Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele ...(Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.
Sugarcane mosaic virus SCMV ( Potyvirus sugarcane mosaic virus ) is an ssRNA virus that negatively affects yield in maize ( Zea mays ) worldwide. Resistance to SCMV is controlled primarily by a ...single dominant gene ( Scm1 ). The goal of this study was to identify sweet corn ( Z. mays ) inbreds that demonstrate resistance to SCMV, confirm the presence of genomic regions previously identified in maize associated with resistance, and identify other resistant loci in sweet corn. Eight plants from each of 563 primarily sweet corn inbred lines were tested for SCMV resistance. Plants were inoculated 14 d after planting and observed for signs of infection 24 d after planting. A subset of 420 inbred lines were genotyped using 7504 high-quality genotyping-by-sequencing single-nucleotide polymorphism markers. Population structure of the panel was observed, and a genome-wide association study was conducted to identify loci associated with SCMV resistance. Forty-six of the inbreds were found to be resistant to SCMV 10 d after inoculation. The Scm1 locus was confirmed with the presence of two significant loci on chromosome 6 ( P = 2.5 × 10 −8 and 1.6 × 10 −8 ), 5 Mb downstream of the Scm1 gene previously located at Chr6: 14194429.14198587 and the surrounding 2.7-Mb presence–absence variation. We did not identify other loci associated with resistance. This research has increased information on publicly available SCMV-resistant germplasm useful to future breeding projects and demonstrated that SCMV resistance in this sweet corn panel is driven by the Scm1 gene.
Breeding programs around the world continually collect data on large numbers of individuals. To be able to combine data collected across regions, years, and experiments, research communities develop ...standard operating procedures for data collection and measurement. One such method is a crop ontology, or a standardized vocabulary for collecting data on commonly measured traits. The ontology is also computer readable to facilitate the use of data management systems such as databases. Blueberry breeders and researchers across the United States have come together to develop the first standardized crop ontology in blueberry ( Vaccinium spp.). We provide an overview and report on the construction of the first blueberry crop ontology and the 178 traits and methods included within. Researchers of Vaccinium species—such as other blueberry species, cranberry, lingonberry, and bilberry—can use the described crop ontology to collect phenotypic data of greater quality and consistency, interoperability, and computer readability. Crop ontologies, as a shared data language, benefit the entire worldwide research community by enabling collaborative meta-analyses that can be used with genomic data for quantitative trait loci, genome-wide association studies, and genomic selection analysis.
Broader Relevance: The purpose of this research is to advance the scientific knowledge of sweet corn (Zea mays) genetics for breeders, growers, and consumers. Finer control of carbohydrates in sweet ...corn would lead to products that are preferable to consumers and contribute to lessening food waste. The wider incorporation of disease resistance in sweet corn means better yields and product quality. Genetic Analysis of Carbohydrates within Sweet Corn: Sweetness, and texture of sweet corn kernels are the most important traits for eating quality. This study investigates the variation and genetic associations of seven endosperm carbohydrates within the largest and most diverse sweet corn diversity panel to date. Predicted kernel carbohydrate composition was generated through high-throughput near-infrared spectroscopy. Two-stage genome-wide association studies (GWAS) were conducted with 77,414 markers on the carbohydrate measurements. We found that carbohydrate content varies widely across the panel and endosperm mutation groups varied significantly for most traits. Genotype was the main source of variance from all factors in the mixed linear model for all phenotypes (52%–73%). Association study found 373 significant markers between the seven carbohydrate traits in addition to the major endosperm mutants shrunken2 and sugary1. The large number of small effect size loci indicated that carbohydrates should be amenable to breeding through genomic prediction. Resistance to Sugar Cane Mosaic Virus: Sugarcane mosaic virus (SCMV) is a ssRNA virus that negatively impacts yield in Zea mays worldwide. The goal of this study was to identify sweet corn inbreds that demonstrate resistance to SCMV, confirm the presence of genomic regions previously identified associated with resistance, and identify other resistant loci in sweet corn. Eight plants from each of 563 primarily sweet corn inbred lines were tested for SCMV resistance. A GWAS was conducted to identify loci associated with SCMV resistance. Forty-six of the inbreds were found to be resistant to SCMV 10 days after inoculation. The Scm1 locus was confirmed with the presence of two significant markers on chromosome 6 (P = 2.5 × 10–8 and 1.6 × 10–8) downstream of the Scm1 gene. This research has increased information on publicly available SCMV resistant germplasm useful to future breeding projects.
