The Functional Change and Deletion of FLC Homologs Contribute to the Evolution of Rapid Flowering in Boechera stricta

Differences in the timing of vegetative-to-reproductive phase transition have evolved independently and repeatedly in different plant species. Due to their specific biological functions and positions in pathways, some genes are important targets of repeated evolution – independent mutations on these genes caused the evolution of similar phenotypes in distantly related organisms. While many studies have investigated these genes, it remains unclear how gene duplications influence repeated phenotypic evolution. Here we characterized the genetic architecture underlying a novel rapid-flowering phenotype in Boechera stricta and investigated the candidate genes BsFLC1 and BsFLC2. The expression patterns of BsFLC1 suggested its function in flowering time suppression, and the deletion of BsFLC1 is associated with rapid flowering and loss of vernalization requirement. In contrast, BsFLC2 did not appear to be associated with flowering and had accumulated multiple amino acid substitutions in the relatively short evolutionary timeframe after gene duplication. These non-synonymous substitutions greatly changed the physicochemical properties of the original amino acids, concentrated non-randomly near a protein-interacting domain, and had greater substitution rate than synonymous changes. Here we suggested that, after recent gene duplication of the FLC gene, the evolution of rapid phenology was made possible by the change of BsFLC2 expression pattern or protein sequences and the deletion of BsFLC1

Reconfigurable Security: Edge Computing-based Framework for IoT

In various scenarios, achieving security between IoT devices is challenging since the devices may have different dedicated communication standards, resource constraints as well as various applications. In this article, we first provide requirements and existing solutions for IoT security. We then introduce a new reconfigurable security framework based on edge computing, which utilizes a near-user edge device, i.e., security agent, to simplify key management and offload the computational costs of security algorithms at IoT devices. This framework is designed to overcome the challenges including high computation costs, low flexibility in key management, and low compatibility in deploying new security algorithms in IoT, especially when adopting advanced cryptographic primitives. We also provide the design principles of the reconfigurable security framework, the exemplary security protocols for anonymous authentication and secure data access control, and the performance analysis in terms of feasibility and usability. The reconfigurable security framework paves a new way to strength IoT security by edge computing.Comment: under submission to possible journal publication

The Maintenance of Genetic Variation by Environmental Selection

<p>Understanding forces creating or maintaining the vast amount of biodiversity has been a major task of biologists. Genetic variation plays a major role in the creation of biodiversity because in contrast to environmental influence, genetic variants can be inherited. For a species in natural environments, genetic variation is generated by mutation, eliminated by genetic drift or selective sweep, and maintained by balancing selection that favors different alleles in different environments or time. In my dissertation, I will address how spatially heterogeneous environmental selection maintains genetic variation in two aspects.</p><p>Genes in the genome vary vastly in their level of polymorphism. Previous studies have used features within the genome, such as recombination rate or expression level, to explain the variation in gene polymorphism. One factor, however, that has often been overlooked is the effect of environmental adaptation on gene polymorphism. Specifically, if different alleles of a gene are responsible for local adaptation to distinct environments, the polymorphism of this gene will be actively maintained by spatially heterogeneous environmental selection. In the first part (Chapter 2) of my dissertation, I used publicly available genomic data from Arabidopsis thaliana to address this question. I found that environmental relevance of a gene has a significantly positive relationship with the variation in polymorphism level among genes in the Arabidopsis genome, consistent with the hypothesis that environmental selection actively maintains the polymorphism of environmentally responsive genes.</p><p>A biological species is formed by a mating pool of individuals, and for two populations of the same species, differentiation is often homogenized by gene flow. Reproductive isolation between populations allows genetic differentiation, and therefore speciation, the process in which full reproductive isolation is achieved between populations, plays important role in generating biodiversity. In the second part of my dissertation I used Boechera stricta to address how environmental selection contributes to speciation. In Chapter 3, I used niche modeling to show that environmental factors have more important roles than geographical distance in the genetic differentiation of EAST and WEST subspecies, and local water availability is the most important factor. In Chapter 4, I performed large-scale greenhouse experiments to identify key traits responsible for the EAST-WEST local adaptation, and that those traits have significantly larger differentiation between subspecies than neutral expectation. In Chapter 5, I performed quantitative trait loci mapping for those important traits and fitness in both parental environments and greenhouse. In summary, the second part of my dissertation provides an example to study ecological speciation from the environment, trait, to the genetic level.</p>Dissertatio

Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci

Background: Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits. Results: Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM. Conclusion: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices

Dynamical climatic model for time to flowering in Vigna radiata

Background: Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development. Results: We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature, precipitation, day length and solar radiation. We obtained model parameters by adaptation to the available experimental data. The models were validated by cross-validation and used to demonstrate that the phenology of adaptive traits, like flowering time, is strongly predicted not only by local environmental factors but also by plant geographic origin and genotype. Conclusions: Of local environmental factors maximal temperature appeared to be the most critical factor determining how faithfully the model describes the data. The models were applied to forecast time to flowering of accessions grown in Taiwan in future years 2020-2030

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

Number of misassemblies for different assembly strategies. Number of misassemblies for the de novo assembly results for E. coli DH1 and S. Parasanguinis FW213 are shown together with their standard errors of the mean. Group A [PE] and Group A [SE] represent all reads assembled as paired-end reads and single end reads, respectively. Group A [PE + SE] represents all the non-overlapped paired-end reads assembled together with merged reads. Group M [PE] and Group M [SE] represent Group M reads assembled as paired-end reads and single end reads, respectively. The numbers of misassemblies fluctuate a lot when depths of read number are low and gradually decreases until they reach a steady number. The paired-end reads (Group A [PE] and Group M [PE]) in S. Parasanguinis FW213 gave the lowest number of misassemblies when depths of read number are high. (TIFF 669 kb

Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)

Background: Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results: We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. Conclusions: The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts

DSAP: deep-sequencing small RNA analysis pipeline

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log2-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw