Analyzing the Nucleotide Variations within the Expressed Sequence Tags of Loblolly Pine (Pinus taeda)

Kong, Fanming; Wang, Xiaolong

doi:10.4172/2329-9029.1000109

Cited by 1 publication

(1 citation statement)

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“…Similarly, in Pinus taeda , Kong et al . [ 128 ] reported that InDels were infrequent with only 0.67% frequency in targeted regions. The probable reason for this variance in the present investigation could be due to the highly divergent genotypes selected in the present study, indicating that InDels could be a useful marker for genetic analysis in Eucalyptus species.…”

Section: Resultsmentioning

confidence: 99%

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

Dasgupta

Dharanishanthi

Agarwal³

et al. 2015

PLoS ONE

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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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Section: Resultsmentioning

confidence: 99%