‘Approaches to genetics for livestock research’ at IASH, University of Edinburgh

A couple of weeks ago, I was at a symposium on the history of genetics in animal breeding at the Institute of Advanced Studies in the Humanities, organized by Cheryl Lancaster. There were talks by two geneticists and two historians, and ample time for discussion.

First geneticists:

Gregor Gorjanc presented the very essence of quantitative genetics: the pedigree-based model. He illustrated this with graphs (in the sense of edges and vertices) and by predicting his own breeding value for height from trait values, and from his personal genomics results.

Then, yours truly gave this talk: ‘Genomics in animal breeding from the perspectives of matrices and molecules’. Here are the slides (only slightly mangled by Slideshare). This is the talk I was preparing for when I collected the quotes I posted a couple of weeks ago.

I talked about how there are two perspectives on genomics: you can think of genomes either as large matrices of ancestry indicators (statistical perspective) or as long strings of bases (sequence perspective). Both are useful, and give animal breeders and breeding researchers different tools (genomic selection, reference genomes). I also talked about potential future breeding strategies that use causative variants, and how they’re not about stopping breeding and designing the perfect animal in a lab, but about supplementing genomic selection in different ways.

Then, historians:

Cheryl Lancaster told the story of how ABGRO, the Animal Breeding and Genetics Research Organisation in Edinburgh, lost its G. The organisation was split up in the 1950s, separating fundamental genetics research and animal breeding. She said that she had expected this split to be do to scientific, methodological or conceptual differences, but instead found when going through the archives, that it all was due to personal conflicts. She also got into how the ABGRO researchers justified their work, framing it as ”fundamental research”, and aspired to do long term research projects.

Jim Lowe talked about the pig genome sequencing and mapping efforts, how it was different from the human genome project in organisation, and how it used comparisons to the human genome a lot. Here he’s showing a photo of Alan Archibald using the gEVAL genome browser to quality-check the pig genome. He also argued that the infrastructural outcomes of a project like the human genome project, such as making it possible for pig genome scientists to use the human genome for comparisons, are more important and less predictable than usually assumed.

The discussion included comments by some of the people who were there (Chris Haley, Bill Hill), discussion about the breed concept, and what scientists can learn from history.

What is a breed? Is it a genetical thing, defined by grouping individuals based on their relatedness, a historical thing, based on what people think a certain kind of animal is supposed to look like, or a marketing tool, naming animals that come from a certain system? It is probably a bit of everything. (I talked with Jim Lowe during lunch; he had noticed how I referred to Griffith & Stotz for gene concepts, but omitted the ”post-genomic” gene concept they actually favour. This is because I didn’t find it useful for understanding how animal breeding researchers think. It is striking how comfortable biologists are with using fuzzy concepts that can’t be defined in a way that cover all corner cases, because biology doesn’t work that way. If the nominal gene concept is broken by trans-splicing, practicing genomicists will probably think of that more as a practical issue with designing gene databases than a something that invalidates talking about genes in principle.)

What would researchers like to learn from history? Probably how to succeed with large research endeavors and how to get funding for them. Can one learn that from history? Maybe not, but there might be lessons about thinking of research as ”basic”, ”fundamental”, ”applied” etc, and about what the long term effects of research might be.

Excerpts about genomics in animal breeding

Here are some good quotes I’ve come across while working on something.

Artificial selection on the phenotypes of domesticated species has been practiced consciously or unconsciously for millennia, with dramatic results. Recently, advances in molecular genetic engineering have promised to revolutionize agricultural practices. There are, however, several reasons why molecular genetics can never replace traditional methods of agricultural improvement, but instead they should be integrated to obtain the maximum improvement in economic value of domesticated populations.

Lande R & Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics.

