Using turbulence scintillation to assist object ranging from a single camera viewpoint.

Image distortions caused by atmospheric turbulence are often treated as unwanted noise or errors in many image processing studies. Our study, however, shows that in certain scenarios the turbulence distortion can be very helpful in enhancing image processing results. This paper describes a novel approach that uses the scintillation traits recorded on a video clip to perform object ranging with reasonable accuracy from a single camera viewpoint. Conventionally, a single camera would be confused by the perspective viewing problem, where a large object far away looks the same as a small object close by. When the atmospheric turbulence phenomenon is considered, the edge or texture pixels of an object tend to scintillate and vary more with increased distance. This turbulence induced signature can be quantitatively analyzed to achieve object ranging with reasonable accuracy. Despite the inevitable fact that turbulence will cause random blurring and deformation of imaging results, it also offers convenient solutions to some remote sensing and machine vision problems, which would otherwise be difficult.

Addition of individual chromosomes of maize inbreds B73 and Mo17 to oat cultivars Starter and Sun II: maize chromosome retention, transmission, and plant phenotype.

Oat-maize addition (OMA) lines with one, or occasionally more, chromosomes of maize (Zea mays L., 2n = 2x = 20) added to an oat (Avena sativa L., 2n = 6x = 42) genomic background can be produced via embryo rescue from sexual crosses of oat x maize. Self-fertile disomic addition lines of different oat genotypes, mainly cultivar Starter, as recipient for maize chromosomes 1, 2, 3, 4, 5, 6, 7, 9, and the short arm of 10 and a monosomic addition line for chromosome 8, have been reported previously in which the sweet corn hybrid Seneca 60 served as the maize chromosome donor. Here we report the production and characterization of a series of new OMA lines with inbreds B73 and Mo17 as maize chromosome donors and with oat cultivars Starter and Sun II as maize chromosome recipients. Fertile disomic OMA lines were recovered for B73 chromosomes 1, 2, 4, 5, 6, 8, 9, and 10 and Mo17 chromosomes 2, 4, 5, 6, 8, and 10. These lines together with non-fertile (oat x maize) F(1) plants with chromosome 3 and chromosome 7 of Mo17 individually added to Starter oat provide DNA of additions to oat of all ten individual maize chromosomes between the two maize inbreds. The Mo17 chromosome 10 OMA line was the first fertile disomic OMA line obtained carrying a complete chromosome 10. The B73 OMA line for chromosome 1 and the B73 and Mo17 OMA lines for chromosome 8 represent disomic OMA lines with improved fertility and transmission of the addition chromosome compared to earlier Seneca 60 versions. Comparisons among the four oat-maize parental genotype combinations revealed varying parental effects and interactions on frequencies of embryo recovery, embryo germination, F(1) plantlets with maize chromosomes, the specific maize chromosomes retained and transmitted to F(2) progeny, and phenotypes of self-fertile disomic addition plants. As opposed to the previous use of a hybrid Seneca 60 maize stock as donor of the added maize chromosomes, the recovered B73 and Mo17 OMA lines provide predictable genotypes for use as tools in physical mapping of maize DNA sequences, including inter-genic sequences, by simple presence/absence assays. The recovered OMA lines represent unique materials for maize genome analysis, genetic, physiological, and morphological studies, and a possible means to transfer maize traits to oat. Descriptions of these materials can be found at http://agronomy.cfans.umn.edu/Maize_Genomics.html .

Maize centromere mapping: a comparison of physical and genetic strategies.

Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies. Surprisingly, the choice of mapping technique was not the critical determining factor. Instead, on 4 chromosomes, results from all techniques were consistent with a single centromere position. On chromosomes 1, 3, and 6, centromere positions were not consistent even in studies using the same technique. The conflicting centromere map positions on chromosomes 1, 3, and 6 could be explained by pericentric inversions or alternative centromere positions on these chromosomes.

Profiling expression changes caused by a segmental aneuploid in maize.

BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that approximately 40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSION: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.

Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize.

