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  • 1
    Online Resource
    Online Resource
    Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn
    Springer Science and Business Media LLC ; 2021
    In:  Nature Communications Vol. 12, No. 1 ( 2021-02-23)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-02-23)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-021-21380-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
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  • 2
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    Online Resource
    Accelerating Biological Insight for Understudied Genes
    Oxford University Press (OUP) ; 2022
    In:  Integrative and Comparative Biology Vol. 61, No. 6 ( 2022-02-05), p. 2233-2243
    Details
    In: Integrative and Comparative Biology, Oxford University Press (OUP), Vol. 61, No. 6 ( 2022-02-05), p. 2233-2243
    Abstract: The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.
    Type of Medium: Online Resource
    ISSN: 1540-7063 , 1557-7023
    URL: Article
    DOI: 10.1093/icb/icab029
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2159110-6
    SSG: 12
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  • 3
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    Theoretical design of a space bioprocessing system to produce recombinant proteins
    Springer Science and Business Media LLC ; 2023
    In:  npj Microgravity Vol. 9, No. 1 ( 2023-09-16)
    Details
    In: npj Microgravity, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2023-09-16)
    Abstract: Space-based biomanufacturing has the potential to improve the sustainability of deep space exploration. To advance biomanufacturing, bioprocessing systems need to be developed for space applications. Here, commercial technologies were assessed to design space bioprocessing systems to supply a liquid amine carbon dioxide scrubber with active carbonic anhydrase produced recombinantly. Design workflows encompassed biomass dewatering of 1 L Escherichia coli cultures through to recombinant protein purification. Non-crew time equivalent system mass (ESM) analyses had limited utility for selecting specific technologies. Instead, bioprocessing system designs focused on minimizing complexity and enabling system versatility. Three designs that differed in biomass dewatering and protein purification approaches had nearly equivalent ESM of 357–522 kg eq. Values from the system complexity metric (SCM), technology readiness level (TRL), integration readiness level (IRL), and degree of crew assistance metric identified a simpler, less costly, and easier to operate design for automated biomass dewatering, cell lysis, and protein affinity purification.
    Type of Medium: Online Resource
    ISSN: 2373-8065
    URL: Article
    DOI: 10.1038/s41526-023-00324-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2823626-9
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  • 4
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    Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 52 ( 2020-12-29), p. 33177-33185
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 52 ( 2020-12-29), p. 33177-33185
    Abstract: Endosperm starch synthesis is a primary determinant of grain yield and is sensitive to high-temperature stress. The maize chloroplast-localized 6-phosphogluconate dehydrogenase (6PGDH), PGD3, is critical for endosperm starch accumulation. Maize also has two cytosolic isozymes, PGD1 and PGD2, that are not required for kernel development. We found that cytosolic PGD1 and PGD2 isozymes have heat-stable activity, while amyloplast-localized PGD3 activity is labile under heat stress conditions. We targeted heat-stable 6PGDH to endosperm amyloplasts by fusing the Waxy1 chloroplast targeting the peptide coding sequence to the Pgd1 and Pgd2 open reading frames (ORFs). These WPGD1 and WPGD2 fusion proteins import into isolated chloroplasts, demonstrating a functional targeting sequence. Transgenic maize plants expressing WPGD1 and WPGD2 with an endosperm-specific promoter increased 6PGDH activity with enhanced heat stability in vitro. WPGD1 and WPGD2 transgenes complement the pgd3 -defective kernel phenotype, indicating the fusion proteins are targeted to the amyloplast. In the field, the WPGD1 and WPGD2 transgenes can mitigate grain yield losses in high–nighttime-temperature conditions by increasing kernel number. These results provide insight into the subcellular distribution of metabolic activities in the endosperm and suggest the amyloplast pentose phosphate pathway is a heat-sensitive step in maize kernel metabolism that contributes to yield loss during heat stress.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2010179117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
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    Classification approaches for sorting maize ( Zea mays subsp. mays ) haploids using single‐kernel near‐infrared spectroscopy
    Wiley ; 2020
    In:  Plant Breeding Vol. 139, No. 6 ( 2020-12), p. 1103-1112
    Details
    In: Plant Breeding, Wiley, Vol. 139, No. 6 ( 2020-12), p. 1103-1112
    Abstract: Doubled haploids (DHs) are an important breeding tool for creating maize inbred lines. One bottleneck in the DH process is the manual separation of haploids from among the much larger pool of hybrid siblings in a haploid induction cross. Here, we demonstrate the ability of single‐kernel near‐infrared reflectance spectroscopy (skNIR) to identify haploid kernels. The skNIR is a high‐throughput device that acquires an NIR spectrum to predict individual kernel traits. We collected skNIR data from haploid and hybrid kernels in 15 haploid induction crosses and found significant differences in multiple traits such as percent oil, seed weight, or volume, within each cross. The two kernel classes were separated by their NIR profile using Partial Least Squares Linear Discriminant Analysis (PLS‐LDA). A general classification model, in which all induction crosses were used in the discrimination model, and a specific model, in which only kernels within a specific induction cross, were compared. Specific models outperformed the general model and were able to enrich a haploid selection pool to above 50% haploids. Applications for the instrument are discussed.
