Search

Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were lhe most differentiated with regional substructuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent CypSIA mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of lhe promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and CypSIA haplotypes with South African isolates, suggesting a recent common origin. [ABSTRACT FROM AUTHOR]

Spot form net blotch, caused by Pyrenophora teres f. maculata, is a major foliar disease of barley worldwide. Knowledge of the pathogen’s genetic diversity and population structure is critical for a better understanding of inherent evolutionary capacity and for the development of sustainable disease management strategies. Genome-wide, single nucleotide polymorphism data of 254 Australian isolates revealed genotypic diversity and an absence of population structure, either between states, or between fields and cultivars in different agro-ecological zones. This indicates there is little geographical isolation or cultivar directional selection and that the pathogen is highly mobile across the continent. However, two cryptic genotypic groups were found only in Western Australia, predominantly associated with genes involved in fungicide resistance. The findings in this study are discussed in the context of current cultivar resistance and the pathogen’s adaptive potential. [ABSTRACT FROM AUTHOR]

Abstract Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

Net formnet blotch disease, caused by Pyrenophora teres f. teres, results in significant yield losses to barley industries. Up-to-date knowledge of the genetic diversity and structure of pathogen populations is critical for elucidating the disease epidemiology and unraveling pathogen survival and dispersal mechanisms. Thus, this study investigated long-distance dispersal and adaptation by analyzing the genetic structure of 250 P. teres f. teres isolates collected from Australia, Canada, Hungary, and Republic of South Africa (RSA), and historical isolates from Canada, Denmark, Japan, and Sweden. The population genetic structure detected by discriminant analysis of principal components, with the use of 5,890 Diversity Arrays Technology markers, revealed the presence of four clusters. Two of these contained isolates from all regions, and all isolates from RSA were grouped in these two. Australia and Hungary showed three clusters each. One of the Australian clusters contained only Australian isolates. One of the Hungarian clusters contained only Hungarian isolates and one Danish isolate. STRUCTURE analysis indicated that some isolates from Australia and Hungary shared recent ancestry with RSA, Canada, and historical isolates and were thus admixed. Subdivisions of the neighbor joining network indicated that isolates from distinct countries were closely related, suggesting that multiple introduction events conferred genetic heterogeneity in these countries. Through a neighbor joining analysis and amplification with form-specific DNA markers, we detected two hybrid isolates, CBS 281.31 from Japan and H-919 from Hungary, collected in 1931 and 2018, respectively. These results provide a foundation for exploring improved management of disease incursions and pathogen control through strategic deployment of resistance. [ABSTRACT FROM AUTHOR]

Phalaris aquatica L. (phalaris) is a cool-season perennial grass originating from the Mediterranean Basin, north-west Africa and Middle Eastern regions that is used for livestock agriculture mainly in temperate areas with dry summers. It has been the subject of breeding programs in Australia, South America, New Zealand and the USA. Increased knowledge of relationships between wild and cultivated germplasm through use of molecular markers has the potential to facilitate future breeding gains. For this purpose, we conducted an analysis of P. aquatica by using 3905 polymorphic DArTseq SNP markers. Genetic diversity as measured by expected heterozygosity was similar for wild (HE = 0.14; n = 57) and cultivated (HE = 0.13; n = 37) accessions. Diversity in wild germplasm was generally continuous in nature, largely related to geographical location, with a division at the broadest scale into eastern and western clades, with more admixture in the western than the eastern clade. Structure analysis of wild germplasm indicated six subpopulations consistent with country of origin, with some admixture among subpopulations likely resulting from natural and human influences. There were nine subpopulations among wild and cultivated accessions combined. This population structure should be considered if genomic selection is applied in P. aquatica. Analysis of molecular variance indicated that 71% of the genetic variation occurred within subpopulations and 29% among subpopulations. Genetic distances were low among cultivated germplasm from most countries except the USA, which was more distinct. Evaluation of material from the US pool by breeding programs in other countries, and additional material from the less utilised eastern clade, may be worthwhile. Knowledge of genetic diversity is important for traditional and genomics-based breeding in the perennial pasture grass Phalaris aquatica. Use of molecular markers indicated the presence of nine groups among wild and cultivated germplasm, with close relationships among cultivars from most countries where P. aquatica is bred. Population structure should be considered for genomic breeding of P. aquatica and more testing of germplasm from less exploited germplasm groups may be worthwhile in future breeding. [ABSTRACT FROM AUTHOR]

Abstract Background Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. Results Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P

