Talk:Quantitative trait locus

Question

Do you have the steps and processes involved in QTL mapping? Thanks... please answer it in the most elementary way as I am quite new on this field.

Comment

I think that this sentence doesn't fit it, nothing has been said about growth hormone before. "In this way, we might find a gene involved in the production of growth hormone." can the author check it please?

Mendelian inheritance

I am quite confused with this statement: Unlike monogenic traits, polygenic traits do not follow patterns of Mendelian inheritance (qualitative traits)because in some websites it states the following:

These traits are controlled by multiple genes, each segregating according to Mendel's laws. These traits can also be affected by the environment to varying degrees.

Copyright © 1998. Phillip McClean from http://www.ndsu.edu/instruct/mcclean/plsc731/quant/quant1.htm

Please clarify. Thank you 00

The number of genes involved and the way they interact (with each other and with the environment) to elicit a phenotype is complex and appears non-Mendelian. Alleles of each of the genes that affect the trait segregate and assort independently according to Mendel's laws, but the trait -- the visible manifestation or phenotype -- is not observed to fall neatly into classes with ratios predicted by Mendel's laws, so the inheritance pattern of the trait appears non-Mendelian. Dr d12 04:18, 2 May 2007 (UTC)

History and confusion

The sentence "The QTL techniques were developed in the late 1980s and can be performed on inbred strains of any species" is very confused. In fact, this entire article seems to think that interval mapping is the same as QTL analysis, which is not the case (although this is the common usage today).

First off, "QTL techniques" were around well before the late 1980s. The first example I know of QTL analysis is from Thoday in the 60s and 70s (see Genetics and Analysis of Quantitative Traits by Lynch and Walsh) -- and there were even chromosomal association studies before that in Drosophila [actually, at 3am I discovered "The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris", Sax K, Genetics 140:201-206]. Between Thoday and Lander and Botstein (see later), QTL analysis got a lot more sophisticated, with more sophisticated marker genotyping methods. The problem with these methods is that while they could detect a QTL, they couldn't tell you where it was (as far as I know).

In the late 1980s Lander and Botstein proposed a new way to use dense markers (in their case, RFLPs, or restriction fragment length polymorphisms). In their method, pairs of flanking markers are used to estimate the likelihood that a QTL exists at every position in the genome. This is how the LOD maps are generated (the pretty images in this article).

So, some advice I have for this article:

• Add in some history of QTL analysis that includes Thoday and the many others after him and before Lander and Botstein.
• Have a better explanation of the statistics behind interval/LOD mapping (what this article calls "QTL mapping"). I.e., an LOD score is the log of the ratio between the maximum likelihood that the data fit a null hypothesis and the maximum likelihood that the data fit a QTL hypothesis, given the observed phenotypes and marker genotypes (see Lander and Botstein, "Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps", 1989).
• Fix the error that QTL mapping can only be performed in inbred strains. If this were the case we wouldn't have QTL maps for human traits (like osteoporosis, the example in the article). What's required is linkage disequilibrium between a QTL and a marker (since, if the traits were in Hardy-Weinberg, there would be no association between a marker genotype and a QTL genotype), which is maximized in inbred strains but can also be achieved in the wild, by examining drift-caused disequilibrium in families or expanding populations.

-- Josh 06:57, 7 March 2007 (UTC)

RE" Evolution and QTL: Needs to elaborate why this poses a problem. According the the Theory of Evolution, small changes are sufficient to create a small adaptation to an environment, which can then change further in small increments. So if an environment is in the process of changing such that an organism in it needs to be in the process of changing its color in order to adapt, QTL would provide a perfect mechanism as opposed to an either/or trait that could be recessive.

-- Zev Greenblatt

It is stated that QTL mapping is only done in inbred lines, but QTL mapping can be done in outbred lines as well, as long as the markers that are used for mapping are consistent within each line but differ between the two lines of interest. It can even be done between closely-related species (to identify QTL for species differences) with the caveat that the species need to still be able to mate and produce viable and fertile offspring.
(-- unsigned)

My complaint is that I would take issue with the claimed fact (reference 4) that one quoted sentence was in fact "Wright's Summarization"

When reading this page I find this section confusing or misleading (to a non-expert in Genetics (IE: most people)):

"In an early summary of the theory of evolution of continuous variation, Sewall Wright, a graduate student who trained under Castle, summarized contemporary thinking about the genetic basis of quantitative natural variation: "As genetic studies continued, ever smaller differences were found to mendelize, and any character, sufficiently investigated, turned out to be affected by many factors."[4] Wright and ..."