    Type of Medium: Online Resource
    ISSN: 0179-9541 , 1439-0523
    URL: Issue
    URL: Article
    DOI: 10.1111/pbr.v139.6
    DOI: 10.1111/pbr.12857
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020488-7
    SSG: 12
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  • 6
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    Characterization of pea seed nutritional value within a diverse population of Pisum sativum
    Public Library of Science (PLoS) ; 2021
    In:  PLOS ONE Vol. 16, No. 11 ( 2021-11-4), p. e0259565-
    Details
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 16, No. 11 ( 2021-11-4), p. e0259565-
    Abstract: Micronutrient malnutrition is a global concern that affects more than two billion people worldwide. Pea ( Pisum sativum ) is a nutritious pulse crop with potential to assist in tackling hidden hunger. Here we report seed ionomic data of 96 diverse pea accessions collected via inductively coupled plasma mass spectrometry (ICP-MS). We found a 100 g serving of peas provides the following average percent daily value for U.S. recommendations: 8% Ca, 39% Mg, 73% Cu, 37% Fe, 63% Mn, 45% Zn, 28% K, and 43% P. Correlations were observed between the majority of minerals tested suggesting strong interrelationships between mineral concentration levels. Hierarchical clustering identified fifteen accessions with high-ranking mineral concentrations. Thirty accessions could be compared to earlier inductively coupled optical emission spectrometry (ICP-OES) data, which revealed significant differences particularly for elements at extreme low or high levels of accumulation. These results improve our understanding of the range of variation in mineral content found in peas and provide additional mineral data resources for germplasm selection.
    Type of Medium: Online Resource
    ISSN: 1932-6203
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.1371/journal.pone.0259565
    DOI: 10.1371/journal.pone.0259565.g001
    DOI: 10.1371/journal.pone.0259565.g002
    DOI: 10.1371/journal.pone.0259565.g003
    DOI: 10.1371/journal.pone.0259565.g004
    DOI: 10.1371/journal.pone.0259565.t001
    DOI: 10.1371/journal.pone.0259565.t002
    DOI: 10.1371/journal.pone.0259565.t003
    DOI: 10.1371/journal.pone.0259565.t004
    DOI: 10.1371/journal.pone.0259565.s001
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2021
    detail.hit.zdb_id: 2267670-3
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  • 7
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    Protein, weight, and oil prediction by single‐seed near‐infrared spectroscopy for selection of seed quality and yield traits in pea ( Pisum sativum )
    Wiley ; 2020
    In:  Journal of the Science of Food and Agriculture Vol. 100, No. 8 ( 2020-06), p. 3488-3497
    Details
    In: Journal of the Science of Food and Agriculture, Wiley, Vol. 100, No. 8 ( 2020-06), p. 3488-3497
    Abstract: Pea ( Pisum sativum ) is a prevalent cool‐season crop that produces seeds valued for their high protein content. Modern cultivars have incorporated several traits that improved harvested yield. However, progress toward improving seed quality has received less emphasis, in part due to the lack of tools for easily and rapidly measuring seed traits. In this study we evaluated the accuracy of single‐seed near‐infrared spectroscopy (NIRS) for measuring pea‐seed weight, protein, and oil content. A total of 96 diverse pea accessions were analyzed using both single‐seed NIRS and wet chemistry methods. To demonstrate field relevance, the single‐seed NIRS protein prediction model was used to determine the impact of seed treatments and foliar fungicides on the protein content of harvested dry peas in a field trial. RESULTS External validation of partial least squares (PLS) regression models showed high prediction accuracy for protein and weight (R 2 = 0.94 for both) and less accuracy for oil (R 2 = 0.74). Single‐seed weight was weakly correlated with protein and oil content in contrast with previous reports. In the field study, the single‐seed NIRS predicted protein values were within 10 mg g −1 of an independent analytical reference measurement and were sufficiently precise to detect small treatment effects. CONCLUSION The high accuracy of protein and weight estimation show that single‐seed NIRS could be used in the dual selection of high‐protein, high‐weight peas early in the breeding cycle, allowing for faster genetic advancement toward improved pea nutritional quality. © 2020 Society of Chemical Industry
