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.

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

“…Additionally, the barley kit has since been used to identify a mutation in the gene HvPHYTOCHROME C which is involved in flowering time, an important agronomic trait (Pankin et al, 2014). Exome sequencing has also been used to analyse variation in 94 eucalyptus genes related to wood properties, identifying 5905 SNPs (Dasgupta et al, 2015). Finally, exome sequencing has helped detect 1 395 501 SNPs in switchgrass (Evans et al, 2014), 97 075 SNPs in Picea mariana (Pavy et al, 2016) and 129 156 sequence variants in potato (Uitdewilligen et al, 2013).…”

Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

“…Exome capture followed by resequencing proved efficient for the highly heterozygous and fully sequenced poplar (Zhou & Holliday ) and eucalypt genomes (Dasgupta et al . ), as well as for large genomes such as the polyploid wheat (Saintenac et al . ; Winfield et al .…”

“…The targeted regions are sequenced, thus reducing the sequencing cost and enabling to reach the high coverage depth of targets needed for the detection of high-confidence SNPs. Exome capture followed by resequencing proved efficient for the highly heterozygous and fully sequenced poplar (Zhou & Holliday 2012) and eucalypt genomes (Dasgupta et al 2015), as well as for large genomes such as the polyploid wheat (Saintenac et al 2011;Winfield et al 2012), the polyploid switchgrass (Evans et al 2014) and loblolly pine (Neves et al 2013). It has been applied as a high-throughput and cost-effective method to identify polymorphisms as well as genome-wide mutations in EMS mutant populations for species with complex genomes (Henry et al 2014).…”

Progress in plant genome sequencing: research directions

“…Разработаны методики анализа целевых геномных об ластей, связанных с агрономически важными признаками, для выявления разнообразия ДНКпоследовательностей кукурузы (Muraya et al, 2015), рапса (Clarke et al, 2013;Schiessl et al, 2014), хлопка (Salmon et et al, 2012) и ма ниоки (Pootakham et al, 2014). Кроме того, целевое обога щение последовательностей и повторное секвенирование проведены для нескольких видов деревьев, а именно ла данной сосны, черного тополя и эвкалипта, с целью вы явления полиморфизмов для построения генетической карты (Neves et al, 2013(Neves et al, , 2014, генотипирования (Zhou et al, 2012), а также разработки маркеров, ассоциированных с ксилогенезом (Dasgupta et al, 2015).…”