Pigeon foot feathering reveals conserved limb identity networks

Abstract

statementIn feather-footed pigeons, mutant alleles of PITX1 and TBX5 drive the partial redeployment of an evolutionarily conserved forelimb genetic program in the hindlimb. AbstractThe tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. 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. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conserved PITX1-and TBX5-regulated components of the limb identity program. 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.

Tbx4 function during hindlimb development reveals a novel mechanism to explain the origins of proximal limb defects

“…Pitx1 also has a Tbx4-independent input into the regulation of In our Tbx4 gene deletion/gene replacement assay, both Tbx4 and Tbx5 can rescue hindlimb formation equally well and a morphologically indistinguishable hindlimb is formed in each case, consistent with our previous observations that these genes have no role in determining forelimb or hindlimb morphologies in mouse (Duboc and Logan 2011b, Minguillon et al 2005, Minguillon et al 2009. Recently in an avian model, the pigeon, cis regulatory alleles mapping to Tbx5 (and Pitx1) have been mapped to loci associated with feathered feet which are believed to represent partial transformations from hindlimb to forelimb identity (Boer et al 2019, Domyan et al 2016. Whether this represents a difference between avians and mammals in how differences between forelimbs and hindlimb morphologies are established remains to be clarified.…”

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology

“…We used protein sequences of A. carolinensis and A. punctatus obtained from NCBI RefSeq to query our reference sequence for homologous proteins. Composite RNA-seq data were prepared by combining eight paired-end RNA-Seq libraries consisting of two libraries from a forelimb and a hindlimb at embryonic stage 7 108 , three libraries from brain, liver, and skin tissue of an adult female 109 (SRA accession number: DRA004457), and three libraries from central, nasal, and temporal regions of eye retina at embryonic stage 16.5. These RNA-seq reads were aligned to AnoSag2.0 using TopHat v2.1.1 110 with the option -- b2-very-sensitive 110 .…”

“…Likewise, composite RNA-Seq data were generated by combining data from 27 RNA-Seq libraries from embryonic (forelimbs, hindlimbs, and retina) and adult tissues (brain, skin, and liver). Embryonic limb (GEO accession GSE128151) and adult tissue RNA-seq data (DDBJ Sequence Read Archive accession DRA004457) were previously published 108,109 . Anole eye RNA-seq datasets were generated from tissues from Sanger Stage 16.5 embryos laid from wild-caught A. sagrei parents from Orlando, FL.…”

Comparative genome and transcriptome integration studies reveal the mechanism of pectoral muscle development and function in pigeons

“…Molecular breeding can accelerate the breeding process of meat pigeons. Most studies investigating quality traits using pigeon genomics have focused on the feather crown[8], feather color [9], and foot feathers [10,11]. Moreover, analyses of complex traits have mainly focused on competition ability [12].…”