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  • 1
    Online Resource
    Online Resource
    Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
    Springer Science and Business Media LLC ; 2007
    In:  BMC Genomics Vol. 8, No. 1 ( 2007-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2007-12)
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/1471-2164-8-116
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2007
    detail.hit.zdb_id: 2041499-7
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  • 2
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    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
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  • 3
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    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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  • 4
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    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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  • 5
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    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
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  • 6
    Online Resource
    Online Resource
    The maize viviparous15 locus encodes the molybdopterin synthase small subunit
    Wiley ; 2006
    In:  The Plant Journal Vol. 45, No. 2 ( 2006-01), p. 264-274
    Details
    In: The Plant Journal, Wiley, Vol. 45, No. 2 ( 2006-01), p. 264-274
    Abstract: A new Zea mays viviparous seed mutant, viviparous15 ( vp15 ), was isolated from the UniformMu transposon‐tagging population. In addition to precocious germination, v p15 has an early seedling lethal phenotype. Biochemical analysis showed reduced activities of several enzymes that require molybdenum cofactor (MoCo) in vp15 mutant seedlings. Because MoCo is required for abscisic acid (ABA) biosynthesis, the viviparous phenotype is probably caused by ABA deficiency. We cloned the vp15 mutant using a novel high‐throughput strategy for analysis of high‐copy Mu lines: We used MuTAIL PCR to extract genomic sequences flanking the Mu transposons in the vp15 line. The Mu insertions specific to the vp15 line were identified by in silico subtraction using a database of MuTAIL sequences from 90 UniformMu lines. Annotation of the vp15 ‐specific sequences revealed a Mu insertion in a gene homologous to human MOCS2A, the small subunit of molybdopterin (MPT) synthase. Molecular analysis of two allelic mutations confirmed that Vp15 encodes a plant MPT synthase small subunit (ZmCNX7). Our results, and a related paper reporting the cloning of maize viviparous10 , demonstrate robust cloning strategies based on MuTAIL‐PCR. The Vp15 / CNX7 , together with other CNX genes, is expressed in both embryo and endosperm during seed maturation. Expression of Vp15 appears to be regulated independently of MoCo biosynthesis. Comparisons of Vp15 loci in genomes of three cereals and Arabidopsis thaliana identified a conserved sequence element in the 5′ untranslated region as well as a micro‐synteny among the cereals.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.2006.45.issue-2
    DOI: 10.1111/j.1365-313X.2005.02620.x
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 2020961-7
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  • 7
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    The maize Viviparous10/Viviparous13 locus encodes the Cnx1 gene required for molybdenum cofactor biosynthesis
    Wiley ; 2006
    In:  The Plant Journal Vol. 45, No. 2 ( 2006-01), p. 250-263
    Details
    In: The Plant Journal, Wiley, Vol. 45, No. 2 ( 2006-01), p. 250-263
    Abstract: Abscisic acid (ABA), auxin and nitrate are important signaling molecules that affect plant growth responses to the environment. The synthesis or metabolism of these compounds depends on the molybdenum cofactor (MoCo). We show that maize ( Zea mays ) viviparous10 ( vp10 ) mutants have strong precocious germination and seedling lethal phenotypes that cannot be rescued with tissue culture. We devised a novel PCR‐based method to clone a transposon‐tagged allele of vp10 , and show that Vp10 encodes the ortholog of Cnx1 , which catalyzes the final common step of MoCo synthesis. The seedling phenotype of vp10 mutants is consistent with disruptions in ABA and auxin biosynthesis, as well as a disruption in nitrate metabolism. Levels of ABA and auxin are reduced in vp10 mutants, and vp10 seedlings lack MoCo‐dependent enzyme activities that are repairable with exogenous molybdenum. vp10 and an Arabidopsis cnx1 mutant, chlorate6 ( chl6 ), have similar defects in aldehyde oxidase (AO) enzyme activity, which is required for ABA synthesis. Surprisingly, chl6 mutants do not show defects in abiotic stress responses. These observations confirm an orthologous function for Cnx1 and Vp10 , as well as defining a characteristic viviparous phenotype to identify other maize cnx mutants. Finally, the vp10 mutant phenotype suggests that cnx mutants can have auxin‐ as well as ABA‐biosynthesis defects, while the chl6 mutant phenotype suggests that low levels of AO activity are sufficient for normal abiotic stress responses.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.2006.45.issue-2
    DOI: 10.1111/j.1365-313X.2005.02621.x
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 2020961-7
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