DOI: 10.5061/dryad.18931zd9n
title: Data from: Expression of <em>SCARB1</em> in feather follicles is necessary but not sufficient for carotenoid-based feather pigmentation in Gouldian finches

description: Carotenoids play fundamental roles in avian ecology and evolution. Full
 expression of carotenoid-based plumage relies on key molecular mechanisms
 that regulate the uptake, processing, and deposition of dietary pigments
 into target tissues. The blue Gouldian finch (Erythrura gouldiae) variety
 is explained by an autosomal recessive locus that affects carotenoid
 colouration. Using whole-genome sequencing data and genetic mapping, we
 identified a splice-acceptor mutation in scavenger receptor B1 (SCARB1)
 that abolishes carotenoid-based pigmentation. Biochemical analyses
 revealed that blue individuals circulate extremely low concentrations of
 dietary carotenoids, confirming a genetic disruption of carotenoid uptake
 and transport in the gut. Through genotyping of the candidate causative
 mutation in carotenoid-containing and carotenoid-free mask feathers of a
 mosaic blue individual, we further demonstrate that somatic reversion of
 blue rescues SCARB1 function and locally restores carotenoid deposition in
 feathers. Finally, by comparing the transcriptomes of
 carotenoid-containing and carotenoid-free feather follicles from different
 plumage regions of wild-type birds, we show that SCARB1 expression alone
 is not sufficient to trigger carotenoid pigmentation. These findings
 reinforce the role of SCARB1 as a key facilitator of carotenoid uptake and
 transport in the gut, while also establishing its necessity for localized
 uptake of carotenoids to developing feather follicles.
description: #### GouldianPlex Assay Design and Genotypes **Associated manuscript:**
 Expression of *SCARB1* in feather follicles is necessary but not
 sufficient for carotenoid-based feather pigmentation in Gouldian finches
 **Authors:** Marques, CI *et al.* #### Data
 File: GouldianPlex_SCARB1-Design_and_Genotypes.xlsx This file encloses two
 Excel spreadsheet tabs with all the necessary information to replicate
 GouldianPlex analysis used for fine genetic mapping of
 "*blue*" *SCARB1* locus in Gouldian finches. These data are
 presented in Figure 1d of the corresponding manuscript. The file is
 formatted for use in Microsoft Excel. 1. iPlex_DesignSCARB1\ Sequenom
 MassARRAY™ Assay Design information. Details on primer sequences used to
 amplify 40 randomly selected loci in 60 Gouldian finch (*Erythrura
 gouldiae*) samples. 1. SNP_ID = Loci genomic coordinates in Gouldian finch
 reference genome (GCA_003676055.1) 2. 2nd-PCRP = Secondary PCR primer
 sequence 3. 1st-PCRP = Primary PCR primer sequence 4. AMP_LEN = Amplicon
 length 5. UP_CONF = Uniplex amplification score 6. MP_CONF = Multiplex
 amplification score 7. EP_SEQ = Extend Primer sequence 8. Tm(NN) = Extend
 primer melting temperature (calculated by Nearest Neighbour method) 9. GC
 = GC content of the extend primer 10. EP_DIR = MassEXTEND™ direction (F =
 Forward, R = Reverse) 11. EXT1_CALL = Genotype 1 (Analyte 1 as identified
 by mass peak 1 in MS analysis) 12. EXT2_CALL = Genotype 2 (Analyte 2 as
 identified by mass peak 2 in MS analysis). 2. iPlex_GenoSCARB1. Genotypes
 for the entire WGS dataset, comprising 11 *blue* birds and 49 wild-type
 birds (N=60). Failure in multiplex reactions resulted in 29 out of 40 SNPs
 being genotyped. 1. Sample_ID = Lab name attributed to Gouldian finch WGS
 samples 2. SNP_ID = Loci genomic coordinates in Gouldian finch reference
 genome (GCA_003676055.1) 3. GENO = Genotype 4. BC_Status = Base-call
 status (base-call confidence and curation, No-Alleles/Low Probability =
 Missing data). #### Data File: Gouldianfinch_GWPairwise_Relatedness.xlsx
 Output from NgsRelate v2. Related to Figure S1b. This file contains
 estimates of relatedness, inbreeding coefficients and other summary
 statistics for all pairs of Gouldian finches (N = 60 individuals; N = 1771
 pairs), inferred from low coverage NGS data by using genotype likelihoods.
 Output description 1. *Sample description and main coefficients:* 1.
 ID_a/ID_b = Individual ID 2. Group = Phenotypic category of the
 individuals 3. nSites = number of genomic sites considered in the analysis
 4. J9 to J1 = maximum likelihood (ML) estimates of the nine jacquard
 coefficients, where K0==J9; K1==J8; K2==J7 in absence of inbreeding 2.
 *Summary statistics calculated based on Jacquard coefficients:* 1. rab =
 pairwise relatedness 2. Fa = inbreeding coefficient of individual a 3. Fb
 = inbreeding coefficient of individual b 4. theta = kinship coefficient 5.
 2of3_IDB = Two-out-of-three Identical by Descent 6. F_diff_a_b =
 Inbreeding difference 7. loglh = the log-likelihood of the ML estimate 8.
 nIter = number of EM-algorithm iterations 9. coverage = fraction of
 genomic sites, with data available for both individuals, used for the
 Maximum Likelihood (ML) estimate 3. *Statistics based on a two-folded
 site-frequency-spectrum (2D-SFS)* 1. 2dsfs =  estimates as implemented in
 ANGSD software 2. R0 = Identity by State (IBS) ratio 3. R1 = Identity by
 Descent (IBD) proportion 4. KING = co-ancestry 5. 2dsfs_loglike = the
 log-likelihood of the 2dsfs estimate 6. 2dsfsf_niter = number of
 iterations for 2dsfs estimation Dataset DOI:
 [10.5061/dryad.18931zd9n](https://doi.org/10.5061/dryad.18931zd9n) ####