find sequence differences among cows, and compare cows with and without the sequence difference. The other way to evaluate importance of mtDNA variation is to look at difference in mtDNA between maternal lineages of cows within our herd.

The experimental material used for our studies was the Iowa State University Dairy Breeding herd. There were 38 different maternal lineages available in the herd that were determined by tracing each cow back to when their ancestor was imported into the United States. When two or more cows had a common ancestor, they were considered to be in a common lineage. This tracing of ancestry was done by using the Holstein Herd Book.

The D-loop (control region) of mtDNA was sequenced for the 38 lineages, and 51 separate sites of sequence variation were found. Some variation also was found within lineages. The most variable was at nucleotide 363 where 29% of the lineages differed. There were other sites that were hypervariable between lineages, and therefore these should not be used as genetic markers.

In addition to mtDNA variation among maternal lineages, there is evidence that mtDNA differs within an oocytes and, thus within a cow. Forty-seven oocytes were isolated from a single Holstein cow, and two were found to have a single insertion of a nucleotide at the same location in the D-loop. The other 45 oocytes did not have this insertion. In addition, there were two sites, other than the original insertion, that showed genetic variation.

Association of Molecular Differences with Economic Traits

Again, these data were obtained from the Dairy Breeding Research herd. Seventeen of the most common sequence polymorphisms in the D-loop of the mtDNA were associated with production and reproduction traits. These polymorphisms were found to be stable when the entire D-Loop was sequenced in all lineages. A comprehensive animal model with full relationships was used. The ranges of significant differences were: 3121 lbs. milk, 28.6 lbs. milk fat, 321 lbs., solids not fat, 978 Mcal lactation energy, and 0.60% milk fat.

The ranges of significant differences for reproductive traits were 64 days open, $19 in reproductive costs, and $40 in total health costs. By using the same data (36 maternal lineages in one herd), analyses that clustered identical mtDNA genotypes across lineages showed that the percentage of milk fat and energy concentrations differed significantly across maternal lineage clusters.

Association of Maternal Lineages with Production

Again, data from the Holstein Breeding Research herd were used to associate maternal lineages with milk production. The data were analyzed with an animal model where lineages were considered as fixed effects and partitioned from the cytoplasmic effects in 53 lineages. The 53 lineages have been in the herd since 1968 when foundation cows were purchased. Data included 1595 production records from 669 cows. The ranges among maternal lineages were 6,454 lbs. of milk, 339 lbs. of fat, and 0.91% fat. The within-herd standard deviations were 3,331 lbs. milk, 13 lbs. of fat, and 0.39% milk for fat. A significance test showed that lineages were significantly different (P< 0.015) for percentage of milk fat and production of calculated milk energy (P<0.028). We attempted to verify these results in another research project in North Carolina and found differences among lineages, but they were not significantly different (P>0.05).

A study of mtDNA variation in beef cattle was conducted by using synthetic lines of beef cattle where the synthetic lines were bred to produce small, medium, and large framed cattle. Unfortunately, these lineages could not be traced back to a common ancestor, which was a problem with the interpretation of the data. Nevertheless, the conclusion was that cytoplasmic (mtDNA) variance failed to be important for preweaning performance of beef calves.

Discussion

Maternal lineages show associations with production traits in dairy cattle. mtDNA polymorphisms in the D-loop are markers for large differences in productive and reproductive traits. Because some nucleotides are hypervariable, they should not be used as genetic markers. There are possible nuclear-by-mitochondrial effects that remain unknown, and these need to be understood more clearly before useing mtDNA variation in dairy breeding programs.



