Dataset Information

Transcriptome-facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Moraceae).

ABSTRACT: PREMISE OF THE STUDY:Single-nucleotide polymorphism (SNP) primers were developed for a native North American desert fig, Ficus petiolaris (Moraceae), to provide markers for population genetic studies designed to quantify patterns of gene flow across a complex landscape. METHODS AND RESULTS:Transcriptome sequencing and bioinformatic protocols were implemented to discover SNPs in single-copy protein-coding genes. Multiplexes of 30 nuclear and 24 organellar (chloroplast and mitochondrial) SNPs were selected for primer development and genotyping on the Sequenom MASSArray System. Of these 54 loci, 49 reliably amplified across a panel of 96 F. petiolaris individuals. CONCLUSIONS:This study has provided SNP primers that can be applied in future studies investigating population genetics of F. petiolaris and its coevolution with associated pollinating and nonpollinating fig wasps.

SUBMITTER: Davis NG

PROVIDER: S-EPMC4504724 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Transcriptome-facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Moraceae).

Davis Nicholas G NG Houston Derek D DD Nason John D JD

Applications in plant sciences 20150604 7

<h4>Premise of the study</h4>Single-nucleotide polymorphism (SNP) primers were developed for a native North American desert fig, Ficus petiolaris (Moraceae), to provide markers for population genetic studies designed to quantify patterns of gene flow across a complex landscape.<h4>Methods and results</h4>Transcriptome sequencing and bioinformatic protocols were implemented to discover SNPs in single-copy protein-coding genes. Multiplexes of 30 nuclear and 24 organellar (chloroplast and mitochond ...[more]

PMID: 26191464

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Project description:BackgroundColor directly affects fruit quality and consumer preference. In fig syconia, the female flower tissue is contained in a receptacle. Anthocyanin pigmentation of this tissue and the peel differs temporally and spatially. A transcriptome study was carried out to elucidate key genes and transcription factors regulating differences in fig coloring.ResultsAnthocyanins in the female flower tissue were identified mainly as pelargonidin-3-glucoside and cyanidin-3-rutinoside; in the peel, the major anthocyanins were cyanidin 3-O-glucoside and cyanidin-3-rutinoside. Anthocyanin content was significantly higher in the female flower tissue vs. peel before fig ripening, whereas at ripening, the anthocyanin content in the peel was 5.39 times higher than that in the female flower tissue. Light-deprivation treatment strongly inhibited peel, but not female flower tissue, anthocyanin pigmentation. RNA-Seq revealed 522 differentially expressed genes (recruited with criteria log2 ≥ 2 and P < 0.05) at fig ripening, with 50 upregulated and 472 downregulated genes in the female flower tissue. Light deprivation upregulated 1180 and downregulated 856 genes in the peel, and upregulated 909 and downregulated 817 genes in the female flower tissue. KEGG enrichment revealed significantly changed expression in the phenylpropanoid-biosynthesis and flavonoid-biosynthesis pathways in the peel, but not in the female flower tissue, with significant repression of FcCHS, FcCHI, FcF3H, FcF3'H, FcDFR and FcUFGT transcripts. Light deprivation led to differential expression of 71 and 80 transcription factor genes in the peel and female flower tissue, respectively. Yeast one-hybrid screen revealed that FcHY5 and FcMYB114 bind the promoter regions of FcCHS and FcDFR, respectively in the flavonoid-biosynthesis pathway.ConclusionsPhenylpropanoid- and flavonoid-biosynthesis pathways were differentially expressed spatially and temporally in the peel and female flower tissue of fig syconia; pathway expression in the peel was strongly regulated by light signal. Differentially expressed transcription factors were recruited as candidates to screen important expression regulators in the light-dependent and light-independent anthocyanin-synthesis pathway. Our study lays the groundwork for further elucidation of crucial players in fig pigmentation.

Dataset Information

Transcriptome-facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Moraceae).

Publications

Transcriptome-facilitated development of SNPs for the Sonoran Desert rock fig, Ficus petiolaris (Moraceae).

Similar Datasets

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