A nonsense mutation inTFECis the likely cause of the recessive piebald phenotype in ball pythons (Python regius)

Abstract

Captive-bred ball pythons (<em>Python regius<em>) represent a powerful model system for studying the genetic basis of colour variation and Mendelian phenotypes in vertebrates. Although hundreds of Mendelian phenotypes (colour morphs) affecting colouration and patterning have been described for ball pythons, the genes causing these colour morphs remain unknown. Here, we used crowdsourcing of samples from commercial ball python breeders to investigate the genetic basis of a classic phenotype found in the pet trade, the piebald [characterized by dorsolateral patches of unpigmented (white) skin]. We used whole-genome sequencing of pooled samples followed by population genetic methods to delineate the genomic region containing the causal gene. We identified TFEC of the MIT-family of transcription factors as a candidate gene. Functional annotation of SNPs identified a nonsense mutation in TFEC, which we conclude is the likely causal variant for the piebald phenotype. Our work shows that ball python colour morphs have the potential to be an excellent model system for studying the genetic basis of pigment variation in vertebrates, and highlights how collaborations with commercial breeders can accelerate discoveries.

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

“…Future studies of ball python color morphs will be aided by our groundwork showing that ball python samples can be recruited effectively from pet owners, and that genetic analyses in ball python can be scaffolded using the genome of Burmese python as a reference. Similar groundwork has also been provided by a recent study characterizing the ball python morph known as Piebald [ 26 ]. We expect that a continued community-science approach will be effective in developing ball pythons into a resource for understanding the genetics of reptile coloration.…”

“…Many color morphs are heritable and show simple dominant or recessive patterns of inheritance. These inheritance patterns are consistent with single-gene causality, but only a single genetic variant associated with a ball python color morph (Piebald) has been identified to date [ 26 ]. Ball pythons therefore represent a tractable yet largely untapped resource for understanding the genetics of coloration in reptiles.…”

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

“…Wild ball pythons exhibit a mottled color pattern, consisting of brown-to-black melanin and red-to-yellow (non-melanin) pigments in the skin (Figure 1). Captive-bred ball pythons, by contrast, include many variants of the normal color pattern (Broghammer, 2019;Garcia-Elfring et al, 2020;Irizarry and Bryden, 2016;McCurley, 2005). These variants, referred to as 'color morphs', include animals having reduced melanin (e.g.…”

“…Color cell development has been characterized to some extent in fish (Huang et al, 2021;Kimura et al, 2014;Nüsslein-Volhard and Singh, 2017), and genes controlling the use of non-melanin pigments have been identified in a few species of fish and birds (Cooke et al, 2017;Gazda et al, 2020;Kwon et al, 2021;Lopes et al, 2016;Mundy et al, 2016;Toomey et al, 2017;Zhang et al, 2021). The genetics and development of non-mammalian color patterns is less well understood in other vertebrates, particularly in reptiles (although see Garcia-Elfring et al, 2020;Guo et al, 2021;McLean et al, 2017;Ullate-Agote et al, 2020).…”

“…Color cell development has been characterized to some extent in fish [16][17][18], and genes controlling the use of non-melanin pigments have been identified in a few species of fish and birds [19][20][21][22][23][24][25]. The genetics and development of non-mammalian color patterns are less well understood in other vertebrates, particularly in reptiles [although see [26][27][28][29].…”