Abstract Background Leaves of Poaceae have a unique morphological feature: they consist of a proximal sheath and a distal blade separated by a ligular region. The sheath provides structural support and protects young developing leaves, whereas the main function of the blade is photosynthesis. The auricles allow the blade to tilt back for optimal photosynthesis and determine the angle of a leaf, whereas the ligule protects the stem from the entry of water, microorganisms, and pests. Liguleless variants have an upright leaf blade that wraps around the culm. Research on liguleless mutants of maize and other cereals has led to identification of genes that are involved in leaf patterning and differentiation. Results We characterized an induced liguleless mutant (LM) of Aegilops tauschii Coss., a donor of genome D of bread wheat Triticum aestivum L.. The liguleless phenotype of LM is under dominant monogenic control (Lg t ). To determine precise position of Lg t on the Ae. tauschii genetic map, highly saturated genetic maps were constructed containing 887 single-nucleotide polymorphism (SNP) markers derived via diversity arrays technology (DArT)seq. The Lg t gene was mapped to chromosome 5DS. Taking into account coordinates of the SNP markers, flanking Lg t , on the pseudomolecule 5D, a chromosomal region that contains this gene was determined, and a list of candidate genes was identified. Morphological features of the LM phenotype suggest that Lg t participates in the control of leaf development, mainly, in leaf proximal–distal patterning, and its dominant mutation causes abnormal ligular region but does not affect reproductive development. Conclusions Here we report characterization of a liguleless Ae. tauschii mutant, whose phenotype is under control of a dominant mutation of Lg t . The dominant mode of inheritance of the liguleless trait in a Triticeae species is reported for the first time. The position of the Lg t locus on chromosome 5DS allowed us to identify a list of candidate genes. This list does not contain Ae. tauschii orthologs of any well-characterized cereal genes whose mutations cause liguleless phenotypes. Thus, the characterized Lg t mutant represents a new model for further investigation of plant leaf patterning and differentiation.

Background: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results: Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion: Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection. [ABSTRACT FROM AUTHOR]

In the current study, significant variations were identified for seven fruit traits of the walnut accessions. The highest correlations were detected between nut height and nut width, and between nut weight and kernel weight. Most traits had a continuous normal binominal distribution. A total of 16,774 single-nucleotide polymorphism (SNP) markers based on diversity arrays technology were generated and after filtering the missing data, the remaining 13,611 SNP data were used for genotyping. STRUCTURE (v.2.2) analysis revealed two possible scenarios (K = 3 and K = 5) according to the results of AK computation. While K = 3 indicated that walnut cultivars were clustered into three different groups, K = 5 revealed five different groups. Results of the dendrogram tree analysis were supported by the results presented in the STRUCTURE analysis. A total of 98 association signals were detected with FDR < 0.05 from MLM (K) using BLUP predictors for the seven agronomic traits. Out of these 98 associations, seven SNPs were associated with nut weight, 26 SNPs with nut length, 15 SNPs with nut height, 18 SNPs with nut width, 18 SNPs with shell thickness, 12 SNPs with kernel weight, and 2 SNPs with kernel ratio. [ABSTRACT FROM AUTHOR]

Abstract Background Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.

Sugarcane is an economically important crop grown for sugar and bioethanol. Most commercial varieties are hybrids of the noble cane Saccharum officinarum and its wild relative S. spontaneum. Sugarcane breeding in the Philippines is focused on the development of new varieties with higher sucrose content and resistance to major fungal diseases. Evaluation of parents for crossing depends on the knowledge of the genetic diversity of the available sugarcane germplasm. In this study, the genetic diversity of 54 local and foreign sugarcane varieties selected from the local germplasm was evaluated through genotyping-by-sequencing (GBS) using diversity arrays technology (DArT). Single nucleotide polymorphisms (SNPs) and silico-DArT (presence/absence) dominant markers were developed using DArT-Seq method, which employs genome complexity reduction method using methylation-sensitive restriction enzymes (REs) and highthroughput next-generation sequencing (NGS). Polymorphism information content (PIC) values of resulting SNP markers range from 0.009 to 0.5 with an average of 0.195, while Silico-DArT markers have PIC values from 0.02 to 0.5 with an average of 0.271. Silico-DArT markers were considered more informative based on higher average reproducibility, call rate, and PIC values. Cluster analysis and principal coordinate analysis using scoring data from SNP and silico- DArT markers showed low-sucrose varieties grouping separately from commercial hybrids developed in the Philippines. However, observed genetic distances among varieties genotyped indicate moderate to high genetic relatedness within the local germplasm, especially among commercially-available varieties in the country. DArT-Seq genotyping was successfully used in analysis of genetic diversity among current commercial varieties and can be a useful tool in the evaluation of new breeding materials for the development of more improved varieties. [ABSTRACT FROM AUTHOR]