William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Feed stuffs ingested by cattle undergoes digestion to volatile fatty acids by rumen fermentation and to long-chain fatty acids, amino acids, and glucose by digestion of fats, protein, and starch. These are the main "fuels" the cells metabolize to liberate the form of energy that can join various molecules into new substances that are used to build and repair the body and to produce its various products.
These fuels are broken down in the cells primarily by aerobic metabolism (an estimated 92% of the total energy produced in the body is generated by this process). The final power form that is produced through this break down is the electron. This form of energy is capable of joining various chemical molecules into various new substances that are used for growth and repair of the body and production of various products. This break down of the "fuel" molecules occurs in a series of usually lighting fast hand offs in a specifically ordered series of enzymes and receptors. The last of these is a protein molecule called by its initials ATP. The electron it receives is very loosely bound and is very easily transferred to the many building stages that produce the new molecules (usually a protein) that the gene template has called for. Loss of this electron changes the ATP molecule into a slightly different compound which is called ADP. The ADP molecule is attracted back and receives another electron which changes it back into ATP and it then heads out to where ever another electron is needed. There are about 60 genes involved in the formation of the molecular assembly line and its components that breaks down the fuels to produce the electrons. About 12 of them are exclusively present in the mitochondria and about 48 of them are in the cell nucleus. Thus the quality of this aerobic metabolism assembly line is dependent on both the quality of genes in the mitochondria and in the nucleus. Both the sire and dam influence the quality of the nuclear genes but only the dam influences the quality of the mitochondria genes.
Let me know if this concept is clear.If not I'll work at it some more. After this one is clear we can tackle another step.
Let me know if this is helpful. I smile as I envision my biochemistry friends frowning over this simplistic explanation of the beautiful process of aerobic metabolism.

Regards
Bill

William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Tonight, as I have been working on some of the recent posts concerning mitochondria two question have been surfacing in my mind so I thought I'd ask the board about them.
1) Have you noticed in your herd that a heifer will often calve within 10 days of the date she was born (but of course in a different years)?
2) Have you noticed how an occasional bull sired by a small testicle size bull will appear that has a normal or above scrotal size and proceeds to transmit normal or above testicle size to his offspring? Almost like he wasn't out of a small testicle linage.

Are these clues telling us to look to the Y chromosome for genes involved in testicle size and to the mitochondria for fertility genes?
The 64 day difference in conception (3 heat cycles?) association reported in Gene and Dons research and the balance side in the sire of the Y chromosome transmission that e.g.Price points out might be at work to cause these differences.
Just an idle thought that doesn't want to go away.
Like to hear your observations about these points.
Regards
Bill


William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[Glenn]

Dr. Gene Freeman's reply to questions I have shared with him follows:

"One expects to detect the most significant mitochondria effects where very large expenditures of energy are needed to express to phenotype. For example, a dairy cow producing 21,000 pounds of milk with 3.2 % protein, 3.6 % fat, and 8.5 % solids (lactose and minerals) not fat in 305 days expends a great deal of energy. The references J. Dairy Sci. 75: 1331-1341 and Livestock Production Science 37:283 -293 are good starting points for this information. Ratios of estimates of variance are of maternal lineages to total phenotypic variance, ratios of cows within maternal lineages to maternal lineages, etc. For example the ratio of the variance of maternal lineages to total phenotypic variance are .052 for ME milk,.041 for ME fat and 0.105 for percentage. This is from the JDS paper referenced above. The mitochondria contribution to the production of aerobic energy is an essential component of the process. Variation in mitochondria contribution had a significant effect on certain of the milk production traits we studied and have reported in the literature."
Posted for Dr. Gene Freeman
Regards
Bill


William P Switzer
DVM MS PhD Dr.h.c.(retired)
2224 Hamilton Dr
Ames Iowa 50014
515 268 5205
fax [phone]

[timbernt]

About 10 years ago I came to believe the majority of ag journalists, extension specialists, and self-proclaimed breed leaders did not have the mental capacity to understand how complex the genotype is behind the phenotype they see. That is the reason behind my wait and see attitude about the current state of genomics and genetic measures like EPD's. We should all embrace DNA science like parentage, congenital defect inheritance, and the few genomic measures that are truly proven. Being from Missouri, my attitude is "show me" about all the articles promoting what a person without manure on their boots can tell me about how to breed cattle. Glenn's reposting in this thread shows the real role academia should play in our thought process. I have a huge amount of respect for these researchers and none for those pseudointellectuals who don't know how little they know.

[strojanherefords]

The other day I went to a bull sale. All the bulls were genomically tested and the sim-angus bulls were tested for hair color. It was a little funny, when the auctioneer got a little tired instead of saying he is homozygous black, he said he's a homo. Well towards the end of the sale the video of a red bull came up but in the catalog the bull tested as homozygous black. Nobody caught it. Genomics is only as good as the data that goes into it.

[woodford]

     Thank you Glenn, for those informative posts. I knew that it would take time to read and try to digest it, and so have only just now read them. 