Smith and Smith suggested that the way to proceed is to map QTL to low resolution using standard mapping methods and then to increase the resolution of the map in these regions in order to locate more closely linked markers. In fact, future developments should make this approach unnecessary and make possible high resolution maps of the whole genome, even, perhaps, to the level of the DNA sequence. In addition to easing the application of selection on loci with appreciable individual effects, we argue further that the level of genomic information available will have an impact on infinitesimal models. Relationship information derived from marker information will replace the standard relationship matrix; thus, the average relationship coefficients that this represents will be replaced by actual relationships. Ultimately, we can envisage that current models combining few selected QTL with selection on polygenic or infinitesimal effects will be replaced with a unified model in which different regions of the genome are given weights appropriate to the variance they explain.

Haley C & Visscher P. (1998) Strategies to utilize marker–quantitative trait loci associations. Journal of Dairy Science.

Instead, since the late 1990s, DNA marker genotypes were included into the conventional BLUP analyses following Fernando and Grossman (1989): add the marker genotype (0, 1, or 2, for an animal) as a fixed effect to the statistical model for a trait, obtain the BLUP solutions for the additive polygenic effect as before, and also obtain the properly adjusted BLUE solution for the marker’s allele substitution effect; multiply this BLUE by 0, 1, or 2 (specic for the animal) and add the result to the animal’s BLUP to obtain its marker-enhanced EBV. A logical next step was to treat the marker genotypes as semi-random effects, making use of several different shrinkage strategies all based on the marker heritability (e.g., Tsuruta et al., 2001); by 2007, breeding value estimation packages such as PEST (Neumaier and Groeneveld, 1998) supported this strategy as part of their internal calculations. At that time, a typical genetic evaluation run for a production trait would involve up to 30 markers.

Knol EF, Nielsen B, Knap PW. (2016) Genomic selection in commercial pig breeding. Animal Frontiers.

Although it has not caught the media and public imagination as much as transgenics and cloning, genomics will, I believe, have just as great a long-term impact. Because of the availability of information from genetically well-researched species (humans and mice), genomics in farm animals has been established in an atypical way. We can now see it as progressing in four phases: (i) making a broad sweep map (~20 cM) with both highly informative (microsatellite) and evolutionary conserved (gene) markers; (ii) using the informative markers to identify regions of chromosomes containing quantitative trait loci (QTL) controlling commercially important traits–this requires complex pedigrees or crosses between phenotypically anc genetically divergent strains; (iii) progressing from the informative markers into the QTL and identifying trait genes(s) themselves either by complex pedigrees or back-crossing experiments, and/or using the conserved markers to identify candidate genes from their position in the gene-rich species; (iv) functional analysis of the trait genes to link the genome through physiology to the trait–the ‘phenotype gap’.

Bulfield G. (2000) Biotechnology: advances and impact. Journal of the Science of Food and Agriculture.

I believe animal breeding in the post-genomic era will be dramatically different to what it is today. There will be massive research effort to discover the function of genes including the effect of DNA polymorphisms on phenotype. Breeding programmes will utilize a large number of DNA-based tests for specific genes combined with new reproductive techniques and transgenes to increase the rate of genetic improvement and to produce for, or allocate animals to, the product line to which they are best suited. However, this stage will not be reached for some years by which time many of the early investors will have given up, disappointed with the early benefits.

Goddard M. (2003). Animal breeding in the (post-) genomic era. Animal Science.

Genetics is a quantitative subject. It deals with ratios, with measurements, and with the geometrical relationships of chromosomes. Unlike most sciences that are based largely on mathematical techniques, it makes use of its own system of units. Physics, chemistry, astronomy, and physiology all deal with atoms, molecules, electrons, centimeters, seconds, grams–their measuring systems are all reducible to these common units. Genetics has none of these as a recognizable component in its fundamental units, yet it is a mathematically formulated subject that is logically complete and self-contained.

Sturtevant AH & Beadle GW. (1939) An introduction to genetics. W.B. Saunders company, Philadelphia & London.

We begin by asking why genes on nonhomologous chromosomes assort independently. The simple cytological story rehearsed above answers the questions. That story generates further questions. For example, we might ask why nonhomologous chromosomes are distributed independently at meiosis. To answer this question we could describe the formation of the spindle and the migration of chromosomes to the poles of the spindle just before meiotic division. Once again, the narrative would generate yet further questions. Why do the chromosomes ”condense” at prophase? How is the spindle formed? Perhaps in answering these questions we would begin to introduce the chemical details of the process. Yet simply plugging a molecular account into the narratives offered at the previous stages would decrease the explanatory power of those narratives.

