Data from: Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation
Data files
Aug 22, 2024 version files 98.89 KB
Abstract
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.
README: 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
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.
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Code/Software
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Methods
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, DFR and an ortholog of TRANSPARENT TESTA8, 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.