Net form of net blotch caused by Pyrenophora teres f. teres (Ptt) is a major foliar disease of barley (Hordeum vulgare) worldwide. Knowledge of the evolution of Ptt pathogen populations is important for development of durable host‐plant resistance. This study was conducted to investigate changes in genetic structure of a Ptt population within a barley field during three cropping years. The susceptible barley cultivar Henley was inoculated with Ptt isolate NB050. Leaf samples were collected during the years 2013–15 and 174 single spore Ptt isolates stored. Genotyping using Diversity Arrays Technology markers identified that 25% of isolates were clones of the inoculated isolate and 75% of isolates were multilocus genotypes (MLGs) differing from the original inoculated genotype. The novel genotypes probably originated from a combination of windborne spores from neighbouring fields, infected seed and sexual recombination in the field. The rapid change in the genotypic composition of the Ptt population in this study suggests adaptive potential of novel genotypes and demonstrates the need for barley breeders to use multiple sources of host‐plant resistance to safeguard against resistance being overcome. [ABSTRACT FROM AUTHOR]

Textural property is one of the most important factors influencing the quality of northern-style Chinese steamed bread (CSB). We detected quantitative trait loci (QTLs) for the textural properties of CSB by using 184 recombinant inbred lines derived from a cross between two Chinese winter wheat (Triticum aestivum L.) varieties, Linmai6 and Tainong18. Eighteen putative QTLs were detected on 14 chromosomes: 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 5B, 6A, 6B, 7B, and 7D. Six textural quality traits, one QTL for hardness (QHa - 4A), three QTLs for springiness (QSp - 3B , QSp - 4B , and QSp - 5B), seven QTLs for cohesiveness (QCo - 6A , QCo - 7B.1 , QCo - 7B.2 , QCo - 3A , QCo - 1D , QCo - 2B.1 , and QCo - 2B.2), four QTLs for resilience (QRe - 2D , QRe - 2A , QRe - 7D , and QRe - 1B), two QTLs for gumminess (QGu - 6B , and QGu - 3B), and one QTL for chewiness (QCh - 7D) were detected. The contributions of the QTLs ranged from 6.19% to 15.74%. The present study enhances understanding of the genetic basis for the textural properties of northern-style CSB and provides the basis for gene mapping of these traits. Quantitative trait loci (QTLs) for the textural properties of Chinese steamed bread were detected. Eighteen putative QTLs referring to six textural quality traits were detected on 14 chromosomes. The contributions of these QTLs ranged from 6.19% to 15.74%. [ABSTRACT FROM AUTHOR]

• Test of genetic differentiation among taxa differing in one character: ± lignotuber. • Obligate-seeder and lignotuberous eucalypts formed discrete phylogenetic lineages. • Lignotuber state shifts have contributed to the evolution of eucalypt diversity. • Lignotuber shifts evolved directionally with respect to environmental conditions. Plant taxa can be broadly divided based on the mechanisms enabling persistence through whole-crown disturbances, specifically whether individuals resprout, populations reseed, or both or neither of these mechanisms are employed. At scales from species through to communities, the balance of disturbance-response types has major ramifications for ecological function and biodiversity conservation. In some lineages, morphologically identical populations except for differences in a disturbance-response trait (e.g. ± lignotuber) occur, offering the opportunity to apply genetic analyses to test whether trait state is representative of broader genetic distinctiveness, or alternatively, variation in response to local environmental conditions. In eucalypts, a globally-significant plant group, we apply dense taxon sampling and high-density, genome-wide markers to test monophyly and genetic divergence among pairs of essentially morphologically-identical taxa excepting lignotuber state. Taxa differing in lignotuber state formed discrete phylogenetic lineages. Obligate-seeders were monophyletic and strongly differentiated from each other and lignotuber-resprouters, but this was not the case for all lignotuber-resprouter taxa. One lignotuber state transition within our sample clade was supported, implying convergence of some non-lignotuber morphology characters. Greater evolutionary rate associated with the obligate-seeder disturbance-response strategy offers a plausible explanation for these genetic patterns. Lignotuber state is an important taxonomic character in eucalypts, with transitions in lignotuber state having contributed to the evolution of the exceptional diversity of eucalypts in south-western Australia. Differences in lignotuber state have evolved directionally with respect to environmental conditions. [ABSTRACT FROM AUTHOR]

