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DNA-based molecular markers are the most effective methods for developing desirable crop varieties in modern plant breeding. However, these markers have a limited use in plant breeding and their impact is insignificant. Developing them requires prior sequence information that is costly, especially for complex genome. Despite advances in sequencing technology, getting the full genome sequence of polyploidy species is still time-consuming and resource-intensive. This led to slow progress in the genetic improvement of these species using DNA-based molecular markers. Diversity Array Technology (DArT) which is a low-cost and quick-genotyping platform offers the opportunity to screen hundreds of highly polymorphic markers without genome sequence data. Because of their high level of diversity, DArT-based methods are popular among different crop genetic improvement programs. In polyploidy crop improvement, DArT markers are still useful, and exploiting their potential to the fullest is necessary. DArT markers can provide deep genetic diversity analysis, entire genome profiling, and high-density mapping of complex features needed for marker-based breeding. Therefore, molecular analyzes using DArT markers significantly contributed to the improvement of various crop species. The markers will prove useful in future crop breeding programs aimed at improving crop quality and yield. Understanding the concept and potential applications of DArT markers is essential for maximizing their potential. This review summarizes the concepts behind DArT markers and their potential future applications for improving crop genetics. [ABSTRACT FROM AUTHOR]

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11–36 and 12–3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed.

Key message: Using DArT analysis, we demonstrated that all Solanum × michoacanum (+) S. tuberosum somatic hybrids contained all parental chromosomes. However, from 13.9 to 29.6 % of the markers from both parents were lost in the hybrids. Abstract: Somatic hybrids are an interesting material for research of nucleus-cytoplasm interaction and sources of new nuclear and cytoplasmic combinations. Analyses of genomes of somatic hybrids are essential for studies on genome compatibility between species, its evolution and are important for their efficient exploitation. Diversity array technology (DArT) permits analysis of the composition of nuclear DNA of somatic hybrids. The nuclear genome compositions of 97 Solanum × michoacanum (+) S. tuberosum [ mch (+) tbr] somatic hybrids from five fusion combinations and 11 autofused 4 x mch were analyzed for the first time based on DArT markers. Out of 5358 DArT markers generated in a single assay, greater than 2000 markers were polymorphic between parents, of which more than 1500 have a known chromosomal location on potato genetic or physical map. DArT markers were distributed along the entire length of 12 chromosomes. We noticed elimination of markers of wild and tbr fusion components. The nuclear genome of individual somatic hybrids was diversified. Mch is a source of resistance to Phytophthora infestans. From 97 mch (+) tbr somatic hybrids, two hybrids and all 11 autofused 4 x mch were resistant to P. infestans. The analysis of the structure of particular hybrids' chromosomes indicated the presence of markers from both parental genomes as well as missing markers spread along the full length of the chromosome. Markers specific to chloroplast DNA and mitochondrial DNA were used for analysis of changes within the organellar genomes of somatic hybrids. Random and non-random segregations of organellar DNA were noted. [ABSTRACT FROM AUTHOR]

Background Ancestral wheat relatives are important sources of genetic diversity for the introduction of novel traits for the improvement of modern bread wheat. In this study the aim was to assess the susceptibility of 34 accessions of the diploid wheat Triticum monococcum (A genome) to Gaeumannomyces graminis var. tritici, the causal agent of take-all disease. The second aim was to explore the susceptibility of tetraploid wheat (T. durum) and the B genome progenitor species Aegilops speltoides to Ggt. Results Field trials, conducted over 5 years, identified seven T. monococcum accessions with a good level of resistance to take-all when exposed to natural inoculum under UK field conditions. All other accessions were highly susceptible or did not exhibit a consistent phenotype across years. DArT marker genotyping revealed that whole genome diversity was not closely related to resistance to take-all within T. monococcum, suggesting that multiple genetic sources of resistance may exist within the species. In contrast the tetraploid wheat cultivars and Ae. speltoides were all highly susceptible to the disease, including those with known elevated levels of benzoxazinoids. Conclusions The diploid wheat species T. monococcum may provide a genetic source of resistance to takeall disease that could be utilised to improve the performance of T. aestivum in high disease risk situations. This represents an extremely valuable resource to achieve economic and sustainable genetic control of this root disease. [ABSTRACT FROM AUTHOR]

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an Fg recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genie markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good ge-nome coverage and were associated with previously identified genie and AFLP markers linked with quanti-tative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies. [ABSTRACT FROM AUTHOR]

