Gulbrun eller Gulsvart?

[bright_sara]

Sv: Gulbrun eller Gulsvart?

Okej, jag uttryckte mig nog lite fel och jag har fått intrycket av mina färgvänner i USA av att man vet att det är olika gener. Nu när jag själv kollade upp det närmare fann jag bara att man visste att det satt på två olika alleler. Men jag lägger ut en förfrågan i maillistan. Men sen har jag hört att man fått fram ny information i vår, ska kolla upp det! Den infom finns inte på nätet iaf.

 

[swebec]

Sv: Gulbrun eller Gulsvart?

Okej, jag uttryckte mig nog lite fel och jag har fått intrycket av mina färgvänner i USA av att man vet att det är olika gener. Nu när jag själv kollade upp det närmare fann jag bara att man visste att det satt på två olika alleler. Men jag lägger ut en förfrågan i maillistan. Men sen har jag hört att man fått fram ny information i vår, ska kolla upp det! Den infom finns inte på nätet iaf.

Spännande! Du kan väl skriva det du får fram här!

 

[bright_sara]

Sv: Gulbrun eller Gulsvart?

Michal jobbar på PET DNA i AZ och forskar just om bay vs. brown. Det verkar som att de kan erbjuda ett inofficiellt test, dvs. inga andra lab kan göra det för det är inte färdigt ännu.

"In every horse which we include in the study, we first run the
conventional Agouti test, before we run the seal brown test. So we
are actually talking about two tests.

Although some of the horses we get into our study have been already
tested for Agouti elsewhere, I find it necessary to retest them so
that I can be sure that we are comparing results produced in the same
lab, using the same hair sample. After all, we are developing a test which would distinguish between the bay 'A' and the brown 'At', so we need to know first if the horse is A/a or A/A in the regular test (we also discovered some horses which tested a/a, which means they must be genetically black, but looked brown probably because of sun bleaching).

That's a great question! Our study was designed to compare initially the Agouti gene between bright bays and obvious seal browns, which all tested A/a in the regular Agouti test (which is specififc to detect the recessive 'a').

We had to select A/a horses with obvious bay or brown phenotypes, and didn't include any light browns. The reason was to prevent any confusion due to a misclassified phenotype (such as a dark bay being mistaken for seal brown and vice versa).

I'd like to add that we tested the "At" marker in close to 100 seal
brown horses from several breeds, to achieve results which would be statistically and scientifically meaningful. These seal browns were compared to obvious bays (A/a), and also black (a/a) horses.
Practically all the seal browns carried the marker, while the bays
and blacks did not have it. If I remember correctly, there were two seal brown QH which didn't carry the marker, and one bay which did have it. Based on this I'm estimating that the test is at least 95% accurate (I prefer to overestimate the error, rather than underestimate it).

With these numbers of horses tested in the study, I feel confident at this point that our test is good enough to differentiate between A and At. Also, it should be possible now to look in light brown horses. IMO such horses would not have been appropriate to include in the study, where the purpose was to find a DNA marker that would clearly associate with the seal brown phenotype.

We are working through the samples from seal brown horses we received from you and others based on when they were received. How fast we can do it depends also on our funds. We have now over 150 horses involved (including browns, and clear bright A/a bays), and practically all of the expenses are paid from my own pocket. Because the current test seems to have about 5% false negative results, I am working very hard
to get more information about the DNA structure of the Agouti gene, which is necessary if we want to develop a better test. Therefore I do not run the test we have now routinely on every horse which is in the study, but rather save the funds for the new test. Eventually, every horse enrolled in this study will be tested, and I'll let the owners know.

Thank you for bringing this up!

Michal Prochazka, MD
www.petdnaservicesaz.com"

 

[bright_sara]

Sv: Gulbrun eller Gulsvart?

"As I mentioned before, we developed a DNA test for the seal brown color which appears at least 95% accurate.

We are just starting to offer this test publicly as a service, and I
am planning to put a page on our website with more information. The introductory cost is $40 per one horse.

Everyone who has contributed samples to our study will get info about the results for their horses, but it just will take some time to get caught up.

So if anyone would like to get their horse(s) tested, you can go
ahead and send us samples. Please contact me if you have any
questions (the easiest is to email me through our website
www.petdnaservicesaz.com).

That is typically the case, to publish the findings in a peer-
reviewed scientific journal. We are planning to write it up and
submit for publication, but that will take a while."

 

[bright_sara]

Sv: Gulbrun eller Gulsvart?

