These two chapters are rather technical, and focussed on the statistical details of estimation procedures. I would encourage you to not "get drowned in the details" but try to see the bigger picture and the biological implications. Much has happened in the past decade, and the estimation procedures that are described have, to some extent, been replaced by more modern and powerful methods, such as the "Animal Model".
Nevertheless, there are some general and interesting questions that should be discussed:
Chapter 18: Why are heritability estimates from full-sib analyses often higher than those from parent-offspring regressions? Which genetic factors are responsible for the higher heritability estimates obtained in full-sib analyses? Which procedures are preferrable: parent-offspring regression, half-sib analyses or full-sib analyses? Discuss and motivate!
Chapter 21: Which factors are responsible for genetic correlations between characters? How is it possible to explain the strong congruence between phenotypic and genetic correlations (Fig. 21.1) in a biologically meaningful way? How does "selection bias" influence the magnitude of genetic correlations (increasing or decreasing it)? Are there any a priori reasons to expect that genetic and phenotypic correlations should differ more for life-history traits than for morphological traits? If so, in what direction? Do we always expect trade-offs between life-history traits to be expressed as negative genetic correlations? Why? Why not?
Third meeting, Linneaus University 2010-11-04
ReplyDeleteQuestions:
We had some difficulties to separate pleiotropy from gametic phase disequilibrium. Is there really a clear cut line between these and how can you tell in a real situation witch one that affects a set of characters?
In the figure 21.1 page 640 there is several points that have there genetic correlation value less than zero. How can that be and what does that mean?
Good questions!
ReplyDelete1. Pleiotropy vs. gametic phase disequilibrium:
Pleiotropy means that it is the SAME gene which affects two different traits and causes a genetic correlation between them. Pleiotropy can be difficult (or impossible) to distinguish from physical linkage, that is, when two genes are sitting close to each other on the same chromosome.
In contrast, gametic phase disequilibrium can arise even without physical linkage, e. g. when two loci are located on different chromsomes and recombination is maximal (r= 0.5). Indeed, the word GAMETIC phase disequilibrium tells you that it is a form of disequilibrium that is present BEFORE recombination and at the gametic stage. Gametic phase disequilibrium will (unless it is built up every generation by either assortative mating, selection or both) decrease as a result of recombination.
There are several ways to distinguish between pleiotropy and gametic phase disequilibrium. I give two possibilities here:
1. Perform a QTL-analysis for two traits that are genetically correlated. If two QTL:s are found, that are physically separated from each other (either on different chromosomes or distantly from each other on the same chromosome), then the genetic correlation is due to gametic phase disequilibrium. In contrast, if both traits can be attributed to a single QTL or linkage group in the same chromosomal region, then the genetic correlation is EITHER due to physical linkage OR pleiotropy.
2. One can also bring in a population that is subject to natural selection or assortative mating in the field, in to the lab and remove both selection and assortative mating (e. g. randomly pollinate plants in a greenhouse). If you estimate the genetic correlation at outset, and then 10-20 generations later (after no selection and random mating), you would expect the genetic correlation to have become reduced or disappeared (because of recombination), if it was due to gametic phase disequilibrium. In contrast, genetic correlations due to pleiotropy are expected to be more stable and will not be affected, as recombination will (per definition) not alter pleiotropy, only linkage disequilibrium.
Regarding the question on p. 640:
ReplyDeleteA genetic correlation need not to be only positive (r > 0), it can often be negative (r < 0). In the example you refer to on p. 640, it happens that most genetic correlations are positive, but that need not necessarily to always be the case. My guess is that the genetic correlations on that page refer to morphological traits, and the positive correlations might mean that families which produce heavy offspring, also produce tall offspring, simply because genes which affect growth rate have pleiotropic effects on many different traits. Or put it in another way: you can predict the relative size of one trait in an organism by measuring another trait, simply because those which are large in one aspect are often large in another aspect as well. In humans, for instance, tall individuals are on average heavier than short individuals, simply because a tall body has a heavier skeleton, more muscle mass etc.