A Diversity Arrays Technology (DArT) marker system was applied for the first time to common beans ( Phaseolus vulgaris L.) and tested on 89 accessions from the IAC and CIAT common bean breeding programs, as well as on landraces from the FAO collection. Seven frequently used restriction endonucleases were tested in combination with a rare-cutting restriction enzyme, PstI, to evaluate their suitability for DArT technology. Two restriction enzyme combinations ( PstI/ BstNI and PstI/ TaqI) were selected to evaluate polymorphisms and PstI/ BstNI, which yielded the most polymorphisms, was used to construct the final array. Genotyping was done by labelling the genomic representations with the fluorescent nucleotides cy3-dUTP and cy5-dUTP. The poly-linker fragment was labelled with 6-FAM and used as a control treatment and standard to determine the amount of DNA spotted on the array for each clone. DArTsoft version 7.3 software was used to analyse, identify and score polymorphic markers. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 97.1% and a scoring reproducibility of at least 99.9%. A total of 2,501 polymorphic markers were found. Neighbour-joining distance matrices were used to create dispersion graphs that distinguished the two major gene pools of common beans and classified the accessions as either Andean or Mesoamerican. A principal coordinate analysis of the DArT marker results explained 82% of the total data variation. These results show that the DArT platform was accurate for studying the genetic diversity of the common bean and efficient for the large-scale detection of polymorphisms. These properties make marker technology a choice for future experiments. This is the first report to describe the use of DArT technology for genotyping the common bean. [ABSTRACT FROM AUTHOR]

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. [ABSTRACT FROM PUBLISHER]

With 1 figure and 4 tables Abstract Cultivated pigeonpea ( Cajanus cajan L. Millsp.) has a narrow genetic base; hence, utilization of wild relatives in the crossing programme would broaden its genetic base and introduce useful traits. Cajanus platycarpus (Benth.) Maesen, an annual wild relative from the tertiary gene pool, was successfully crossed with the cultigen, utilizing hormone-aided pollinations, embryo rescue and tissue culture techniques, and backcrossed using cultigen as the recurrent parent. Advance generation progeny showed a range of useful traits such as resistance to phytophthora blight, pod borer, bruchid and podfly resistance. Variation was also observed for plant type, growth habit and seed colour. A new source of cytoplasmic male sterility was identified in one of the progeny lines. Molecular analysis of the progeny after four backcrosses showed the presence of genomic segments from C. platycarpus accompanied by the presence of recombinant DNA sequences signifying recombination between the parental genomes. [ABSTRACT FROM AUTHOR]

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed. [ABSTRACT FROM AUTHOR]

Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice ( Oryza sativa L.)genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a general-purpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc (Numerical taxonomy system for cluster and ordination analysis, v. 2.02j) software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple sequence repeats genotyping outline and varieties' pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers. (Managing editor: Ya-Qin Han) [ABSTRACT FROM AUTHOR]

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11–36 and 12–3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars. [ABSTRACT FROM AUTHOR]

Abstract Background Phytophthora infestans (Mont.) de Bary, the causal organism of late blight, is economically the most important pathogen of potato and resistance against it has been one of the primary goals of potato breeding. Some potentially durable, broad-spectrum resistance genes against this disease have been described recently. However, to obtain durable resistance in potato cultivars more genes are needed to be identified to realize strategies such as gene pyramiding or use of genotype mixtures based on diverse genes. Results A major resistance gene, Rpi-rzc1, against P. infestans originating from Solanum ruiz-ceballosii was mapped to potato chromosome X using Diversity Array Technology (DArT) and sequence-specific PCR markers. The gene provided high level of resistance in both detached leaflet and tuber slice tests. It was linked, at a distance of 3.4 cM, to violet flower colour most likely controlled by the previously described F locus. The marker-trait association with the closest marker, violet flower colour, explained 87.1% and 85.7% of variance, respectively, for mean detached leaflet and tuber slice resistance. A genetic linkage map that consisted of 1,603 DArT markers and 48 reference sequence-specific PCR markers of known chromosomal localization with a total map length of 1204.8 cM was constructed. Conclusions The Rpi-rzc1 gene described here can be used for breeding potatoes resistant to P. infestans and the breeding process can be expedited using the molecular markers and the phenotypic marker, violet flower colour, identified in this study. Knowledge of the chromosomal localization of Rpi-rzc1 can be useful for design of gene pyramids. The genetic linkage map constructed in this study contained 1,149 newly mapped DArT markers and will be a valuable resource for future mapping projects using this technology in the Solanum genus.