DOI: 10.5061/dryad.qbzkh18qt
title: Data from: Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation

description: Members of the genus Clivia show considerable variation in flower
 pigmentation and morphology. Such variation is effected by mutations that
 emerge in candidate flower development genes over time. Besides population
 history, mutations can further illuminate the effects of demographic
 events in populations in addition to population genetic parameters
 including selection, recombination, and linkage disequilibrium (LD). The
 current study aimed to find sequence variants in two anthocyanin
 biosynthetic genes (DFR and bHLH) of Clivia miniata and use the data to
 assess population genetic factors from a random collection of orange/red-
 and yellow-flowered specimens. Overall, average nucleotide diversity in
 the two anthocyanic genes was moderate (π = 0.00646), whereas haplotypes
 differed significantly (Hd ≥ 0.9). Gene evolution was seemingly driven by
 mutations (CmiDFR) or recombination (CmibHLH001). LD decayed swiftly
 within the analyzed gene regions and supported the feasibility of
 assessing trait-variant associations via the association/linkage mapping
 approach. In the end, most associations were found to be spurious, but one
 haplotype in CmibHLH001 showed a promising correlation to the orange/red
 flower phenotype in Clivia specimens. In all, the present study is the
 first to measure gene-level diversity in C. miniata – data that had never
 been reported so far. Further, the study also identified allelic and
 haplotypic variants that may be beneficial in future association genetic
 studies of Clivia. Such studies, however, consider large diverse
 populations to control for statistical bias intrinsic to the analysis of
 small datasets.
description: Plants were randomly sourced from a private collector's pool
 as well as landscaped gardens of a university campus. After RNA isolation
 and cDNA synthesis, regions of two pigmentation-related genes,
 <em>DFR</em> and an ortholog of <em>TRANSPARENT
 TESTA8</em>, were PCR amplified and sequenced. The generated
 sequences were manually checked, edited and used to phase haplotypes using
 PHASE algorithms in the software DnaSP v5. Haplotype sequences were then
 used to calculate various population genetic parameters as well as to test
 for the possible correlation between the identified sequence variants and
 flower colour through case/control association tests. 
description: # Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.)
 reveal evidence of selection and possible association with flower
 pigmentation
 [https://doi.org/10.5061/dryad.qbzkh18qt](https://doi.org/10.5061/dryad.qbzkh18qt) Haplotype sequences of *CmiDFR* and *CmibHLH001*, which are two key pigmentation genes in *Clivia miniata*. ## Description of the data and file structure The uploaded FASTA files comprise phased haplotype sequences from two pigmentation genes of *Clivia miniata*, *CmiDFR* and *CmibHLH001*. For each gene, sequence identifiers show the name of the gene, the sample name and annotation of the sample's flower colour. Also, each individual has two phased haplotypes, corresponding to the two alleles at the locus. ## Sharing/Access information Not applicable. ## Code/Software Not applicable.