High resolution genetic and physical mapping of the I-3 region of tomato chromosome 7 reveals almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with duplications on Arabidopsis chromosomes 1, 2 and 3

The tomato I-3 gene introgressed from the Lycopersicon pennellii accession LA716 confers resistance to race 3 of the fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici. We have improved the high-resolution map of the I-3 region of tomato chromosome 7 with the development and mapping of 31 new PCR-based markers. Recombinants recovered from L. esculentum cv. M82 × IL7-2 F2 and (IL7-2 × IL7-4) × M82 TC1F2 mapping populations, together with recombinants recovered from a previous M82 × IL7-3 F2 mapping population, were used to position these markers. A significantly higher recombination frequency was observed in the (IL7-2 × IL7-4) × M82 TC1F2 mapping population based on a reconstituted L. pennellii chromosome 7 compared to the other two mapping populations based on smaller segments of L. pennellii chromosome 7. A BAC contig consisting of L. esculentum cv. Heinz 1706 BACs covering the I-3 region has also been established. The new high-resolution map places the I-3 gene within a 0.38 cM interval between the molecular markers RGA332 and bP23/gPT with an estimated physical size of 50-60 kb. The I-3 region was found to display almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with Arabidopsis thaliana chromosomes 1, 2 and 3. An S-receptor-like kinase gene family present in the I-3 region of tomato chromosome 7 was found to be present in the microsyntenous region of grape chromosome 12 but was absent altogether from the A. thaliana genome.

Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.)

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important biological processes was used to detect polymorphic EST–RFLP loci in the F1(NA6 × AU6) population. A comprehensive set of EST–SSR markers was developed from the analysis of 14,767 unigenes, with 310 primer pairs showing efficient amplification and detecting 113 polymorphic loci. Two parental genetic maps were produced: the NA6 genetic map contains 88 EST–RFLP and 71 EST–SSR loci with a total map length of 963 cM, while the AU6 genetic map contains 67 EST–RFLP and 58 EST–SSR loci with a total map length of 757 cM. Bridging loci permitted the alignment of homologous chromosomes between the parental maps, and a sub-set of genomic DNA-derived SSRs was used to relate linkage groups to the perennial ryegrass reference map. Regions of segregation distortion were identified, in some instances in common with other perennial ryegrass maps. The EST-derived marker-based map provides the basis for in silico comparative genetic mapping, as well as the evaluation of co-location between QTLs and functionally associated genetic loci.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H, was mapped to the telomere region of chromosome 7HS in an Alexis/Sloop doubled haploid barley population. The closest marker to Ruh.7H, abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identified by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of different size while two further loci contained SNPs that were identified using the recently developed high resolution melting (HRM) technique. Two of these markers flanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the first report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved amplified polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should find widespread use in the fine-mapping of genetic regions of interest in complex cereal and other plant genomes.

Odour sampling 1: Physical chemistry considerations

The selection of an odour sampling device may influence the composition of the resulting odour sample. Limited comparison of emission rates derived from turbulent and essentially quiescent sampling devices confirms that the emission rates derived from these devices are quite different. There is therefore compelling evidence that current odour sampling practice should have greater regard for fundamental physical and chemical principles, the nature of the odour source and the conditions created by the sampling device. Such consideration may identify the most appropriate situations under which the use of these devices may or may not be correct.

Odour sampling. 2. Comparison of physical and aerodynamic characteristics of sampling devices: A review

Sampling devices differing greatly in shape, size and operating condition have been used to collect air samples to determine rates of emission of volatile substances, including odour. However, physical chemistry principles, in particular the partitioning of volatile substances between two phases as explained by Henrys Law and the relationship between wind velocity and emission rate, suggests that different devices cannot be expected to provide equivalent emission rate estimates. Thus several problems are associated with the use of static and dynamic emission chambers, but the more turbulent devices such as wind tunnels do not appear to be subject to these problems. In general, the ability to relate emission rate estimates obtained from wind tunnel measurements to those derived from device-independent techniques supports the use of wind tunnels to determine emission rates that can be used as input data for dispersion models.

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Species and Hybrids: Chemical and Physical Foliar Attributes and Implications for Herbivory.

Hybridization is an important biological phenomenon that can be used to understand the evolutionary process of speciation of plants and their associated pests and diseases. Interactions between hybrid plants and the herbivores of the parental taxa may be used to elucidate the various cues being used by the pests for host location or other processes. The chemical composition of plants, and their physical foliar attributes, including leaf thickness, trichome density, moisture content and specific leaf weight were compared between allopatric pure and commercial hybrid species of Corymbia, an important subtropical hardwood taxon. The leaf-eating beetle Paropsis atomaria, to which the pure taxa represented host (C. citriodora subsp. variegata) and non-host (C. torelliana) plants, was used to examine patterns of herbivory in relation to these traits. Hybrid physical foliar traits, chemical profiles, and field and laboratory beetle feeding preference, while showing some variability, were generally intermediate to those exhibited by parent taxa, thus suggesting an additive inheritance pattern. The hybrid susceptibility hypothesis was not supported by our field or laboratory studies, and there was no strong relationship between adult preference and larval performance. The most-preferred adult host was the sympatric taxon, although this species supported the lowest larval survival, while the hybrid produced significantly smaller pupae than the pure species. The results are discussed in relation to plant chemistry and physical characteristics. The findings suggest a chemical basis for host selection behavior and indicate that it may be possible to select for resistance to this insect pest in these commercially important hardwood trees.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Mile-a-minute (Mikania micrantha): its distribution, growth and physical and socio-economic impacts in Papua New Guinea

Mikania micrantha, Kunth. H.B.K (Asteraceae) or mile-a-minute is a weed of Neotropical origin in 17 Pacific Island countries. It is becoming increasingly regarded as an invasive weed in Papua New Guinea and is now the focus of an Australian Government-funded biological control program. As part of the program, growth rates, distribution and physical and socia-economic impacts were studied to obtain baseline data and to assist with the field release of biological control agents. Through public awareness campaigns and dedicated surveys, mikania has been reported in most lowland provinces. It is particularly widespread in East New Britain and West New Britain Province. In field trials, mikania grew more than 1 metre per month in open sunny areas but slightly slower when growing under cocoa. The weed invades a wide range of land types, impacting on plantations and food gardens, smothering pawpaw, young cocoa, banana, taro, young oil palms and ornamental plants. In socia-economic surveys, mikania was found to have severe impacts on crop production and income generated through reduced yields and high weeding costs. These studies suggest that there would be substantial benefits to the community if biological control of mikania is successful.

Mikania micrantha Kunth (Asteraceae) (Mile-a-Minute): Its Distribution and Physical and Socioeconomic Impacts in Papua New Guinea

Mikania micrantha or mile-a-minute is regarded as a major invasive weed in Papua New Guinea (PNG) and is now the target of a biological control program. As part of the program, distribution and physical and socioeconomic impacts of M. micrantha were studied to obtain baseline data and to assist with field release of biological control agents. Through public awareness campaigns and dedicated surveys, M. micrantha has been reported in all 15 lowland provinces. It is particularly widespread in East New Britain, as well as in West New Britain and New Ireland. A CLIMEX model suggests that M. micrantha has the potential to continue to spread throughout all lowland areas in PNG. The weed was found in a wide range of land uses, impacting on plantations and food gardens and smothering papaya, young cocoa, banana, taro, young oil palms, and ornamental plants. In socioeconomic surveys, M. micrantha was found to have severe impacts on crop production and income generated through reduced yields and high weeding costs, particularly in subsistence mixed cropping systems. About 89% of all respondents had M. micrantha on their land, and 71% of respondents had to weed monthly. Approximately 96% of respondents in subsistence mixed cropping systems used only physical means of control compared with 68% of respondents in other farming systems. About 45% of all respondents estimated that M. micrantha causes yield losses in excess of 30%. These studies suggest that there would be substantial benefits to landholders if biological control of M. micrantha were to be successful.

High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC7F3 nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

Evaluation of restoration of vegetation infested with cat's claw creeper vine (Dolichandra unguis-cati): soil seed bank response to herbicide and physical removal

Cat’s claw creeper vine, Dolichandra unguis-cati (L.) L.G.Lohmann (formerly known as Macfadyena unguis-cati (L.) A.H.Gentry), a Weed of National Significance (WoNS), is a structural woody parasite that is highly invasive along sensitive riparian corridors and native forests of coastal and inland eastern Australia. As part of evaluation of the impact of herbicide and mechanical/physical control techniques on the long-term reduction of biomass of the weed and expected return of native flora, we have set-up permanent vegetation plots in: (a) infested and now chemically/physically treated, (b) infested but untreated and (c) un-infested patches. The treatments were set up in both riparian and non-riparian habitats to document changes that occur in seed bank flora over a two-year post-treatment period. Response to treatment varied spatially and temporally. However, following chemical and physical removal treatments, treated patches exhibited lower seed bank abundance and diversity than infested and patches lacking the weed, but differences were not statistically significant. Thus it will be safe to say that spraying herbicides using the recommended rate does not undermine restoration efforts.

Modified Atmosphere Packaging (MAP) for Control of Black Spot Formation in Chilled Prawns

The marketing of organically labeled prawns is predominately in a cooked or raw frozen form to avoid the development of melanosis (black spot). Certification for organic status prohibits the use of any added chemicals. The application of 60% CO2/40%N2 modified atmosphere to chilled (raw) prawns using two species of prawn was investigated for the ability to control black spot formation. Sensory assessment and microbiological counts were used to determine the end of product shelf life. Modified atmosphere packaged (MAP) prawns exhibited no melanosis for up to 16 days. The high quality life was retained for 12 days; shelf life of 16 days, according to standard microbiological criteria, was achieved, which is more than twice previously reported for non-MAP prawns. Results suggest MAP may be an effective method for the marketing of organically grown prawns as well as those produced by conventional prawn aquaculture without application of the normal chemicals used to prevent black spot. Copyright © 2014 Crown Copyright.