. It is not that "any character" is "affected by many factors", but rather what is quoted from the next line in the source referenced:

"A reaction from this viewpoint was led by CASTLE, who demonstrated the effectiveness of selection of small variations in carrying the average of a stock beyond the original limits of variation.

This effectiveness turned out to depend not so much on variability of the principal genes concerned as on residual heredity. As genetic studies continued, ever smaller differences were found to mendelize, and any character, sufficiently investigated, turned out to be affected by many factors. The work of NILSSON-EHLE, EAST, SHULL, and others established on a firm basis the multiple factor hypothesis in cases of apparent blending inheritance of quantitative variation. The work of MORGAN and his school securely identified Mendelian heredity with chromosomal behavior and made possible researches which further strengthened the view that the Mendelian mechanism is the general mechanism of heredity in sexually reproducing organisms.

The only exceptions so far discovered have been a few plastid characters of plants."

.My "confusion or misunderstanding" is that in Wright's 1930 book, the above attributed comment was not proven at the time (nor am I guessing it is currently proven) and it was not Wright's summarization (or last word, since it was written on page 3) upon the subject. It was simply one comment within the book; with the following lines showing both a greater refinement of what is proposed (by Wright) AND a counterexample that is not mentioned on this Wikipedia page.

Should I read that section and leave it thinking "... ever smaller differences were found to mendelize, and any character, sufficiently investigated, turned out to be affected by many factors ..." or is that commonly thought to be untrue (then, and now). Would I be better educated to think " ... (there is) multiple factor hypothesis in cases of apparent blending inheritance of quantitative variation ... " (IE: the contents of the line one after the one quoted from Wright's (85 year old) book.

Perhaps this section is too confusing (to me) for me to be able to formulate the question properly.

The note "that this section requires expansion" was placed by another but I agree with it. The "History" section MUST have some contents covering the past few decades, how can we be without. An expert can put a link to visit a particular site for more info on a particular subject covered on this page without having to rewrite it's content to a great extent. With difficult subjects a few Links is always better than no links or textual explanation. 96.48.222.120 (talk) 07:48, 8 April 2015 (UTC)

Merge Quantitative trait gene into Quantitative trait locus

Both major textbooks, Falconer & Mackay, 4th ed., and Lynch & Walsh, do not use the term "quantitative trait gene". Locus is a general term that can refer to a gene or any other genomic feature. "Fine mapping" can equally well apply to QTL mapping.

In my MSc course on quantitative genetics (possibly the only full course on the subject) at Edinburgh Uni (where much of this theory was developed), I did not come across the term. It does seem to be used by at least one academic, namely any one or several of Z-B. Zeng, C. J. Basten, R. Doerge, B. Yandell and I. Hoeschele [1]. - Samsara _contrib ^talk 12:53, 11 February 2006 (UTC)

I would suggest to delete it entierly, and just explain the term when needed at spots where it is used. If as all, it is more used in molecular genetics to indicates a specific gene that contributes to a quantitative trait determined by many genes. If not delete, to quantitative genetics --KimvdLinde 15:45, 11 February 2006 (UTC)

I've made that change. I've also suggested merging polygenic inheritance into quantitative trait locus - any thoughts on that? - Samsara _contrib ^talk 08:54, 15 February 2006 (UTC)

I do not agree with merging polygenic inheritance with quantitative trait locus as the first one deserves its own page with a lot more text than it has now - though, one will have to write that. 08:26 (CET) 2006-10-27

I also believe polygenic inheritance deserves its own article as it is fundamentally different from quantitative trait loci. I have added a brief overview to polygenic inheritance and have also redirected polygenic to that page. Raetzsch 05:50, 15 November 2006 (UTC)

Suggested merges

I am suggesting to merge both candidate gene and polygenic inheritance into this article, since

1. neither article goes beyond the remit of a dictionary entry
2. the candidate gene approach is an integral and exclusive part to trait mapping exercises, of which QTL mapping is the more general and powerful version
3. it is intellectually more elegant and leads to a better understanding to accommodate polygenic inheritance within a quantitative/discrete/threshold trait framework (oh dear, this one may be controversial...)

