One of our members was curious about the genetics behind feathered shanks and stubs. A few of their Ameraucana have been hatching with stubs.
Stubs, as discussed in the following thread, are a disqualification.
http://ameraucanabreedersclub.org/forum/index.php/topic,4282.0.htmlI have been gathering information on the subjects. I’ll gradually update this thread as I gather additional info and then will summarize it.
Feathered shank research:
“Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet.”
“By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.”
https://pubmed.ncbi.nlm.nih.gov/32344429/Bortoluzzi C, Megens HJ, Bosse M, Derks MFL, Dibbits B, Laport K, Weigend S, Groenen MAM, Crooijmans RPMA. Parallel Genetic Origin of Foot Feathering in Birds. Mol Biol Evol. 2020 Sep 1;37(9):2465-2476. doi: 10.1093/molbev/msaa092. PMID: 32344429; PMCID: PMC7475038.
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“Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15.”
“Here, we present genetic evidence for the identification of candidate causal mutations at these loci.”
“The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located ∼200 kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. The feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds.”
https://pubmed.ncbi.nlm.nih.gov/32344431/Li J, Lee M, Davis BW, Lamichhaney S, Dorshorst BJ, Siegel PB, Andersson L. Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken. Mol Biol Evol. 2020 Sep 1;37(9):2477-2486. doi: 10.1093/molbev/msaa093. PMID: 32344431; PMCID: PMC7475036.
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“Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species.”
https://pubmed.ncbi.nlm.nih.gov/26977633/Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. Elife. 2016 Mar 15;5:e12115. doi: 10.7554/eLife.12115. PMID: 26977633; PMCID: PMC4805547.
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“By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways.”
https://pubmed.ncbi.nlm.nih.gov/32344429/Bortoluzzi C, Megens HJ, Bosse M, Derks MFL, Dibbits B, Laport K, Weigend S, Groenen MAM, Crooijmans RPMA. Parallel Genetic Origin of Foot Feathering in Birds. Mol Biol Evol. 2020 Sep 1;37(9):2465-2476. doi: 10.1093/molbev/msaa092. PMID: 32344429; PMCID: PMC7475038.
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“In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors, PITX1 and TBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation of PITX1 and TBX5 expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream of PITX1 and TBX5 in the partial transformation from HL to FL identity. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.”
https://pubmed.ncbi.nlm.nih.gov/31247188/Boer EF, Van Hollebeke HF, Park S, Infante CR, Menke DB, Shapiro MD. Pigeon foot feathering reveals conserved limb identity networks. Dev Biol. 2019 Oct 15;454(2):128-144. doi: 10.1016/j.ydbio.2019.06.015. Epub 2019 Jun 24. PMID: 31247188; PMCID: PMC6726567.
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“Two QTL with 1% genome-wide significant level for feathered feet trait, one 9-cM/2.80-Mb (48.0-57.0/13.40-16.20 Mb) region on GGA13, and another 12-cM/1.45-Mb (41.0-53.0 cM/11.37-12.82 Mb) region on GGA15 were identified.”
“A single nucleotide substitution, g.12465322T>G on chromosome 15, located on the downstream of the TBX5 gene, was strongly associated with fully feathered-leg. A second genomic region on chromosome 12, which contains two Wnt genes, was also associated with intermediate feathered-leg.”
“Two dominant genes at separate loci when presented together produce the heavy feathered-legs of the Cochin, Sultan, Belgian d’Uccle Bantam and Botted Bantam breeds (Somes 1990). Either of these genes will result in the weak feathered-leg common to Langshan, Faverolles, and Breda breeds. The slightly heavier feathered-leg observed in Brahma and Silkie breeds may be due to one of these two loci (Dunn & Jull 1927; Warren 1933), or both of them with a different allele at one locus in other lines (Punnett & Bailey 1918; Dunn & Jull 1927). The Pavloff feathering was suggested to be due to a recessive gene. The gene symbols Pti-1, Pti-2 and pti-3 for ptilopody were assigned to these loci (Somes 1990). Linkage mapping has shown that only one chromosome region (15.3Mb in chromosome 13) is significantly associated with feathered-leg in the Silkie (Dorshorst et al., 2010). Compared with the report of Dunn and Jull (1927), this region should be either Pti-1 or Pti-2. The other feathered-leg gene in the Silkie may be in a micro-chromosome, or may not exist in the Silkie line used in the study reported by Dorshorst et al. (2010). Sun et al. (2015) observed two chromosomal regions that were significantly associated with feathered-leg in Beijing-You chickens. The first region in chromosome 15 contained 5 genes including TBX3 and TBX5. The second region was consistent with the one reported by Dorshorst et al. (2010). The domestic pigeon is another avian species that has striking variation in feathered-leg phenotypes. By matings of different breeds of pigeons and expression studies, Domyan et al. (2016) reported that the decreased expression of paired-like homeodomain 1 (PITX1) and ectopic expression of T-box 5 (TBX5) were associated with feathered-leg. They also studied the expression of TBX5 and PITX1 in the hindlimb buds of feathered-leg Cochin and Silkie chickens. The ectopic expression of TBX5 was observed which may be responsible to either Pti-1 or Pti-2. Although there was no association between PITX1 expression and feathered-leg in chickens (Domyan et al., 2016), the position of PITX1 (15.7Mb in chromosome 13) suggests it may responsible for the candidate region reported by Dorshorst et al. (2010) and Sun et al. (2015). Thus, while the causal mutation affecting TBX5 expression (in chromosome 15) in feathered-leg chickens needs to be identified, the association between PITX1 and feathered-leg needs to be confirmed.”
https://pubmed.ncbi.nlm.nih.gov/26248982/Sun Y, Liu R, Zhao G, Zheng M, Sun Y, Yu X, Li P, Wen J. Genome-Wide Linkage Analysis Identifies Loci for Physical Appearance Traits in Chickens. G3 (Bethesda). 2015 Aug 6;5(10):2037-41. doi: 10.1534/g3.115.020883. PMID: 26248982; PMCID: PMC4592986.
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In a study completed by Somes (1992), crosses were done on lightly, heavily, and non-feather shanked chickens.
The Pti-1 locus was designated.
He identified two alleles on the Pti-1 locus.
-Pti-1L being the Langshan allele
-Pti-1B the Brahma allele.
The Brahma allele was shown to be dominant over the Langshan allele.
https://pubmed.ncbi.nlm.nih.gov/1624770/Somes RG Jr. Identifying the ptilopody (feathered shank) loci of the chicken. J Hered. 1992 May-Jun;83(3):230-4. doi: 10.1093/oxfordjournals.jhered.a111200. PMID: 1624770.
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A single nucleotide substitution, g.12465322T>G on chromosome 15, located on the downstream of the TBX5 gene, was strongly associated with fully feathered-leg. A second genomic region on chromosome 12, which contains two Wnt genes, was also associated with intermediate feathered-leg.
https://vtechworks.lib.vt.edu/bitstream/handle/10919/85397/Li_J_D_2017.pdf?isAllowed=y&sequence=1———
Stub research:
•sb-1
•sb-2
The two genes listed came from a study on Rhode Island Reds (Crawford, 1990). It was mentioned that these stub genes may be partially sex-limited, as stubs expression was more prominent in males. Other studies indicated a polygenic basis for the stubs trait (ie, multiple genes involved, acummulative effect on expression).
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