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A , QIT.sicau-4B , QDS.sicau-4B.2 , QDS.sicau-6A.3 , and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance. [ABSTRACT FROM AUTHOR]

Polyphenol oxidase (PPO) causes undesirable darkening in wheat products such as Asian noodles. The inheritance of PPO activity was investigated in a doubled haploid (DH) population derived from a hybrid between a null PPO genotype VAW08-A17 and Australian wheat variety QALBis. The observed genetic ratio indicated three genes controlling high PPO activity. Quantitative trait loci (QTL) mapping was performed in this DH population using diversity arrays technology (DArT) to genotype the population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL with additive mode of action. Three closely associated DArT markers, wPt-7024, wPt-0094 and wPt-2544, were identified corresponding to these QTLs. Collectively, these loci explained 74% of the observed variation in PPO activity. Identification of DArT markers associated with PPO genes will accelerate the development of null or very low PPO cultivars that exhibit reduced time-dependent darkening of Asian noodles. [ABSTRACT FROM AUTHOR]

Background: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was~88 kbp, while for the Andean gene pool was ~395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches. [ABSTRACT FROM AUTHOR]

We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria , Exsertaria , Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies. [ABSTRACT FROM AUTHOR]

Rust, caused by the fungus Puccinia substriata var. indica, is one of the most important production constraints of pearl millet worldwide, leading to grain yield losses of up to 76 % as well as major losses in fodder yield and quality. Here, we report the development of a linkage map integrating Diversity Arrays Technology (DArT) markers and simple sequence repeat (SSR) markers, using this to identify quantitative trait loci (QTLs) for pearl millet rust resistance. Genotyping data from 256 DArT and 70 SSR markers on 168 F recombinant inbred lines from cross 81B-P6 × ICMP 451-P8 were used to construct a linkage map comprised of 286 loci (229 DArT and 57 SSR markers) spanning a total length of 740.3 cM (Haldane) with an average adjacent marker distance of 2.7 cM. Linkage group 7 (LG7) (153.5 cM) was the longest and LG6 the shortest (45.0 cM). The map was used to identify a major QTL for rust resistance with an LOD score of 27 on LG1, which explained 58 % of the observed phenotypic variation. In addition, two putative modifiers of small effect were detected, one each on LG4 and LG7. The novel rust resistance QTL identified on LG1 is thought to confer a durable slow-rusting phenotype, which is still effective in India more than 20 years after it was first deployed in the previously popular single-cross hybrid MH 179 (ICMH 451). The flanking markers reported here provide a framework for marker-assisted selection and possible future map-based cloning of this resistance gene. [ABSTRACT FROM AUTHOR]

Eucalyptus is a genus that occurs in a range of habitats in Australia, Papua New Guinea, Timor, Sulawesi and the Philippines, with several species being used as sources of timber and fibre. However, despite its ecological and commercial significance, understanding its evolutionary history remains a challenge. The focus of the present study is the green ashes (subgenus Eucalyptus section Eucalyptus). Although previous studies, based primarily on morphology, suggest that the green ashes form a monophyletic group, there has been disagreement concerning the divergence of taxa. The present study aims to estimate the phylogeny of the green ashes and closely related eucalypts (37 taxa from over 50 locations in south-eastern Australia), using genome-wide analyses based on Diversity Arrays Technology (DArT). Results of analyses were similar in topology and consistent with previous phylogenies based on sequence data. Many of the relationships supported those proposed by earlier workers. However, other relationships, particularly of taxa within the Sydney region and Blue Mountains, were not consistent with previous classifications. These findings raise important questions concerning how we define species and discern relationships in Eucalyptus and may have implications for other plant species, particularly those with a complex evolutionary history where hybridisation and recombination have occurred. [ABSTRACT FROM AUTHOR]

