DArT markers for the rye genome - genetic diversity and mapping

Abstract

BackgroundImplementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers available for the species is limited. Diversity Arrays Technology (DArT) is a microarray-based method allowing for detection of DNA polymorphism at several thousand loci in a single assay without relying on DNA sequence information. The objective of this study was the development and application of Diversity Arrays technology for rye.ResultsUsing the PstI/TaqI method of complexity reduction we created a rye diversity panel from DNA of 16 rye varieties and 15 rye inbred lines, including parents of a mapping population consisting of 82 recombinant inbred lines. The usefulness of a wheat diversity panel for identification of DArT markers for rye was also demonstrated. We identified 1022 clones that were polymorphic in the genotyped ILs and varieties and 1965 clones that differentiated the parental lines L318 and L9 and segregated in the mapping population. Hierarchical clustering and ordination analysis were performed based on the 1022 DArT markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. Chromosomal location of 1872 DArT markers was determined using wheat-rye addition lines and 1818 DArT markers (among them 1181 unique, non-cosegregating) were placed on a genetic linkage map of the cross L318 × L9, providing an average density of one unique marker every 2.68 cM. This is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest.ConclusionThe Diversity Arrays Technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. The 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species.

DArT Markers Effectively Target Gene Space in the Rye Genome

“…In our opinion, there are two major reasons for the relatively high sequence redundancy of the rye DArT markers. Firstly, with its 1520 clones the rye genotyping array is one of the largest operational DArT arrays, and, apart from 768 clones rearrayed from the wheat genotyping array, the majority of the clones included in the array were not subjected to prescreening with respect to polymorphism detection efficiency nor the distinctness of observed segregation patterns (Bolibok-Bragoszewska et al, 2009). Secondly, for the sequencing we have chosen all the DArT markers, which segregated in at least one mapping population, even if multiple markers mapped to the same map position.…”

“…The first high-throughput genotyping technology was established for rye in 2009 with the development of a 1520-clone DArT genotyping panel (Bolibok-Bragoszewska et al, 2009). Since then, it was successfully applied for high density genetic map construction, both in rye and triticale (Bolibok-Bragoszewska et al, 2009; Milczarski et al, 2011; Tyrka et al, 2011, 2015), genome-wide germplasm characterization (Bolibok-Bragoszewska et al, 2014), QTL/gene mapping (Stojałowski et al, 2011; Miedaner et al, 2012; Myśków et al, 2012; Milczarski et al, 2016), and genomic selection (Wang et al, 2014, 2015; Schulthess et al, 2015). Following transcriptome sequencing a Rye5K SNP genotyping panel was developed and used for construction of high density transcript map (Haseneyer et al, 2011; Martis et al, 2013).…”

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…The DArTseq method is used to discriminate diverse species for population studies, genetic diversity studies, germplasm characterization (Cruz et al, 2013), association studies (Courtois et al, 2013;Phuong Phung et al, 2014), and genetic mapping (Ren et al, 2015). To date, DArTseq genotyping has also been used for genetic analysis in species genomes, including Sorghum bicolor (Mace et al, 2008), rye (Bolibok-Brągoszewska et al, 2009), Lesquerella and related species (Cruz et al, 2013), japonica rice (Courtois et al, 2013), watermelon (Ren et al, 2015), and pineapple (Kilian et al, 2016).…”

Genetic composition of interspecific potato somatic hybrids and autofused 4x plants evaluated by DArT and cytoplasmic DNA markers

“…DArT maps have been constructed for a variety of plant species, including rice (Jaccoud et al 2001), thale cress (Wittenberg et al 2005), wheat (Crossa et al 2007), barley (Li et al 2008), rye (Bolibok-Brągoszewska et al 2009) and others (Varshney et al 2010). DArT linkage maps of potato were created for Solanum   ×   michoacanum ( mch ) (Śliwka et al 2012a), Solanum ruiz - ceballosii (Śliwka et al 2012b) and a doubled haploid DM1–3 of Solanum phureja , for which a physical map is available, too (Sharma et al 2013).…”