     Some of the details that interest me most, are those about milk production, and fertility. As an aside, nearly all milk is classed as A-1, but there are a few instances that milk is A-2. A-2 milk is, from what I have been told, useful for people that are lactose intolerant, and those who are autistic. A-2 milk comes as a recessive trait, so it is easily lost in a breeding program. While focus has often been upon quantity of milk produced, it will be interesting what information will come to light about the qualities of milk in lesser quantities, particularly within the Hereford breed.

     I want to thank Dr. Switzer for simplifying his explanation of the various details that he has outlined. If I understand correctly, it looks like the mitochondrial DNA has a relationship to cell activity. If this is true, I wonder if greater cell activity wouldn't improve disease resistance as well?

    As for his 2 questions: for number 1 is an emphatic yes. Part of my numbering system to identify my cattle is consecutive, so that part always starts at 1 for the first calf born that year. Often times daughters from my better female lines will have the same, or nearly the same number as their mother, which indicates the time of year they were born in. However, there are instances this does not play out the same, and this has always been a result of what I have found to be an inferior influence through a sire line. A female can keep the trait going, but an inferior sire can still mess it all up.

     Question 2, I think is also a yes to a lessor degree than question 1.


     Woodford

      

   
     

[Jobulls]

I try to stay out of the discussion, but I too have concerns with the geneticists marketing that they have figured all of these interactions out. I think the Mitochondrial DNA discussion was interesting, but the variation of a few (under 40) out of 20,000 genes is not that significant. (I might be wrong on these numbers). I realize there is some effect from the small amount of Mitochondrial DNA from the mother, but I think a more interesting discussion would be that mammals are more influenced actually by their father's DNA (is this true)? If 10% more of the father's DNA is going to be displayed by the offspring, would it be better to focus on sire selection rather than embryo flushing? Would it be better to use a brother than flush his sister? Just a thought to get everyone going.

"Overall, they found that most genes showed parent-of-origin effects in their levels of expression, and that paternal genes consistently won out. For up to 60 percent of the mouse’s genes, the copy from dad was more active than the copy from mom. This imbalance resulted in mice babies whose brains were significantly more like dad’s, genetically speaking."

blogs.discovermagazine.com/d-brief/2015/03/03/genetically-more-like-dad/#.W7GoLi-ZMnU

I also think it is interesting that the age and condition of the father at different points in life can change development.

"In rodents, changing the quantity or quality of a male's diet at various developmental time points has also been found to induce phenotypic changes in male offspring. For example, males exposed to prenatal dietary restriction (through reductions in caloric intake of their mother during late gestation), who are then fed ad libitum throughout the rest of their life, sire offspring with reduced birth weights and impaired glucose tolerance compared to fathers who were born to control dams"

"In one of the first studies of paternal age effects, rats born to very old fathers (>22 months) performed poorly on a conditioned avoidance test compared to rats born to younger males, though no changes in anxiety-like behavior were found (Auroux, 1983). "

www.ncbi.nlm.nih.gov/pmc/articles/PMC2975825/

I am not a geneticist but it is interesting to think that a male calf that was not fed properly will not produce progeny that is as good. It is also interesting to think that an old decrepit bull may sire worse offspring than he did in the prime of his life? We need to have older bulls to promote longevity, but is there an argument for bull rotation? Paternal Nutrition and Paternal Influence could have more effect on offspring than Maternal Mitochondrial DNA? Then you have to throw in Offspring Development and the effect that the mother will have on training the calf how to live and grow. Sometimes I think this has more effect on temperament than genetics. A high headed recip cow is not good for calf development. What about a mother that does not know how to range and is not efficient?

Here is another crazy thought. The feed for the female could be effecting multiple generations.

"For instance, in the case of pregnant dams who are exposed to some perturbation (e.g. high fat diet, endocrine disruptors, ethanol), there are three generations being exposed to the same environmental experience."

With all of these genetic factors, how valuable are genomic EPDs or genomic profiles?

Just a thought. The DNA discussion leads to so many variables, I am not sure the scientists know what they are looking at. Again, this is not my area of expertise. I know cows and telecommunication. You will notice a lot of question marks in this post.

[timbernt]

About 23,000 genes on cattle, each gene effecting multiple traits. My thought is the environment does a much better job of selecting the right type than a computer.

[rockmillsherefords]

I was looking around the web for some follow on what's been posted here on Mitochondria, couldn't find what I was looking for. I did see where Dr. Switzer died about a year ago.