The objectives of this study were to evaluate the usefulness of DArT markers in genotypic identification of willow species and describe genetic relationships between four willow species: Salix viminalis, S. purpurea, S. alba and S. triandra. The experimental plant material comprised 53 willow genotypes of these four species, which are popularly grown in Poland. DArT markers seem to identify Salix species with a high degree of accuracy. As a result, the examined species were divided into four distinct groups which corresponded to the four analyzed species. In our study, we observed that S. triandra was very different genetically from the other species, including S. alba which is generally classified into the same subgenus of Salix. The above corroborates the findings of other authors who relied on molecular methods to reveal that the classification of S. triandra to the subgenus Salix was erroneous. The Principal Coordinate Analysis (PCoA) and the neighbor-joining dendrogram also confirmed the clear division of the studied willow genotypes into four clusters corresponding to individual species. This confirmed the usefulness of DArT markers in taxonomic analyses and identification of willow species. [ABSTRACT FROM AUTHOR]

Wheat ( Triticum aestivum L.) flour functionality during the dough development and baking processes is an important quality attribute considered by the baking industry. A flour with high water absorption during mixing means more water and less flour is needed, compared to a flour with less water absorption. The objective of this study was to identify quantitative trait loci (QTL) influencing water absorption and dough rheological properties of hard red spring wheat. QTL were mapped on a genetic linkage map that comprised 531 simple sequence repeats (SSRs) and diversity array technology (DArT) marker loci. Composite interval mapping with 139 recombinant inbred lines (RILs) was used to identify QTL within and across two field environments. Six QTL on chromosomes 1A, 1B, 4B, 4D, and 5A were detected for farinograph water absorption. These QTL also confirmed earlier studies that flour water absorption is a function of protein content, starch damage, and gluten strength. In this study, dough rheological properties such as dough development time, dough stability, mixing tolerance index, and time to breakdown were influenced by the high-molecular weight glutenin genes Glu- B1 and Glu- D1. [ABSTRACT FROM AUTHOR]

Abstract: A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species. [Copyright &y& Elsevier]

Wild barley-specific genomic libraries were developed for the purpose of creating a 'comprehensive' genomic representation of the primary Hordeum genepool capable of more robust genotyping of barley. In order to enrich for wild barley-specific sequences in the DArT libraries, suppression subtraction hybridization (SSH) was performed using cultivated barley as the subtraction driver and wild barley as the tester. Four doubled-haploid populations were genotyped with the comprehensive barley DArT array, including two from wild × cultivated crosses (Damon/Harrington and Shechem/Harrington) and two from cultivated × cultivated crosses (Albacete/Barbarrouse and TX9425/Naso Nijo). Analysis of genotyping data revealed that the SSH process was somewhat ineffective at enriching for unique sequences in this application of DArT marker development. However, the addition of markers derived from wild barley proved to be an effective means for increasing the number of polymorphic markers obtainable from a single DArT assay. Genetic maps of the four component populations were developed and 607 newly developed DArT markers were integrated with a barley consensus map to create a new synthetic map of the barley genome containing 3542 markers. This significantly increased the resolution of the consensus map and improved the power of the map to provide a reference for profiling genetic diversity within the primary Hordeum genepool. The improvement in the genotyping capability of the comprehensive DArT genomic representation and the higher resolution of the synthetic map facilitates an even greater flexibility of DArT markers to be utilized as a fast, high-throughput platform for molecular marker-based barley breeding. [ABSTRACT FROM AUTHOR]

A genetic linkage mapping study was conducted in 93 doubled-haploid lines derived from a cross between Triticum aestivum L. em. Thell 'Arina' and a Norwegian spring wheat breeding line, NK93604, using diversity arrays technology (DArT), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR) markers. The objective of this study was to understand the distribution, redundancy, and segregation distortion of DArT markers in comparison with AFLP and SSR markers. The map contains a total of 624 markers with 189 DArTs, 165 AFLPs and 270 SSRs, and spans 2595.5 cM. All 3 marker types showed significant (p < 0.01) segregation distortion, but it was higher for AFLPs (24.2%) and SSRs (22.6%) than for DArTs (13.8%). The overall segregation distortion was 20.4%. DArTs showed the highest frequency of clustering (27.0%) at < 0.5 cM intervals between consecutive markers, which is 3 and 15 times higher than SSRs (8.9%) and AFLPs (1.8%), respectively. This high proportion of clustering of DArT markers may be indicative of gene-rich regions and (or) the result of inclusion of redundant clones in the genomic representations, which was supported by the presence of very high correlation coefficients (r > 0.98) and multicollinearity among the clustered markers. The present study is the first to compare the utility of DArT with AFLP and SSR markers, and the present map has been successfully used to identify novel QTLs for resistance to Fusarium head blight and powdery mildew and for anther extrusion, leaf segment incubation, and latency. [ABSTRACT FROM AUTHOR]