Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

Тип публикации: статья из журнала

Год издания: 2015

Идентификатор DOI: 10.1371/journal.pone.0116528

Ключевые слова: genomic DNA, genetic marker, Article, controlled study, DNA hybridization, DNA isolation, Eucalyptus, Eucalyptus camaldulensis, Eucalyptus grandis, Eucalyptus tereticornis, exome sequencing, gene sequence, genetic procedures, high throughput sequencing, indel mutation, nonhuman, plant gene, plant genome, plant tissue, quantitative trait locus, sequence alignment, sequence analysis, single nucleotide polymorphism, species comparison, target enrichment, exome, genetics, Genetic Markers, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide

Аннотация: The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family-based QTL and association analysis in Eucalyptus.

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Издание

Журнал: PLOS ONE

Выпуск журнала: Vol. 10, Is. 1

ISSN журнала: 19326203

Место издания: SAN FRANCISCO

Издатель: PUBLIC LIBRARY SCIENCE

Авторы

  • Dasgupta Modhumita Ghosh (Inst Forest Genet & Tree Breeding, Div Plant Biotechnol, Coimbatore 641002, Tamil Nadu, India)
  • Dharanishanthi Veeramuthu (Inst Forest Genet & Tree Breeding, Div Plant Biotechnol, Coimbatore 641002, Tamil Nadu, India)
  • Agarwal Ishangi (Genotyp Technol Private Ltd, Bangalore 560094, India)
  • Krutovsky Konstantin V. (Univ Gottingen, Dept Forest Genet, D-37077 Gottingen, Germany; Univ Gottingen, Busgen Inst, D-37077 Gottingen, Germany; Texas A&M Univ, Dept Ecosystem Sci & Management, College Stn, TX 77843 USA; Russian Acad Sci, NI Vavilov Inst Gen Genet, Moscow 119333, Russia)

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