Accession-specific Parent-of-origin Dependent and Independent Genome Dosage Effects on Salt Tolerance in Arabidopsis Thaliana

Improving the salt stress tolerance of crops is an important goal in plant breeding. Changes in the number of chromosome pairs (i.e. ploidy level) cause genome dosage effects which can result in improved traits or emergence of novel traits. The genetic and epigenetic contribution of maternal or paternal chromosomes can differentially affect physiological and metabolic characteristics of F1 offspring. Hence genome dosage effects can be parent-of-origin independent or dependent. The model plant Arabidopsis thaliana displays both genome dosage and parent-of-origin effects on plant growth under normal, non-stress conditions. Using an insogenic ploidy series of diploid, triploid and tetraploid lines we investigate the extent of genome dosage effects and their parent-of-origin dependency on in vitro salt stress tolerance of seedlings across ten different A. thaliana accessions (genetic backgrounds). We demonstrate genome dosage effects on salt stress tolerance in five accessions, and using reciprocal triploid lines demonstrate parent-of-origin dependent genome dosage effects on salt stress tolerance in three accessions. Our results indicate that epigenetic genome dosage and genome dosage balance effects can have significant impacts on abiotic stress tolerance in plants.

EARBOX: An open tool for high-throughput measurements of the spatial organization of maize ears and inference of novel traits

Background: Characterizing plant genetic resources and their response to the environment through accurate measurement of relevant traits is crucial to genetics and breeding. The spatial organization of the maize ear provides insights into the response of grain yield to environmental conditions. Current automated methods for phenotyping the maize ear do not capture these spatial features. Results: We developed EARBOX, a low-cost, open-source system for automated phenotyping of maize ears. EARBOX integrates open-source technologies for both software and hardware that facilitate its deployment and improvement for specific research questions. The imaging platform consists of a customized box in which ears are repeatedly imaged as they rotate via motorized rollers. With deep learning based on convolutional neural networks, the image analysis algorithm uses a two-step procedure: ear-specific grain masks are first created and subsequently used to extract a range of trait data per ear, including ear shape and dimensions, the number of grains and their spatial organization, and the distribution of grain dimensions along the ear. The reliability of each trait was validated against ground-truth data from manual measurements. Moreover, EARBOX derives novel traits, inaccessible through conventional methods, especially the distribution of grain dimensions along grain cohorts, relevant for ear morphogenesis, and the distribution of abortion frequency along the ear, relevant for plant response to stress, especially soil water deficit. Conclusions: The proposed system provides robust and accurate measurements of maize ear traits including spatial features. Future developments include grain type and colour categorization. This method opens avenues for high-throughput genetic or functional studies in the context of plant adaptation to a changing environment.

The Role of Analogy in Adaptive Explanation

<p>Cases of 'convergence' (traits which have independently evolved in two or more lineages) could play an important role in the construction and corroboration of adaptive hypotheses. In particular, they could inform us about the evolutionary histories of novel traits. However, there is a problem of causal depth in the use of analogies. Natural Selection's affect on phenotype is constrained by phylogenetic history to a degree that we are unfounded in projecting adaptive stories from one lineage to another. I will argue for two approaches to resolve this issue. First, by constraining our catchment area to closely related lineages we can control for developmental noise. Second, by integrating analogies into explanations which incorporate other streams of evidence or bootstrapping an analogous model across many instantiations, we can overcome the problem of causal depth.</p>

The Role of Analogy in Adaptive Explanation

<p>Cases of 'convergence' (traits which have independently evolved in two or more lineages) could play an important role in the construction and corroboration of adaptive hypotheses. In particular, they could inform us about the evolutionary histories of novel traits. However, there is a problem of causal depth in the use of analogies. Natural Selection's affect on phenotype is constrained by phylogenetic history to a degree that we are unfounded in projecting adaptive stories from one lineage to another. I will argue for two approaches to resolve this issue. First, by constraining our catchment area to closely related lineages we can control for developmental noise. Second, by integrating analogies into explanations which incorporate other streams of evidence or bootstrapping an analogous model across many instantiations, we can overcome the problem of causal depth.</p>

Estimation of Pool Construction and Technical Error

Pooling animals with extreme phenotypes can improve the accuracy of genetic evaluation or provide genetic evaluation for novel traits at relatively low cost by exploiting large amounts of low-cost phenotypic data from animals in the commercial sector without pedigree (data from commercial ranches, feedlots, stocker grazing or processing plants). The average contribution of each animal to a pool is inversely proportional to the number of animals in the pool or pool size. We constructed pools with variable planned contributions from each animal to approximate errors with different numbers of animals per pool. We estimate pool construction error based on combining liver tissue, from pulverized frozen tissue mass from multiple animals, into eight sub-pools containing four animals with planned proportionality (1:2:3:4) by mass. Sub-pools were then extracted for DNA and genotyped using a commercial array. The extracted DNA from the sub-pools was used to form super pools based on DNA concentration as measured by spectrophotometry with planned contribution of sub-pools of 1:2:3:4. We estimate technical error by comparing estimated animal contribution using sub-samples of single nucleotide polymorphism (SNP). Overall, pool construction error increased with planned contribution of individual animals. Technical error in estimating animal contributions decreased with the number of SNP used.

