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Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (7: turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from ~3,341 [cR.sub.35,000] for five major linkage groups to 11,773 [cR.sub.35,000] for a comprehensive map. The mapping resolution was estimated to be ~199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

Genes interacting with seed developmental environments control primary dormancy. To understand how a multigenic system evolved to adapt to the changing environments in weedy rice, we evaluated genetic components of three dormancy QTL in a synchronized nondormant genetic background. Two genetically identical populations segregating for qSD1, qSD7-1, and qSD12 were grown under greenhouse and natural conditions differing in temperature, relative humidity, and light intensity during seed development. Low temperatures tended to enhance dormancy in both conditions. However, genotypes responded to the environments divergently so that two populations displayed similar distributions for germination. Additive and/or dominance effects of the three loci explained ~90% of genetic variances and their epistases accounted for the remainder in each environment. The qSD1 and qSD7-1 main effects were increased, while the qSD12 additive effect was decreased by relatively low temperatures. Both gene main and epistatic effects were involved in G X E interactions, which in magnitude were greater than environmental main effect. The divergent responses of dormancy genes observed in this simple multigenic system presumably have selective advantages in natural populations adapted to changing environments and hence represent a genetic mechanism stabilizing the dormancy level of weedy rice ripened in different seasons or temperature regimes.

Association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting. A phenotypic selection and recurrent backcrossing technique was used to introduce dormancy genes from a wild-like weedy rice to a breeding line to determine their effects and linkage with the other traits. Five generations of phenotypic selection alone for low germination extremes simultaneously retained dormancy alleles at five independent QTL, including qSD12 ([R.sup.2] > 50%), as determined by genome-wide scanning for their main and/or epistatic effects in two B[C.sub.4][F.sub.2] populations. Four dormancy loci with moderate to small effects colocated with QTL/genes for one to three of the associated traits. Multilocus response to the selection suggests that these dormancy genes are cumulative in effect, as well as networked by epistases, and that the network may have played a 'sheltering' role in maintaining intact adaptive haplotypes during the evolution of weeds. Tight linkage may prevent the dormancy genes from being used in breeding programs. The major effect of qSD12 makes it an ideal target for map-based cloning and the best candidate for imparting resistance to preharvest sprouting.

Wild related Triticum species have been and will be a useful reservoir of genetic diversity for solving problems in the development of improved durum (Triticum turgidum L. var. durum) and bread wheat (T. aestivum L.) cultivars. The alien germplasm may be used to reduce vulnerability of cultivars to pests, and improve agronomic fitness and grain quality. However, lack of genetic recombination and hybrid sterility are two obstacles to the use of alien germplasms. Nuclear-cytoplasmic (NC) incompatibility is known to exist between the T. longissimum S. & M. cytoplasm and T. turgidum nucleus. A two-gene system has been found that restores fertility in this situation: the species cytoplasm specific (scs) gene and the vitality (Vi) gene. This gene system can also be used for the production of hybrid wheat. Effects of these genes on euplasmic (true cytoplasm) durum wheat under a field environment had not been previously investigated. In this study, lines with two copies of the sc[s.sup.ti] gene, derived from T. timopheevii Zhnk., were compared to lines without the copy of the gene, the parents, and four durum cultivars for five agronomic characteristics: days to heading, plant height, lodging resistance, grain yield, and kernel test weight. Comparison of genotypes homozygous for the sc[s.sup.ti] gene and those containing no sc[s.sup.ti] gene indicated minor differences among them, confirming that the sc[s.sup.ti] gene does not confer any detrimental effects in the euplasmic situation. Thus, the sc[s.sup.ti] gene could be useful in the production of hybrids in durum wheat., IN THE PAST, alien cytoplasms and chromosomes have been introduced into wheat by cytologically monitoring the chromosomal constitution of backcross progenies in interspecific hybrids (Maan et al., 1999). However, NC [...]