Kitcher, P. (1984) 1953 and all that. A tale of two sciences. Philosophical Review.

And, of course, this great quote by Jay Lush.

‘Hard cash paid down, over and over again’

The whole subject of inheritance is wonderful. When a new character arises, whatever its nature may be, it generally tends to be inherited, at least in a temporary and sometimes in a most persistent manner. What can be more wonderful than that some trifling peculiarity, not primordially attached to the species, should be transmitted through the male or female sexual cells, which are so minute as not to be visible to the naked eye, and afterwards through the incessant changes of a long course of development, undergone either in the womb or in the egg, and ultimately appear in the offspring when mature, or even when quite old, as in the case of certain diseases? Or again, what can be more wonderful than the well-ascertained fact that the minute ovule of a good milking cow will produce a male, from whom a cell, in union with an ovule, will produce a female, and she, when mature, will have large mammary glands, yielding an abundant supply of milk, and even milk of a particular quality?

Today is Charles Darwin’s birthday. I’m not such a serious Darwin reader, but it’s fun how it seems like you can open a Darwin book at almost any chapter and find something interesting or amusing. This is from The Variation of Animals And Plants Under Domestication, chapter twelve, ‘Inheritance’. Here we find Darwin overflowing with enthusiasm when trying to convince a sceptic about the importance of inheritance. In true Darwin style he launches into a long list of examples:

Some writers, who have not attended to natural history, have attempted to show that the force of inheritance has been much exaggerated. The breeders of animals would smile at such simplicity; and if they condescended to make any answer, might ask what would be the chance of winning a prize if two inferior animals were paired together? They might ask whether the half-wild Arabs were led by theoretical notions to keep pedigrees of their horses? Why have pedigrees been scrupulously kept and published of the Shorthorn cattle, and more recently of the Hereford breed? Is it an illusion that these recently improved animals safely transmit their excellent qualities even when crossed with other breeds? have the Shorthorns, without good reason, been purchased at immense prices and exported to almost every quarter of the globe, a thousand guineas having been given for a bull? With greyhounds pedigrees have likewise been kept, and the names of such dogs, as Snowball, Major, &c., are as well known to coursers as those of Eclipse and Herod on the turf. Even with the Gamecock, pedigrees of famous strains were formerly kept, and extended back for a century. With pigs, the Yorkshire and Cumberland breeders ”preserve and print pedigrees;” and to show how such highly-bred animals are valued, I may mention that Mr. Brown, who won all the first prizes for small breeds at Birmingham in 1850, sold a young sow and boar of his breed to Lord Ducie for 43 guineas; the sow alone was afterwards sold to the Rev. F. Thursby for 65 guineas; who writes, ”She paid me very well, having sold her produce for 300l., and having now four breeding sows from her.” Hard cash paid down, over and over again, is an excellent test of inherited superiority. In fact, the whole art of breeding, from which such great results have been attained during the present century, depends on the inheritance of each small detail of structure. But inheritance is not certain; for if it were, the breeder’s art would be reduced to a certainty, and there would be little scope left for that wonderful skill and perseverance shown by the men who have left an enduring monument of their success in the present state of our domesticated animals.

For the rest of the chapter, he will go on to talk about humans, again with long lists of examples, and then mixing in domestic animals and plants again. A lot of these examples of heredity surely hold up, and others seem like anecdotes. Here and even more in the following chapters–with subtitles including ‘reversion to atavism’, ‘prepotency’ and ‘on the good effects of crossing, and the evil effects of close interbreeding’–Darwin is trying hard to make sense of heredity. Why are certain features heritable? Why do they sometimes go away in the offspring but reappear in later generations? Why are offspring sometimes more like one parent than the other? In chapter 27, he will present his ‘provisional hypthesis of pangenesis’.

Literature

Darwin. 1875. The variation of animals and plants under domestication.