Genetic Analysis of Various Traits in Oilseed Brassicas

Background: The combining ability and manifestation of heterosis within and among the species of oilseed brassicas (B. campestris, B. napus and B. juncea) were studied for yield and yield related traits in 12F1 combinations. Methods: All crosses (12F1) along with their parents (7 parents) were sown in randomized complete block design (RCBD) with three replications. Result: The analysis of variance showed extensive variability among the genotypes. The physical appearance of interspecific crosses was intermediate. B. campestris showed significant GCA effects among lines and B. juncea among testers for seed yield per plant. General combining behaviour of B. campestris was better as compared to B. napus and B. juncea. The SCA effects were higher within species than among the species. This also revealed that within the species B. juncea had more SCA (17.45) than B. napus (9.82) and B. campestris (8.01) for seed yield. The SCA showed the improvement of B. Juncea, is the best than other two species. It is also concluded that to obtain better yield, crossing within the species is more appropriate than among the species. Moreover, to introduce novel traits in brassica species is possible through interspecific hybridization.

Parallel evolution of urban-rural clines

Urbanization is the dominant trend of global land use change. The replicated nature of environmental change associated with urbanization should drive parallel evolution, yet insight into the repeatability of evolutionary processes in urban areas has been limited by a lack of multi-city studies. Here we leverage community science data on coat color in >60,000 eastern gray squirrels (Sciurus carolinensis) across 43 North American cities to test for parallel clines in melanism, a genetically based trait associated with thermoregulation and crypsis in gray squirrels. We show the prevalence of melanism in these mammals was positively associated with urbanization. Urban-rural clines in melanism were strongest in the largest cities with extensive forest cover and weakest or absent in cities with warm winter temperature, where thermal selection likely limits the prevalence of melanism. Our results demonstrate that novel traits can evolve in a highly repeatable manner among urban areas, modified by factors intrinsic to individual cities, including size, land cover, and climate.

The use of biotechnology in hop (Humulus lupulus L.) improvement

Hop (Humulus lupulus L.) is a clonally propagated, dioecious, perennial, climbing plant used commercially for their secondary metabolites. The resins containing α- and β-acids, and essential oils produced by the lupulin glands, present on the female flowers are used to add bitterness, aroma and flavour to beer. Recently, flavonoids, including chalcones and flavanones, of hops have been shown to exert a variety of biological activities, including oestrogenic and anticancerogenic characteristics. In this review, we provide a overview of the techniques and opportunities presented by the integration of plant biotechnology into hop improvement. The use of tissue culture techniques such as micropropagation, meristem culture, in vitro storage, adventitious shoot induction, callus culture and cell suspension culture in hops are briefly reviewed. The usefullness of genetic transformation technology to introduce novel traits into hop is also discussed.

Comparison of Analog Performance of AlN/β-Ga2O3 HEMT by Variation in Dielectric Materials

In the present paper, a high electron mobility transistor based on β-Gα2O3 material (BGO-HEMT) with different dielectrics (Si3N4, Al2O3, and HfO2) at the interface of aluminum nitride (AlN) and the gate is demonstrated. The device has a 10nm AlN layer with 50 nm barrier width, 50nm gate-length, and a value of 5 nm as gate-to-barrier thickness.A highly doped n+ material with a wider gap in between ohmic contact-barrier layers reveals the proposed device's novel traits. The performance is computd in terms of transfer characteristic, transconductance, gate capacitance, 2nd, and 3rd order transconductance values. The proposed structure reduced the dynamic & access resistance and provided a high gm value equal to 0.15S/µm,drain current density value of 650 A/mm (maximum) at Vds= 5 V. In the future, the proposed device can be utilized in high power radio frequency and microwave applications.

A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

BackgroundAn outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype—Lamiales flower monosymmetry—defined by a developmental program that relies on regulatory interaction among CYCLOIDEA , RADIALIS , DIVARICATA , and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. ResultsWe found that RADIALIS , DIVARICATA , and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. Additionally, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. ConclusionOur results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.