دورية أكاديمية
أعرض في EDS

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

التفاصيل البيبلوغرافية
العنوان: Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.
المؤلفون: Evans J; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA., Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR
المصدر: The Plant journal : for cell and molecular biology [Plant J] 2014 Sep; Vol. 79 (6), pp. 993-1008. Date of Electronic Publication: 2014 Aug 11.
نوع المنشور: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology Country of Publication: England NLM ID: 9207397 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-313X (Electronic) Linking ISSN: 09607412 NLM ISO Abbreviation: Plant J Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford : Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology, c1991-
مواضيع طبية MeSH: Genetic Variation*, DNA Copy Number Variations/*genetics , Exome/*genetics , Genome, Plant/*genetics , Panicum/*genetics, Alleles ; Base Sequence ; Ecotype ; Genotype ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Polyploidy ; Sequence Analysis, DNA
مستخلص: Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent approximately 50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next-generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8173 putative copy number variants and 3336 presence/absence variants. While the majority of the SNPs (84%) detected was bi-allelic, a substantial number was tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.
(© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)
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فهرسة مساهمة: Keywords: Panicum virgatum; copy number variant; exome; polyploidy; presence/absence variant; switchgrass
سلسلة جزيئية: BioProject PRJNA244250
تواريخ الأحداث: Date Created: 20140621 Date Completed: 20150527 Latest Revision: 20211021
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC4309430
DOI: 10.1111/tpj.12601
PMID: 24947485
قاعدة البيانات: MEDLINE
الوصف
تدمد:1365-313X
DOI:10.1111/tpj.12601