Loci Controlling Resistance to High Plains Virus and Wheat Streak Mosaic Virus in a B73 × Mo17 Population of Maize

High Plains disease has the potential to cause significant yield loss in susceptible corn (Zea mays L.) and wheat (Triticum aestivum L.) genotypes, especially in the central and western USA. The primary causal agent, High Plains virus (HPV), is vectored by wheat curl mite (WCM; Aceria tossicheila Keifer), which is also the vector of wheat streak mosaic virus (WSMV). In general, the two diseases occur together as a mixed infection in the field. The objective of this research was to characterize the inheritance of HPV and WSMV resistance using B73 (resistant to HPV and WSMV) × Mo17 (moderately susceptible to HPV and WSMV) recombinant inbred lines. A population of 129 recombinant inbred lines scored for 167 molecular markers was used to evaluate resistance to WSMV and to a mixed infection of WSMV and HPV. Loci conferring resistance to systemic movement of WSMV in plants mapped to chromosomes 3, 6, and 10, consistent with the map position of wsm2, wsm1, and wsm3, respectively. Major genes for resistance to systemic spread of HPV in doubly infected plants mapped to chromosomes 3 and 6, coincident or tightly linked with the WSMV resistance loci. Analysis of doubly infected plants revealed that chromosome 6 had a major effect on HPV resistance, consistent with our previous analysis of B73 × W64A and B73 × Wf9 populations. Quantitative trait loci (QTL) affecting resistance to localized symptom development mapped to chromosomes 4 (umc66), 5 (bnl5.40), and 6 (umc85), and accounted for 24% of the phenotypic variation. Localized symptoms may reflect the amount of mite feeding or the extent of virus spread at the point of infection. Identification of cosegregating markers may facilitate selection for HPV and WSMV resistance in corn breeding programs

Differential Gene Expression and Epiregulation of Alpha Zein Gene Copies in Maize Haplotypes

Multigenic traits are very common in plants and cause diversity. Nutritional quality is such a trait, and one of its factors is the composition and relative expression of storage protein genes. In maize, they represent a medium-size gene family distributed over several chromosomes and unlinked locations. Two inbreds, B73 and BSSS53, both from the Iowa Stiff Stock Synthetic collection, have been selected to analyze allelic and non-allelic variability in these regions that span between 80–500 kb of chromosomal DNA. Genes were copied to unlinked sites before and after allotetraploidization of maize, but before transposition enlarged intergenic regions in a haplotype-specific manner. Once genes are copied, expression of donor genes is reduced relative to new copies. Epigenetic regulation seems to contribute to silencing older copies, because some of them can be reactivated when endosperm is maintained as cultured cells, indicating that copy number variation might contribute to a reserve of gene copies. Bisulfite sequencing of the promoter region also shows different methylation patterns among gene clusters as well as differences between tissues, suggesting a possible position effect on regulatory mechanisms as a result of inserting copies at unlinked locations. The observations offer a potential paradigm for how different gene families evolve and the impact this has on their expression and regulation of their members

Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice

An endogenous 0.6-kb rice DNA transposon, nDart1-0, was found as an active nonautonomous element in a mutable virescent line, pyl-v, displaying leaf variegations. Here, we demonstrated that the active autonomous element aDart in pyl-v corresponds to Dart1-27 on chromosome 6 in Nipponbare, which carries no active aDart elements, and that aDart and Dart1-27 are identical in their sequences and chromosomal locations, indicating that Dart1-27 is epigenetically silenced in Nipponbare. The identification of aDart in pyl-v was first performed by map-based cloning and by detection of the accumulated transposase transcripts. Subsequently, various transposition activities of the cloned Dart1-27 element from Nipponbare were demonstrated in Arabidopsis. Dart1-27 in Arabidopsis was able to excise nDart1-0 and Dart1-27 from cloned sites, generating footprints, and to integrate into new sites, generating 8-bp target site duplications. In addition to Dart1-27, Nipponbare contains 37 putative autonomous Dart1 elements because their putative transposase genes carry no apparent nonsense or frameshift mutations. Of these, at least four elements were shown to become active aDart elements in transgenic Arabidopsis plants, even though considerable sequence divergence arose among their transposases. Thus, these four Dart1 elements and Dart1-27 in Nipponbare must be potential autonomous elements silenced epigenetically. The regulatory and evolutionary implications of the autonomous Dart1 elements and the development of an efficient transposon-tagging system in rice are discussed

