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

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

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

Design and fabrication of adjustable red-green-blue LED light arrays for plant research

BACKGROUND: Although specific light attributes, such as color and fluence rate, influence plant growth and development, researchers generally cannot control the fine spectral conditions of artificial plant-growth environments. Plant growth chambers are typically outfitted with fluorescent and/or incandescent fixtures that provide a general spectrum that is accommodating to the human eye and not necessarily supportive to plant development. Many studies over the last several decades, primarily in Arabidopsis thaliana, have clearly shown that variation in light quantity, quality and photoperiod can be manipulated to affect growth and control developmental transitions. Light emitting diodes (LEDs) has been used for decades to test plant responses to narrow-bandwidth light. LEDs are particularly well suited for plant growth chambers, as they have an extraordinary life (about 100,000 hours), require little maintenance, and use negligible energy. These factors render LED-based light strategies particularly appropriate for space-biology as well as terrestrial applications. However, there is a need for a versatile and inexpensive LED array platform where individual wavebands can be specifically tuned to produce a series of light combinations consisting of various quantities and qualities of individual wavelengths. Two plans are presented in this report. RESULTS: In this technical report we describe the practical construction of tunable red-green-blue LED arrays to support research in plant growth and development. Two light fixture designs and corresponding circuitry are presented. The first is well suited for a laboratory environment for use in a finite area with small plants, such as Arabidopsis. The second is expandable and appropriate for growth chambers. The application of these arrays to early plant developmental studies has been validated with assays of hypocotyl growth inhibition/promotion and phototropic curvature in Arabidopsis seedlings. CONCLUSION: The presentation of these proven plans for LED array construction allows the teacher, researcher or electronics aficionado a means to inexpensively build efficient, adjustable lighting modules for plant research. These simple and effective designs permit the construction of useful tools by programs short on electronics expertise. These arrays represent a means to modulate precise quality and quantity in experimental settings to test the effect of specific light combinations in regulating plant growth, development and plant-product yield

U.S. public opinion about the safety of gene editing in the agriculture and medical fields and the amount of evidence needed to improve opinions

Introduction: Implementation of gene editing in agriculture and medicine hinges on public acceptance. The objectives of this study were to explore U.S. public opinion about gene editing in agricultural and medical fields and to provide more insight into the relationship between opinions about the safety of gene editing and the potential impact of evidence to improve opinions about safety.Methods: Data were from two samples of U.S. respondents: 1,442 respondents in 2021 and 3,125 respondents in 2022. Survey respondents provided their opinions about the safety of gene editing in the agricultural and medical fields and answered questions about the number of studies or length of time without a negative outcome to improve opinions about the safety of gene editing in the agricultural and medical fields.Results: Results indicated that respondents in both samples were more familiar, more likely to have an opinion about safety, and more positive about the safety of gene editing in the agricultural field than in the medical field. Also, familiarity was more closely associated with opinions about safety than the strength of opinions.Discussion: These findings add to the literature examining perceptions of gene editing in the agricultural or medical fields separately. Opinions about the safety of gene editing were generally more favorable for respondents who were aware of the use of gene editing. These results support a proactive approach for effective communication strategies to inform the public about the use of gene editing in the agricultural and medical fields

Gene content and distribution in the nuclear genome of Fragaria vesca

Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.EEA BalcarceFil: Pontaroli, Ana Clara. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. University of Georgia. Department of Genetics; Estados UnidosFil: Rogers, Rebekah L. Harvard University. Department of Organismic and Evolutionary Biology; Estados Unidos. University of Georgia. Department of Genetics; Estados UnidosFil: Qian, Zhang. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Shields, Melanie E. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Davis, Thomas M. University of New Hampshire. Department of Biological Sciences; Estados UnidosFil: Folta, Kevin M. University of Florida. Horticultural Sciences Department; Estados UnidosFil: SanMiguel, Phillip. Purdue University. Department of Horticulture and Landscape Architecture; Estados UnidosFil: Bennetzen, Jeffrey L. University of Georgia. Department of Genetics; Estados Unido