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  • Settles, A. Mark  (4)
  • 2005-2009  (4)
  • 1
    Online Resource
    Online Resource
    High‐Throughput Near‐Infrared Reflectance Spectroscopy for Predicting Quantitative and Qualitative Composition Phenotypes of Individual Maize Kernels
    Wiley ; 2009
    In:  Cereal Chemistry Vol. 86, No. 5 ( 2009-09), p. 556-564
    Details
    In: Cereal Chemistry, Wiley, Vol. 86, No. 5 ( 2009-09), p. 556-564
    Abstract: Near‐infrared reflectance (NIR) spectroscopy can be used for fast and reliable prediction of organic compounds in complex biological samples. We used a recently developed NIR spectroscopy instrument to predict starch, protein, oil, and weight of individual maize ( Zea mays ) seeds. The starch, protein, and oil calibrations have reliability equal or better to bulk grain NIR analyzers. We also show that the instrument can differentiate quantitative and qualitative seed composition mutants from normal siblings without a specific calibration for the constituent affected. The analyzer does not require a specific kernel orientation to predict composition or to differentiate mutants. The instrument collects a seed weight and a spectrum in 4–6 sec and can collect NIR data alone at a 20‐fold faster rate. The spectra are acquired while the kernel falls through a glass tube illuminated with broad spectrum light. These results show significant improvements over prior single‐kernel NIR systems, making this instrument a practical tool to collect quantitative seed phenotypes at high throughput. This technology has multiple applications for studying the genetic and physiological influences on seed traits.
    Type of Medium: Online Resource
    ISSN: 0009-0352 , 1943-3638
    URL: Article
    DOI: 10.1094/CCHEM-86-5-0556
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2016053-7
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  • 2
    Online Resource
    Online Resource
    Development of a calibration to predict maize seed composition using single kernel near infrared spectroscopy
    Elsevier BV ; 2006
    In:  Journal of Cereal Science Vol. 43, No. 2 ( 2006-3), p. 236-243
    Details
    In: Journal of Cereal Science, Elsevier BV, Vol. 43, No. 2 ( 2006-3), p. 236-243
    Type of Medium: Online Resource
    ISSN: 0733-5210
    URL: Article
    DOI: 10.1016/j.jcs.2005.11.003
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2006
    detail.hit.zdb_id: 1469001-9
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  • 3
    Online Resource
    Online Resource
    A novel genome-scale repeat finder geared towards transposons
    Oxford University Press (OUP) ; 2008
    In:  Bioinformatics Vol. 24, No. 4 ( 2008-02-15), p. 468-476
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 4 ( 2008-02-15), p. 468-476
    Abstract: Motivation: Repeats are ubiquitous in genomes and play important roles in evolution. Transposable elements are a common kind of repeat. Transposon insertions can be nested and make the task of identifying repeats difficult. Results: We develop a novel iterative algorithm, called Greedier, to find repeats in a target genome given a repeat library. Greedier distinguishes itself from existing methods by taking into account the fragmentation of repeats. Each iteration consists of two passes. In the first pass, it identifies the local similarities between the repeat library and the target genome. Greedier then builds graphs from this comparison output. In each graph, a vertex denotes a similar subsequence pair. Edges denote pairs of subsequences that can be connected to form higher similarities. In the second pass, Greedier traverses these graphs greedily to find matches to individual repeat units in the repeat library. It computes a fitness value for each such match denoting the similarity of that match. Matches with fitness values greater than a cutoff are removed, and the rest of the genome is stitched together. The similarity cutoff is then gradually reduced, and the iteration is repeated until no hits are returned from the comparison. Our experiments on the Arabidopsis and rice genomes show that Greedier identifies approximately twice as many transposon bases as those found by cross_match and WindowMasker. Moreover, Greedier masks far fewer false positive bases than either cross_match or WindowMasker. In addition to masking repeats, Greedier also reports potential nested transposon structures. Contact:  xli@cise.ufl.edu
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btm613
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    The Maize Viviparous8 Locus, Encoding a Putative ALTERED MERISTEM PROGRAM1-Like Peptidase, Regulates Abscisic Acid Accumulation and Coordinates Embryo and Endosperm Development  
    Oxford University Press (OUP) ; 2008
    In:  Plant Physiology Vol. 146, No. 3 ( 2008-03-03), p. 1193-1206
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 146, No. 3 ( 2008-03-03), p. 1193-1206
    Abstract: We describe a mutant of Zea mays isolated from a W22 inbred transposon population, widow's peak mutant1 (wpk1), with an altered pattern of anthocyanin synthesis and aleurone cell differentiation in endosperm. In addition, a failure of the developing mutant embryo to form leaf initials is associated with decreased expression of a subset of meristem regulatory genes that includes Abphyl1 and Td1. We show that the viviparous8 (vp8) mutant has a similar pleiotropic phenotype in the W22 inbred background in contrast to the viviparous embryo phenotype exhibited in the standard genetic background, and we confirmed that wpk1 is allelic to vp8. Further genetic analysis revealed that the standard vp8 stock contains an unlinked, partially dominant suppressor of the vp8 mutation that is not present in W22. Consistent with the early-onset viviparous phenotype of vp8, expression of several embryonic regulators, including LEC1/B3 domain transcription factors, was reduced in the mutant embryo. Moreover, reduced abscisic acid (ABA) content of vp8/wpk1 embryos was correlated with altered regulation of ABA biosynthesis, as well as ABA catabolic pathways. The ABA biosynthetic gene Vp14 was down-regulated in the nonsuppressed background, whereas the ZmABA8′oxA1a ABA 8′-hydroxylase gene was strongly up-regulated in both genetic backgrounds. Molecular analysis revealed that Vp8 encodes a putative peptidase closely related to Arabidopsis thaliana ALTERED MERISTEM PROGRAM1. Because the Vp8 regulates meristem development as well as seed maturation processes, including ABA accumulation, we propose that VP8 is required for synthesis of an unidentified signal that integrates meristem and embryo formation in seeds.
    Type of Medium: Online Resource
    ISSN: 1532-2548
    URL: Article
    DOI: 10.1104/pp.107.114108
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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