title: Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing.
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.
authors.affiliation: Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore-641002, India.
authors.forename: Modhumita Ghosh
authors.initials: MG
authors.lastname: Dasgupta
authors.affiliation: Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore-641002, India.
authors.forename: Veeramuthu
authors.initials: V
authors.lastname: Dharanishanthi
authors.affiliation: Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India.
authors.forename: Ishangi
authors.initials: I
authors.lastname: Agarwal
authors.affiliation: Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany; Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America; N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia; Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia.
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Krutovsky
mesh_terms: D005052:Eucalyptus / Q000235:genetics*; D059472:Exome / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
chemical_list: D005819:Genetic Markers