Your thoughts? - Samsara _contrib ^talk 18:36, 15 February 2006 (UTC)

Candidate gene approach can be the same as QTL, but can leave QTL's out of the picture as well. So, leave than one out. polygenic inheritance and Quantitatve trait gene should come here. --KimvdLinde 18:43, 15 February 2006 (UTC)

Several different methods, including chipa assays, LD mapping, QTL, and standard molecular population genetics can all use a candidate gene approach. I don not think it is in any way synonymous with QTL mapping. Understanding polygenic inheritance is clearly important for an appreciation of QTL mapping, but it is more general and shouuld not be merged here. Rather, polygenic inheritance should be merged with the article on Quantitative Genetics.

Rename article

After several merges, this article is no longer exclusively about QTLs. Rather, it includes all aspects of quantitative inheritance, including QTLs. Thus, I believe a better name for this article would be "Quantitative inheritance" or "Quantitative traits." QTL could then redirect to here. - Raetzsch 17:47, 10 December 2006 (UTC)

Faulty redirection of "polygenetic" - Please fix

This page is the destination of redirection for the word "polygenetic" for wiki links of that word from other articles, which use the word in its common English usage of "origin from more than one source" and which have no association with genetics. Please fix this redirection to avoid such pages coming to this page in error. I do not know enough about genetics to be confident enough to fix it myself (e.g. I'm not sure if a redirection from "polygenic" rather than "polygenetic" was the intention). GeoWriter 14:33, 1 August 2007 (UTC)

Intelligence

The comments on "Intelligence" should be removed. The definition of "Intelligence" has nothing to do with "Quantitative Trait Locus". I'm sure a separate article on the "Genetics of Intelligence" would be of great interest. —Preceding unsigned comment added by 24.60.239.250 (talk) 23:58, 19 October 2007 (UTC)

The article simply says that "some authors include intelligence" as a multifactorial trait, and then explains the definitional problems in doing so. The statements are cited with credible sources. It doesn't declare anything about intelligence to be fact in relation to QTL. Where is the problem? Ward3001 01:45, 20 October 2007 (UTC)

If you're serious about it, you can look up the work of Robert Plomin on the heritability of intelligence - or you can read any one of the many books by Deary, Jensen, Eysenck, Brody, or Carroll. —Preceding unsigned comment added by 24.60.239.250 (talk) 21:19, 21 October 2007 (UTC)

I've read those authors, but I don't think you get my point. You say that the "comments on 'Intelligence' should be removed", yet the comments do not express a point of view, they are not unverified, and they are not original research. The comments just state that "some authors include intelligence" within the concept of QTL without stating that intelligence should or should not be included. I don't see a problem. Why should the comments be removed? Ward3001 21:46, 21 October 2007 (UTC)

I agree distinctly with the comments about removing commentary on intelligence, mostly from a structure/authoring standpoint. The section is about "Multifactorial traits in general," and describes continuous traits well with some examples. That seems to be the purpose of the section. The comments on intelligence, as they stand are really about whether intelligence is a continuous trait, something great for an article discussing intelligence, but certainly out of place in a paragraph whose point is to explain the concept of a continuous trait rather than debate the origins of intelligence and the strength of scientists' arguments about them. 205.209.73.247 (talk) 17:31, 6 June 2008 (UTC)

Hip dysplasia

I added a link to Hip dysplasia (human). There is no page for "congenital dislocation", but the subject is covered on the page I linked. In the long run you might want to consider taking that out of the "congenital" list.--Lisa4edit (talk) 15:20, 25 April 2008 (UTC)

This sentence is confusing: If n is the number of involved loci, then the coefficients of the binomial expansion of (a + b)2n will give the frequency of distribution of all n allele combinations. 71.161.126.67 (talk) 11:17, 16 August 2011 (UTC)Chuck

Citations list useful for updating this article

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Locus or Loci

The difference seems important between Locus and Loci. One is singular and the other one is plural. Quantitative trait locus would mean that there is only one region contributing to the quantitative aspect of a trait. In the case of a single locus, wouldn't it be a Mendelian inherited trait?

For QTL studies, we are generally interested in knowing the outlier loci; the ones loci that contains genetic markers (such as SNPs, microsatellites, etc.), contributing the most to determine the variation of a phenotype.

"Quantitative trait loci (QTL): regions of the genome that contribute to differences in phenotypic traits" Source: Hendry, A. P. 2016. Eco-evolutionary Dynamics. Princeton University Press. — Preceding unsigned comment added by Beausoleilmo (talk • contribs) 17:33, 30 November 2016 (UTC)