Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane

Abstract

Diversity Arrays Technology (DArT) provides whole genome profiling for hundreds to thousands of polymorphic markers in a single assay using a high-throughput microarray platform. The presented work aimed to establish DArT genotyping for the genetically challenging genome of sugarcane. Due to the genome complexity of this sugar-producing crop of high economic importance, an application of DArT genotyping to this species required extensive testing and optimization. As the method of genome complexity reduction determines the efficiency of polymorphism identification in DArT, various approaches and several methods were tested, in order to establish the most optimal. The sugarcane DArT markers generated with these established methods identified high genetic differentiation of sugarcane ancestral species from modern cultivars, in agreement with the data available for other types of molecular markers for this crop. The majority of sugarcane DArT markers segregated in a Mendelian fashion and were readily incorporated into the framework genetic map. As the DArT markers are sequence-ready genomic clones, we sequenced 384 clones and found that one-third of sequenced markers came from the transcribed portion of the sugarcane genome. The presented results further validate the potential of DArT technology in providing cost-effective genetic profiles for plants, irrespective of their genome complexity, for effective applications in molecularassisted breeding, diversity analysis or genetic identity testing. (Résumé d'auteur

Breeding of Sugarcane

“…With transcriptome studies, the abundance of microsatellite sequence ESTs allowed the emergence of EST-derived SSRs (EST-SSRs). New techniques using a high-throughput microarray platform, like DART (Diversity Arrays Technology), were implemented in sugarcane and can generate a final array comprising 5,000-7,000 polymorphic markers [28]. More recently, next-generation sequencing (NGS) technologies have been used for whole-genome sequencing to discover large numbers of single nucleotide polymorphisms (SNPs).…”

Comparative analysis of genetic variation in kava (Piper methysticum) assessed by SSR and DArT reveals zygotic foundation and clonal diversification

“…Diversity Array Technology (DArT) are dominant markers but are useful because they offer deep coverage of the genome and high effectiveness without the need for prior sequence information (Jaccoud et al 2001;Wenzl et al 2004), and they have been successfully used in polyploid species such as wheat (Akbari et al 2006), banana (Risterucci et al 2009), and sugarcane (Heller-Uszynska et al 2011). These two molecular markers may contribute to a better understanding of the genetic relationships among P. methysticum cultivars.…”

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

“…After printing, slides were processed as described by Sharma et al (2014) to construct a DArT array. The clones were constructed using PstI and TaqI digestions according to principles described at http://www.diversityarrays.com/ dart-application-microarray-process-complexity-reduction as described by Mace et al (2008) and Heller-Uszynska et al (2011). Sample complexity reduction for each Miscanthus accessions was performed with a combination of two restriction enzymes, a rare cutter (PstI) and a frequent cutter (TaqI), adaptor ligation and PCR amplification, essentially as reported by Wenzl et al (2004).…”