An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae

<p>Abstract</p> <p>Background</p> <p>The diploid woodland strawberry (<it>Fragaria vesca</it>) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for <it>Fragaria </it>and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry), and brambles and roses as well as with the cultivated octoploid strawberry, <it>F</it>. ×<it>ananassa</it>. <it>F. vesca </it>may be used to quickly address questions of gene function relevant to these valuable crop species. Although some <it>F. vesca </it>lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid <it>Fragaria </it>line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry.</p> <p>Results</p> <p>A highly inbred line, YW5AF7, of a diploid strawberry <it>Fragaria vesca </it>f. <it>semperflorens </it>line called "Yellow Wonder" (Y2) was developed and examined. Botanical descriptors were assessed for morphological characterization of this genotype. The plant line was found to be rapidly transformable using established techniques and media formulations.</p> <p>Conclusion</p> <p>The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses. These day-neutral plants have a small genome, a seed to seed cycle of 3.0 - 3.5 months, and produce fruit in 7.5 cm pots in a growth chamber. YW5AF7 is runnerless and therefore easy to maintain in the greenhouse, forms abundant branch crowns for vegetative propagation, and produces highly aromatic yellow fruit throughout the year in the greenhouse. <it>F. vesca </it>can be transformed with <it>Agrobacterium tumefaciens</it>, making these plants suitable for insertional mutagenesis, RNAi and overexpression studies that can be compared against a stable baseline of phenotypic descriptors and can be readily genetically substantiated.</p

Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry.

Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in host-pathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. We reveal the presence of 15 RALF genes in F. vesca genotype Hawaii 4 and 50 in Fragaria x ananassa cv. Camarosa, showing a non-homogenous localization of genes among the different Fragaria x ananassa subgenomes. Expression analysis of Fragaria x ananassa RALF genes upon infection with Colletotrichum acutatum or Botrytis cinerea showed that FanRALF3-1 was the only fruit RALF gene upregulated after fungal infection. In silico analysis was used to identify distinct pathogen inducible elements upstream of the FanRALF3-1 gene. Agroinfiltration of strawberry fruit with deletion constructs of the FanRALF3-1 promoter identified a 5' region required for FanRALF3-1 expression in fruit, but failed to identify a region responsible for fungal induced expression

What’s Trust Got to Do with It? Exploring Agricultural Science Podcast Producers’, Guests’, and Listeners’ Perceptions and Levels of Trust in Science

Little research to this point has examined food, agricultural, natural resource, and human science (FANRHS) podcast creation, the trustworthiness of the information presented, and the credibility of the individuals speaking on the podcast. The purpose of this study was to explore the level of trust in science of FANRHS podcast producers, guests, and listeners. The study followed an explanatory sequential mixed-method design beginning with an online survey instrument to measure trust in science and later, semi-structured interviews to further explore participants’ perceptions of trust and trust in science. Results showed participants had moderate to moderately high levels of trust in science. The study produced recommendations for podcast producers and guests regarding how to increase the credibility of their content and how to better foster science engagement. Future research should delineate trust based on various sub-topics within FANRHS and further explore specific communication tactics and framing strategies to create trusting relationships with podcast listeners

Podcasts in Production: An Examination of Current and Best Practices for Agricultural and Natural Resource Podcast Producers

Little research has been done on the production and use of podcasts in the fields of food, agriculture, natural resource, or human sciences (FANRHS). Currently, there is limited information for best practices on creating an effective FANRHS podcast to reach a target public audience. The purpose of this study was to examine existing practices and experiences of FANRHS podcast producers. The findings of this study will be of interest to organizations, institutions, and individuals who currently produce or are interested in producing an educational or science-based podcast. This study provided foundational information on podcast creation and maintenance. Future research should explore optimal podcast formats and content design to influence listeners’ perception and knowledge level on FANRHS science topics