This study evaluates the potential of flow cytometry for chromosome sorting in durum wheat (Triticum turgidum Desf. var. durum, 2n = 4x = 28). Histograms of fluorescence intensity (flow karyotypes) obtained after the analysis of DAPI-stained chromosomes consisted of three peaks. Of these, one represented chromosome 3B, a small peak corresponded to chromosomes 1A and 6A, and a large peak represented the remaining 11 chromosomes. Chromosomes sorted onto microscope slides were identified after fluorescence in situ hybridization (FISH) with probes for GAA microsatellite, pSc119.2, and Afa repeats. Genomic distribution of these sequences was determined for the first time in durum wheat and a molecular karyotype has been developed for this crop. Flow karyotyping in double-ditelosomic lines of durum wheat revealed that the lines facilitated sorting of any arm of the wheat A- and B-genome chromosomes. Compared to hexaploid wheat, flow karyotype of durum wheat is less complex. This property results in better discrimination of telosomes and high purities in sorted fractions, ranging from 90 to 98%. We have demonstrated that large insert libraries can be created from DNA purified using flow cytometry. This study considerably expands the potential of flow cytogenetics for use in wheat genomics and opens the possibility of sequencing the genome of this important crop one chromosome arm at a time.

Seed dormancy, a major adaptive trait in plants, facilitates the survival of weeds and provides for resistance to preharvest sprouting (PHS) in cereal crops. Seventeen weedy strains and 24 cultivars of rice (Oryza sativa L.) were evaluated for germinability to screen for donors of dormancy genes. Extremely dormant genotypes were identified from the weedy strains. These genotypes displayed hulland pericarp/testa-imposed dormancy. Three dormant weedy strains, LD, TKN12-2, and SS18-2, were crossed and backcrossed with the nondormant breeding line EM93-1 to determine the relationship between dormancy and the shattering, awn, hull color, and pericarp/ testa color characteristics. All these characteristics interrelated to the covering-imposed dormancy; the weedy forms of the characteristics significantly reduced germination in the B[C.sub.1][F.sub.1] populations. Moreover, multiple linear regression analyses revealed significant effects of interaction between the characteristics on dormancy in the populations. The interrelation and interaction reflect the importance of combined effects of dormancy and other weedy characteristics in the adaptation of weedy populations to agroecosystems, and suggest that domestication and breeding activities have eliminated dormancy alleles at loci near the genes for shattering and the morphological characteristics from improved cultivars., WEEDS ARE ORGANISMS adapted to human disturbances (Harlan, 1965). Many characteristics contribute to the adaptation and persistence of weeds (Baker, 1974). For example, shattering enables weed seeds to escape harvest, [...]

Radiation hybrid (RH) mapping is based on radiation-induced chromosome breakage and analysis of chromosome segment retention or loss using molecular markers. In durum wheat (Titicum turgidum L., AABB), an alloplasmic durum line [(lo) durum] has been identified with chromosome 1D of T. aestivum L. (AABBDD) carrying the species cytoplasm-specific ([scs.sup.ae]) gene. The chromosome 1D of this line segregates as a whole without recombination, precluding the use of conventional genome mapping. A radiation hybrid mapping population was developed from a hemizygous (lo) [scs.sup.ae_] line using 35 krad gamma rays. The analysis of 87 individuals of this population with 39 molecular markers mapped on chromosome 1D revealed 88 radiation-induced breaks in this chromosome. This number of chromosome 1D breaks is eight times higher than the number of previously identified breaks and should result in a 10-fold increase in mapping resolution compared to what was previously possible. The analysis of molecular marker retention in our radiation hybrid mapping panel allowed the localization of [scs.sup.ae] and 8 linked markers on the long arm of chromosome 1D. This constitutes the first report of using RH mapping to localize a gene in wheat and illustrates that this approach is feasible in a species with a large complex genome.

Weedy rice has much stronger seed dormancy than cultivated rice. A wild-like weedy strain SS18-2 was selected to investigate the genetic architecture underlying seed dormancy, a critical adaptive trait in plants. A framework genetic map covering the rice genome was constructed on the basis of 156 B[C.sub.1] [EM93-1 (nondormant breeding line)//EM93-1/SS18-2] individuals. The mapping population was replicated using a split-tiller technique to control and better estimate the environmental variation. Dormancy was determined by germination of seeds after 1, 11, and 21 days of after-ripening (DAR). Six dormancy QTL, designated as qS[D.sup.S]-4, -6, -7-1, -7-2, -8, and -12, were identified. The locus qS[D.sup.S]-7-1 was tightly linked to the red pericarp color gene Rc. A QTL x DAR interaction was detected for qS[D.sup.S]-12, the locus with the largest main effect at 1, 11, and 21 DAR ([R.sup.2] = 0.14, 0.24, and 0.20, respectively). Two, three, and four orders of epistases were detected with four, six, and six QTL, respectively. The higher-order epistases strongly suggest the presence of genetically complex networks in the regulation of variation for seed dormancy in natural populations and make it critical to select for a favorable combination of alleles at multiple loci in positional cloning of a target dormancy gene.

The compatibility-inducing action of the sc[s.sup.ti] (species cytoplasm-specific gene derived from Triticum timopheevii) and Vi (vitality) genes can be observed when a durum (T. turgidum) nucleus is placed in T. longissimum cytoplasm. These two genes restore compatibility between an otherwise incompatible nucleus and cytoplasm. The objective of this study was to localize the sc[s.sup.ti] gene on a linkage map of chromosome 1A, which could eventually be used to clone the gene. The mapping population consisted of 110 [F.sub.2] individuals derived from crossing a Langdon-T. dicoccoides chromosome 1A substitution line with a euplasmic (normal cytoplasm) line homozygous for the sc[s.sup.ti] gene. Through a series of testcrosses the genotypes of the 110 individuals were determined: 22 had two copies, 59 bad one copy, and 29 had no copy of the sc[s.sup.ti] gene. Data from RFLP, AFLP, and microsatellite analysis were used to create a linkage map. The flanking marker loci found for the sc[s.sup.ti] gene were Xbcd12 and Xbcd1449-1A.2 with distances of 2.3 and 0.6 cM, respectively. Nearly 10% of individuals in this population were double recombinant for a genetic interval of

Abstract Background The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps. Results A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells. Conclusions The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.

Summary: Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20–25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange–yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat‐growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. Control: Most crown rust management strategies involve the use of rust‐resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust‐resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/. [ABSTRACT FROM AUTHOR]

Key message: Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs.Abstract: A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing. Resistance was incorporated into hexaploid oat by embryo rescue, colchicine chromosome doubling followed by backcrosses with a hexaploid parent, and selection for stable transmission of resistance. To mitigate flag leaf and panicle chlorosis/necrosis associated with the resistance, crosses were made with derived resistant lines to breeding lines of divergent parentage followed by selection. Subsequently, two F2 sister lines, termed MNBT1020-1 and MNBT1021-1, were identified in which the chlorosis/necrosis was reduced. These two lines performed well in replicated multi-location state trials in 2015 and 2016 out-yielding all cultivar entries. Segregating F2:3 plants resulting from crosses of MNBT lines to susceptible parents were genotyped with the oat 6K SNP array, and SNP loci with close linkage to the resistance were identified. KASP assays generated from linked SNPs showed accurate discrimination of the resistance in derivatives of the resistant MNBT lines crossed to susceptible breeding lines. A TaqMan marker was developed and correctly identified homozygous resistance in over 95% of 379 F4 plants when rust was scored in F4:5 plants in the field. Thus, a novel highly effective resistance and associated molecular markers are available for use in breeding, genetic analysis, and functional studies. [ABSTRACT FROM AUTHOR]

Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome. [ABSTRACT FROM AUTHOR]