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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: Red and yellow parrot feathers
Date: Sun, 3 Nov 2024 15:38:54 -0600
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On 11/3/2024 12:13 PM, John Harshman wrote:
> On 11/3/24 9:49 AM, RonO wrote:
>> On 11/3/2024 10:07 AM, John Harshman wrote:
>>> On 11/3/24 6:13 AM, RonO wrote:
>>>> https://www.science.org/content/article/why-are-parrots-so-colorful- 
>>>> study-points-simple-chemical-tweak
>>>>
>>>> There is a link to the research article in this news piece, but it 
>>>> may not be open access.  It is a pretty amazing molecular genetic 
>>>> analysis coming out of an ecology and evolution group of 
>>>> researchers.  They utilized genomic sequence, long read RNA Seq, 
>>>> single cell RNA Seq, and regulatory sequences involved in gene 
>>>> expression in feather cells.
>>>>
>>>> They identified the causative gene for turning red feathers yellow, 
>>>> and the possible causative mutation that is segregating in one 
>>>> species that is responsible for the recessive red feather 
>>>> expression.  The difference in expression levels for the gene are 
>>>> not that great, but there is a larger difference in single cell 
>>>> types. The enzyme is expressed in all cells, but has higher 
>>>> expression in the yellow feathers.  This increase in expression is 
>>>> enough to convert enough red pigment to yellow to make yellow feathers.
>>>>
>>>> The only issue that I see in this paper is that they may not have 
>>>> the causative mutation.  They mapped the causative gene because 
>>>> there were 3 SNP (single nucleotide polymorphisms) found to be 
>>>> significant.  They mapped to possibly a small region of the genome 
>>>> flanking the ALDH3A2 gene, but two of the SNPs were on one contig 
>>>> and 1 SNP was on another containing the gene.  This means that there 
>>>> are issues with not having continuous sequence in this region.  It 
>>>> could be repetitive sequence or issues with genome assembly.  What 
>>>> they needed to do was long read genomic sequencing of the region to 
>>>> obtain the continuous sequence in order to determine if they were 
>>>> dealing with something like a retroviral insertion or some other 
>>>> assembly issue.  The causative mutation may exist in the missing 
>>>> sequence between the two contigs.
>>>>
>>>> In my own experience we have the recessive white allele at the C 
>>>> locus in chickens.  This mutation turns out to be due to a 
>>>> retroviral insertion in an intron of the Tyrosinase gene that causes 
>>>> differential splicing in epidermal cells, but normal splicing in 
>>>> other tissues. When you assemble a genome out of short reads using a 
>>>> reference genome if the reference genome (in our case it was Red 
>>>> Junglefowl that did not have recessive white) you get two contigs 
>>>> cleanly separated from each other with the retroviral insertion 
>>>> sequence missing.  These researchers may be having issues with 
>>>> something similar.
>>>
>>> Do you know what causes the defective splicing in epidermal cells?
>>
>> They do not know the cause.  For some reason the retroviral sequence 
>> continues to be successfully spliced in certain tissues, but for some 
>> cell types like epidermal cells there is a mess up and incorrect 
>> splicing occurs so that a functional tyrosinase transcript is not 
>> produced.  It is the reason why the early protein work on recessive 
>> white found functional tyrosinase expressed in recessive white birds. 
>> That is the reason that recessive white was a black eyed white. 
>> Tyrosinase was still produced in the retina, but it wasn't produced in 
>> the feathers or leg scutes.  Tyrosinase is produced in the dermis.  
>> That is why the normal junglefowl dermal pigmentation of the shank can 
>> be express in white feathered breeds like the French Bresse breed of 
>> chickens and recessive white Silkie that has pigmented dermal and 
>> internal tissue pigmentation.  Silkies have black muscles, connective 
>> tissue and bones.
>>
>> The retroviral insertion affects splicing in a tissue specific manner.
>>
>> https://www.ambresse.com/french-bresse- 
>> chicken.html#:~:text=Bresse%20growth%20rate%20outstrips%20the,higher%20prices%20in%20the%20marketplace.
>>
>> Ron Okimoto
>>>
>>
> Perhaps the mutation introduces a binding site for some transcription 
> factor or regulatory RNA that's expressed only in epidermal cells, and 
> this happens to interfere with splicing?
> 

My take is that it will eventually be figured out because it is an 
unusually regulated mutation.  Something is interferring in epidermal 
cells, and it should be some type of tissue specific regulation.  The 
crazy thing is that it might have something to do with temperature 
sensitvity like a reverse of siamese cats tyrosinase (active enzyme is 
only produced at below body temperature in affected cats).  In this case 
recessive white chicks can hatch with black down for some chicks, so the 
correct splicing can occur when the skin is 37 degrees C, but not for 
all cases.  Most of the time the down lacks black pigment.  The black 
downed chicks feather out white.  The same feather folicles that 
produced black down before hatch produce white chick, juvenile and adult 
feathers.

Ron Okimoto