We report on focus group feedback regarding the services provided by existing education-related Digital Libraries (DL). Participants provided insight into how they seek educational resources online, ...and what they perceive to be the shortcomings of existing educational DLs. Along with useful content, social interactions were viewed as important supplements for educational DLs. Such interactions lead to both an online community and new forms of content such as reviews and ratings. Based on our analysis of the focus group feedback, we propose DL 2.0, the next generation of digital library, which integrates social knowledge with DL content.
NSF’s NSDL is composed of domain-oriented pathways. Ensemble is the pathway for computing and supports the full range of computing education communities, providing a base for the development of ...programs that blend computing with other STEM areas (e.g., X-informatics and Computing + X), and producing digital library innovations that can be propagated to other NSDL pathways. Computing is a distributed community, including computer science, computer engineering, software engineering, information science, information systems, and information technology. Ensemble aims to provide much needed support for the many distinct yet overlapping educational programs in computing and their associated communities. To do this, Ensemble takes the form of a distributed portal providing access to the broad range of existing educational resources while preserving the collections and their associated curatorial processes. Ensemble encourages contribution, use, reuse, review, and evaluation of educational materials at multiple levels of granularity.
Ensemble Cassel, Lillian; Delcambre, Lois; Hislop, Gregory
Proceedings of the 45th ACM technical symposium on Computer science education,
03/2014
Conference Proceeding
The Ensemble computing portal originated under the NSF NSDL program and enjoys the respect and continued interest of the computing education community. The project has reached a maturity level at ...which it is time to focus on the long-term viability of the activity. The original proposal included a commitment from the Villanova University library to adopt the system and keep in running in perpetuity. However, merely keeping the system running will not preserve nor extend the true promise of the project. That requires an active, engaged community. The leaders of the Ensemble project invite our partner projects and the SIGCSE community to join us in an initial meeting of an organization devoted to the continued development and support of the Ensemble vision: that of a community of educators sharing their best efforts, showcasing the best resources, and archiving materials that deserve long term preservation.
Ensemble is a new NSF NSDL Pathways project working to establish a distributed digital library for computing education. This project is funded by the National Science Foundation. The project includes ...the CSTA portal for teaching materials for teachers in schools.
Ensemble Lillian (Boots), Cassel; Gregory, Hislop; Nadella, Bharath
Proceedings of the 14th annual ACM SIGCSE conference on Innovation and technology in computer science education,
07/2009
Conference Proceeding
Ensemble is a new NSF NSDL Pathways project working to establish a distributed digital library for computing education. This project is funded by the National Science Foundation. The project includes ...the CSTA portal for teaching materials for teachers in schools.
Ensemble Hislop, Gregory W.; Cassel, Lillian; Delcambre, Lois ...
Proceedings of the 10th ACM conference on SIG-information technology education,
10/2009
Conference Proceeding
Ensemble is a new NSF NSDL Pathways project working to establish a national, distributed digital library for computing education. Our project is building a distributed portal providing access to a ...broad range of existing educational resources for computing while preserving the collections and their associated curation processes. We want to encourage contribution, use, reuse, review and evaluation of educational materials at multiple levels of granularity and we seek to support the full range of computing education communities including computer science, computer engineering, software engineering, information science, information systems and information technology as well as other areas often called "computing + X" or "X informatics".
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