ArticlePloS one2015
Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 36 citations in OpenAlex.
- Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Identification of induced mutations in hexaploid wheat genome using exome capture assay.PloS one · 2018Article
- Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway.Scientific reports · 2017Article
- Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application.Plant biotechnology journal · 2017Review
- From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement.Frontiers in plant science · 2017Review
- Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis.Molecular biology reports · 2016Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- Current and new approaches in GMO detection: challenges and solutions.BioMed research international · 2015Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.