"I just wanted to clarify a little bit better what I said about the
bay allele A. Here is the annotation of the official sequence of the
bay Agouti A allele, which was defined by the French group. I copied
this from the GenBank database, but left the actual sequence out,
because it's a couple of pages of letters.

So this is one of the sequences I am using as a guide to analyze the
Agouti gene in the seal browns. There are now more sequences
available for this gene/locus, which were made public at the
beginning of this year as a part of the horse genome sequencing
project.

I realize that this and the papers about the different color gene
mutations in horses are quite technical. If you have any questions,
please let me know and I can try to explain it.

Michal Prochazka


Here is the annotation for Agouti allele A

LOCUS AF288358 4994 bp DNA linear MAM
05-JUL-2001
DEFINITION Equus caballus agouti-signaling protein (ASIP) gene,
ASIP-A allele,
complete cds.
ACCESSION AF288358
VERSION AF288358.1 GI:14599451
KEYWORDS .
SOURCE Equus caballus (horse)
ORGANISM Equus caballus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
Mammalia; Eutheria; Laurasiatheria; Perissodactyla;
Equidae; Equus.
REFERENCE 1 (bases 1 to 4994)
AUTHORS Rieder,S., Taourit,S., Mariat,D., Langlois,B. and
Guerin,G.
TITLE Mutations in the agouti (ASIP), the extension (MC1R),
and the brown
(TYRP1) loci and their association to coat color
phenotypes in
horses (Equus caballus)
JOURNAL Mamm. Genome 12 (6), 450-455 (2001)
PUBMED 11353392
REFERENCE 2 (bases 1 to 4994)
AUTHORS Rieder,S., Taourit,S., Mariat,D., Langlois,B. and
Guerin,G.
TITLE Direct Submission
JOURNAL Submitted (19-JUL-2000) Laboratoire de Genetique
Biochimique et de
Cytogenetique, INRA, Centre de Recherche de Jouy, Jouy-
en-Josas
78350, France
FEATURES Location/Qualifiers
source 1..4994
/organism="Equus caballus"
/mol_type="genomic DNA"
/db_xref="taxon:9796"
/chromosome="22"
/map="22q15-q16"
gene <683..>4684
/gene="ASIP"
/allele="A"
mRNA join(<683..842,2144..2208,4508..>4684)
/gene="ASIP"
/allele="A"
/product="agouti-signaling protein"
CDS join(683..842,2144..2208,4508..4684)
/gene="ASIP"
/allele="A"
/codon_start=1
/product="agouti-signaling protein"
/protein_id="AAK70925.1"
/db_xref="GI:14599452"
/translation="MDVIHLFLATLLVSLCFLTAYSHLSPEEKPKDDR
SLRNNSSMNL

LDSPSVSIMALNKKSKKISRKEAEKKKRSSKKKASMTKVARPRLLQPAPCVATRDSCK
PPAPACCDPCASCQCRFFRSACSCRVLTRTC"
exon <683..842
/gene="ASIP"
/allele="A"
/number=1
exon 2144..2208
/gene="ASIP"
/allele="A"
/number=2
exon 4508..>4684
/gene="ASIP"
/allele="A"
/number=3
"

 

[bright_sara]

Sv: Gulbrun eller Gulsvart?

"My research is based on the assumption that the regular bay horses
have the normal ('default') Agouti allele, and the seal browns have
a change in the gene which is specific for the brown color.

Therefore, I started the study by comparing the Agouti gene sequence
in a small number of selected Aa horses: some are bright bays, and
some are seal browns. Any DNA difference I found between these two
colors are then tested in larger groups of seal browns, bays, and
also some blacks (used as a control group), to look for association
of the marker(s) with the color.

The marker I found is nearly unique to Aa seal browns (so far I have
about 50 horses tested, representing various breeds), whereas it's
practically absent in Aa bays (so far, I didn't find the marker in
the black = aa horses). Because this marker is nearly specific for
the brown horses (which are A/a in the conventional Agouti test),
then I am assuming that it is a marker for the At allele, whereas
the bay A/a horses carry the bay allele A (which doesn't have this
marker).

I am not really sure how else one would identify the bay allele A.
It must have the normal sequence of the Agouti gene, which is used as the default information when searching for any other alleles (It's my understanding that this is how the 'a' was identified, by comparing the sequence between bay and black horses).

Michal Prochazka"

 

[bright_sara]

Sv: Gulbrun eller Gulsvart?

Det sista inlägget är äldst, från den 21 july -07. Det första inlägget är från maj i år. Så de har kommit en bit på vägen.