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A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze.

التفاصيل البيبلوغرافية
العنوان: A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze.
المؤلفون: Silva PIT; Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil.; University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil., Silva-Junior OB; Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil., Resende LV; Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil., Sousa VA; Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA Florestas, PR, Colombo, Brazil., Aguiar AV; Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA Florestas, PR, Colombo, Brazil., Grattapaglia D; Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil.; University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil.; Graduate Program in Genomic Sciences, Universidade Católica de Brasília, Brasília, DF, Brazil.
المصدر: PloS one [PLoS One] 2020 Aug 31; Vol. 15 (8), pp. e0230404. Date of Electronic Publication: 2020 Aug 31 (Print Publication: 2020).
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Araucaria/*genetics, Brazil ; Genome, Plant/genetics ; Genomics/methods ; Genotype ; Microsatellite Repeats/genetics ; Polymorphism, Single Nucleotide/genetics ; Tracheophyta/genetics ; Transcriptome/genetics ; Trees/genetics
مستخلص: High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.
Competing Interests: The authors have declared that no competing interests exist.
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سلسلة جزيئية: figshare 10.6084/m9.figshare.11861712; 10.6084/m9.figshare.11861682; 10.6084/m9.figshare.11861754; 10.6084/m9.figshare.11861718
تواريخ الأحداث: Date Created: 20200901 Date Completed: 20200928 Latest Revision: 20231104
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC7458329
DOI: 10.1371/journal.pone.0230404
PMID: 32866150
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0230404