    Type of Medium: Online Resource
    ISSN: 0022-5142 , 1097-0010
    URL: Issue
    URL: Article
    DOI: 10.1002/jsfa.v100.8
    DOI: 10.1002/jsfa.10389
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2001807-1
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  • 8
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    Table_1.XLSX
    Frontiers Media SA ; 2020
    In:  Frontiers in Plant Science Vol. 11 ( 2020-5-25)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 11 ( 2020-5-25)
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2020.00631
    DOI: 10.3389/fpls.2020.00631.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 9
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    Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize
    Springer Science and Business Media LLC ; 2022
    In:  Nature Communications Vol. 13, No. 1 ( 2022-09-13)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-09-13)
    Abstract: Historically, xenia effects were hypothesized to be unique genetic contributions of pollen to seed phenotype, but most examples represent standard complementation of Mendelian traits. We identified the imprinted dosage-effect defective1 ( ded1 ) locus in maize ( Zea mays ) as a paternal regulator of seed size and development. Hypomorphic alleles show a 5–10% seed weight reduction when ded1 is transmitted through the male, while homozygous mutants are defective with a 70–90% seed weight reduction. Ded1 encodes an R2R3-MYB transcription factor expressed specifically during early endosperm development with paternal allele bias. DED1 directly activates early endosperm genes and endosperm adjacent to scutellum cell layer genes, while directly repressing late grain-fill genes. These results demonstrate xenia as originally defined: Imprinting of Ded1 causes the paternal allele to set the pace of endosperm development thereby influencing grain set and size.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-022-33055-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
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  • 10
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    Protein, weight, and oil prediction by single-seed near-infrared spectroscopy for selection of seed quality and yield traits in pea ( Pisum sativum ).
    CABI Publishing ; 2020
    In:  agriRxiv Vol. 2020 ( 2020-01)
    Details
    In: agriRxiv, CABI Publishing, Vol. 2020 ( 2020-01)
    Abstract: Background: Pea ( Pisum sativum ) is a prevalent cool season crop that produces seeds valued for high protein content. Modern cultivars have incorporated several traits that improved harvested yield. However, progress toward improving seed quality has received less emphasis, in part due to the lack of tools for easily and rapidly measuring seed traits. In this study we evaluated the accuracy of single-seed near-infrared spectroscopy (NIRS) for measuring pea seed weight, protein, and oil content. A total of 96 diverse pea accessions were analyzed using both single-seed NIRS and wet chemistry methods. To demonstrate field relevance, the single-seed NIRS protein prediction model was used to determine the impact of seed treatments and foliar fungicides on protein content of harvested dry peas in a field trial. Results: External validation of Partial Least Squares (PLS) regression models showed high prediction accuracy for protein and weight (R 2 = 0.94 for both) and less accuracy for oil (R 2 = 0.75). Single seed weight was not significantly correlated with protein or oil content in contrast to previous reports. In the field study, the single-seed NIRS predicted protein values were within 1% of an independent analytical reference measurement and were sufficiently precise to detect small treatment effects. Conclusion: The high accuracy of protein and weight estimation show that single-seed NIRS could be used in the dual selection of high protein, high weight peas early in the breeding cycle allowing for faster genetic advancement toward improved pea nutritional quality.
    Type of Medium: Online Resource
    ISSN: 2791-1969
    URL: Article
    DOI: 10.31220/osf.io/7j9cy
    Language: Spanish
    Publisher: CABI Publishing
    Publication Date: 2020
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