U.S. adult attitudes about biotechnology and risk aversion to gene editing

While attitudes toward genetically modified (GM) foods have a long study history, there is still much to learn about U.S. adults’ attitudes toward gene edited (GnEd) food. We combine results from two online surveys; one study of 1,331 respondents used a randomized approach to compare views between GnEd and GM foods, and the other study of 1,442 respondents used a framing approach to compare GnEd and fungicide as a solution to combat an agricultural fungus. Overall, respondents viewed GnEd and GM similarly. However, the results provide hints that there are more positive attitudes about the capability of GnEd to positively impact the food system. There was no obvious preference for using either GnEd or fungicide to combat an agricultural disease; however, there were some small framing effects. Combined, our results show some differences emerging in the discussion of GnEd versus GM and reduced some of the risk aversion for GnEd compared to fungicide use.Brandon R. McFadden (Department of Agricultural Economics and Agribusiness, University of Arkansas), Joy N. Rumble (Department of Agricultural Communication, Education, and Leadership, The Ohio State University), Kathryn A. Stofer (Department of Agricultural Education and Communication, University of Florida), Kevin M. Folta (Department of Agricultural Education and Communication, University of Florida), Madison Dyment (Horticultural Sciences Department, University of Florida), Corresponding author: Brandon R. McFaddenIncludes bibliographical reference

A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae, Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing

Fragaria iinumae Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for F. iinumae. The F. iinumae linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter “Array”), and genotyping by sequencing (GBS). The F2 generation mapping population was derived by selfing F. iinumae hybrid F1D, the product of a cross between two divergent F. iinumae accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the Fragaria vesca ssp. vesca L. ‘Hawaii 4’ pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between F. iinumae and F. vesca, and/or to F. vesca genomic assembly errors. The Fii map provides a basis for anchoring a F. iinumae genome assembly as a prerequisite for constructing a second diploid reference genome for Fragaria

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry's complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement

A Randomized Group Approach to Identifying Label Effects

Motivated by the National Bioengineered Food Disclosure Standard (NBFDS), which requires companies to label bioengineered food products, this paper examines the choice effects of using a symbol approved by the standard relative to using text to disclose that a food product has bioengineered contents. Choice effects were determined using a randomized group design that assigned respondents to one-of-two labeled choice experiment groups. One group selected products that used the symbol disclosure and the other group selected products using text disclosure. Besides a label, the price was the only attribute displayed to respondents during the choice experiment and varied at three levels. The same price levels were used for all labels, and prices were balanced within a label, and balanced and orthogonal across labels. This randomized design using a discrete choice experiment allows for the identification of group effects, which in this paper are the choice effects associated with the form of bioengineering disclosure

Can Anyone Hear Us? An Exploration of Echo Chambers at a Land-Grant University

Faculty at land-grant universities are expected to engage in some form of Extension, or science communication, as part of the land-grant mission. However, critics have claimed these institutions are out of touch with their stakeholders’ needs and faculty mainly communicate with others in academia. This engagement with a homogenous group reflects the concepts of echo chambers, where people are only exposed to information that aligns with their beliefs and current knowledge and discredit opposing information. An explanatory mixed-methods design was used to understand land-grant faculty’s engagement in echo chambers. A survey was distributed to a census of tenure-track faculty in the University of Florida’s Institute of Food and Agricultural Sciences to understand respondents’ engagement in echo chambers. Follow-up interviews were conducted with 13 of the survey respondents to further explore their audiences and channels used in science communication to understand their engagement in echo chambers. Survey results indicated faculty did not necessarily participate in echo chambers, but they also did not contribute to an open communication network. However, the interviews found participants were interested in reaching new audiences yet struggled to communicate with stakeholders. The participants also reported wanting to find alternative channels to peer reviewed journals to help disseminate their work. The findings from this study indicated faculty contributed to a type of echo chamber, but rather than viewing their stakeholders’ opinions as false, they simply did not hear the opinions. Agricultural communicators should work with land-grant faculty administrators to identify appropriate audiences and channels for science communication