Towards disappearing user interfaces for ubiquitous computing: human enhancement from sixth sense to super senses

The enhancement of human senses electronically is possible when pervasive computers interact unnoticeably with humans in Ubiquitous Computing. The design of computer user interfaces towards “disappearing” forces the interaction with humans using a content rather than a menu driven approach, thus the emerging requirement for huge number of non-technical users interfacing intuitively with billions of computers in the Internet of Things is met. Learning to use particular applications in Ubiquitous Computing is either too slow or sometimes impossible so the design of user interfaces must be naturally enough to facilitate intuitive human behaviours. Although humans from different racial, cultural and ethnic backgrounds own the same physiological sensory system, the perception to the same stimuli outside the human bodies can be different. A novel taxonomy for Disappearing User Interfaces (DUIs) to stimulate human senses and to capture human responses is proposed. Furthermore, applications of DUIs are reviewed. DUIs with sensor and data fusion to simulate the Sixth Sense is explored. Enhancement of human senses through DUIs and Context Awareness is discussed as the groundwork enabling smarter wearable devices for interfacing with human emotional memories

Genetic analysis of the interaction between Allium species and arbuscular mycorrhizal fungi

The response of Alliumcepa, A. roylei, A. fistulosum, and the hybrid A. fistulosum × A. roylei to the arbuscular mycorrhizal fungus (AMF) Glomus intraradices was studied. The genetic basis for response to AMF was analyzed in a tri-hybrid A. cepa × (A. roylei × A. fistulosum) population. Plant response to mycorrhizal symbiosis was expressed as relative mycorrhizal responsiveness (R′) and absolute responsiveness (R). In addition, the average performance (AP) of genotypes under mycorrhizal and non-mycorrhizal conditions was determined. Experiments were executed in 2 years, and comprised clonally propagated plants of each genotype grown in sterile soil, inoculated with G. intraradices or non-inoculated. Results were significantly correlated between both years. Biomass of non-mycorrhizal and mycorrhizal plants was significantly positively correlated. R′ was negatively correlated with biomass of non-mycorrhizal plants and hence unsuitable as a breeding criterion. R and AP were positively correlated with biomass of mycorrhizal and non-mycorrhizal plants. QTLs contributing to mycorrhizal response were located on a linkage map of the A. roylei × A. fistulosum parental genotype. Two QTLs from A. roylei were detected on chromosomes 2 and 3 for R, AP, and biomass of mycorrhizal plants. A QTL from A. fistulosum was detected on linkage group 9 for AP (but not R), biomass of mycorrhizal and non-mycorrhizal plants, and the number of stem-borne roots. Co-segregating QTLs for plant biomass, R and AP indicate that selection for plant biomass also selects for enhanced R and AP. Moreover, our findings suggest that modern onion breeding did not select against the response to AMF, as was suggested before for other cultivated species. Positive correlation between high number of roots, biomass and large response to AMF in close relatives of onion opens prospects to combine these traits for the development of more robust onion cultivars

Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

[EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.This work has been funded in part by European Unions Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website:http://www.cwrdiversity.org/. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolia Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Acquadro, A.; Barchi, L.; Gramazio, P.; Portis, E.; Vilanova Navarro, S.; Comino, C.; Plazas Ávila, MDLO.... (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS ONE. 12(7). https://doi.org/10.1371/journal.pone.0180774Se018077412