DArT for high-throughput genotyping of Cassava (Manihot esculenta) and its wild relatives

Abstract

Understanding the distribution of genetic diversity within and among individuals, populations, species and gene pools is crucial for the efficient management of germplasm collections. Molecular markers are playing an increasing role in germplasm characterization, yet their broad application is limited by the availability of markers, the costs and the low throughput of existing technologies. This is particularly true for crops of resource-poor farmers such as cassava, Manihot esculenta. Here we report on the development of Diversity Arrays Technology (DArT) for cassava. DArT uses microarrays to detect DNA polymorphism at several hundred genomic loci in a single assay without relying on DNA sequence information. We tested three complexity reduction methods and selected the two that generated genomic representations with the largest frequency of polymorphic clones (PstI/TaqI: 14.6%, PstI/BstNI: 17.2%) to produce large genotyping arrays. Nearly 1,000 candidate polymorphic clones were detected on the two arrays. The performance of the PstI/TaqI array was validated by typing a group of 38 accessions, 24 of them in duplicate. The average call rate was 98.1%, and the scoring reproducibility was 99.8%. DArT markers displayed fairly high polymorphism information content (PIC) values and revealed genetic relationships among the samples consistent with the information available on these samples. Our study suggests that DArT offers advantages over current technologies in terms of cost and speed of marker discovery and analysis. It can therefore be used to genotype large germplasm collections.

Impact of Genomic Technologies on Chickpea Breeding Strategies

“…The number of polymorphic markers in intra-and inter-specific chickpea populations ranged from 35-496 and 210-906, respectively. Polymorphism information content (PIC) values obtained for chickpea were comparable to other crops, such as sorghum and cassava [61,62].…”

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

“…DArT generates genetic fingerprints by scoring the presence versus absence of DNA fragments in genomic representations generated from samples of genomic DNA. Hence, DArT was rapidly applied to a number of other plants and animals such as: apple, Arabidopsis thaliana, banana, barley, cassava, chickpea, coconut, eucalyptus, several fungal pathogens, lupin, pigeon pea, potato, quinoa, rice, ryegrass, sorghum, tomato, mouse, sheep and cattle (Jaccoud et al 2001;Lezar et al 2004;Wenzl et al 2004;Kilian et al 2005;Wittenberg et al 2005;Xia et al 2005;Yang et al 2006;Akbari et al 2006;www.diversityarrays.com). The other advantage of DArT is the speed of development in a new species.…”

“…DArT marker system has been developed as a technology for whole-genome profiling in barley (Wenzl et al 2004), cassava (Xia et al 2005), Arabidopsis thaliana (Wittenberg et al 2005), bread wheat (Akbari et al 2006), etc. As very few (∼10%) polymorphisms have been identified in cultivated pigeon pea lines using a limited number of SSR and DArT markers (Burns et al 2001;Yang et al 2006), an interspecific mapping population was developed by using pigeon pea (C. cajan) accession ICP 28 and ICPW 94 from a wild relative species of pigeon pea (C. scarabaeoides) to avail maximum polymorphism and to generate the first generation linkage map.…”

Development of DArT markers for a linkage map of flue-cured tobacco

“…A library was prepared from the amplification products as described previously [24]. The amplification reactions were dried at 37°C, washed with 70% ethanol, dissolved in DArT Spotter 2 spotting buffer, and then printed on polylysine-coated slides (Erie Scientific, Portsmouth, NH, USA) using a MicroGrid II arrayer (Biorobotics, Cambridge, UK).…”