Flowering time is a fundamental trait of maize adaptation to different agricultural environments. Although a large body of information is available on the map position of quantitative trait loci for flowering time, little is known about the molecular basis of quantitative trait loci. Through positional cloning and association mapping, we resolved the major flowering-time quantitative trait locus, Vegetative to generative transition 1 (Vgt1), to an approximately 2-kb noncoding region positioned 70 kb upstream of an Ap2-like transcription factor that we have shown to be involved in flowering-time control. Vgt1 functions as a cis-acting regulatory element as indicated by the correlation of the Vgt1 alleles with the transcript expression levels of the downstream gene. Additionally, within Vgt1, we identified evolutionarily conserved noncoding sequences across the maize-sorghum-rice lineages. Our results support the notion that changes in distant cis-acting regulatory regions are a key component of plant genetic adaptation throughout breeding and evolution.

Mapping QTLs contributing to Ustilago maydis resistance in specific plant tissues of maize.

Quantitative trait loci (QTL) contributing to the frequency and severity of Ustilago maydis infection in the leaf, ear, stalk, and tassel of maize plants were mapped using an A188 x CMV3 and W23 x CMV3 recombinant inbred (RI) populations. QTLs mapped to genetic bins 2.04 and 9.04-9.05 of the maize genome contributed strongly (R (2) = 18-28%) to variation in the frequency and severity of U. maydis infection over the entire plant in both populations and within the majority of environments. QTLs mapped to bins 3.05, 3.08, and 8.00 in the A188 x CMV3 population and bin 4.05 in both populations significantly contributed to the frequency or severity of infection in only the tassel tissue. QTLs mapped to bin 1.07 in the A188 x CMV3 population and bin 7.00 in the W23 x CMV3 population contributed to U. maydis resistance in only the ear tissue. Interestingly, the CMV3 allele of the QTL mapped to bin 1.10 in the A188 x CMV3 population significantly contributed to U. maydis susceptibility in the ear and stalk but significantly increased resistance in the tassel tissue. Digenic epistatic interactions between the QTL mapped to bin 5.08 and four distinct QTLs significantly contributed to the frequency and severity of infection over the entire plant and within the tassel tissue of the A188 x CMV3 population. Several QTLs detected in this study mapped to regions of the maize genome containing previously mapped U. maydis resistance QTLs and genes involved in plant disease resistance.

Reduction of Escherichia coli O157:H7 populations in cattle by addition of colicin E7-producing E. coli to feed.

A cattle trial using artificially inoculated calves was conducted to determine the effect of the addition of colicinogenic Escherichia coli strains capable of producing colicin E7 (a 61-kDa DNase) to feed on the fecal shedding of serotype O157:H7. The experiment was divided into three periods. In period 1, which lasted 24 days, six calves were used as controls, and eight calves received 10(7) CFU of E. coli (a mixture of eight colicinogenic E. coli strains) per g of feed. Both groups were orally inoculated with nalidixic acid-resistant E. coli O157:H7 strains 7 days after the treatment started. In periods 2 and 3, the treatment and control groups were switched, and the colicinogenic E. coli dose was increased 10-fold. During period 3, which lasted as long as period 1, both groups were reinoculated with E. coli O157:H7. The numbers of E. coli O157:H7 were consistently greater in the control groups during the three periods, but comparisons within each time period determined a statistically significant (P < 0.05) difference only at day 21 of period 1. However, when the daily average counts were compared between the period 1 control group and the period 3 treatment group that included the same six animals, an overall reduction of 1.1 log(10) CFU/g was observed, with a maximum decrease of 1.8 log(10) CFU/g at day 21 (overall statistical significance, P = 0.001). Serotype O157:H7 was detected in 44% of the treatment group's intestinal tissue samples and in 64% of those from the control group (P < 0.04). These results indicated that the daily addition of 10(8) CFU of colicin E7-producing E. coli per gram of feed could reduce the fecal shedding of serotype O157:H7.

Dissecting the maize genome by using chromosome addition and radiation hybrid lines.

We have developed from crosses of oat (Avena sativa L.) and maize (Zea mays L.) 50 fertile lines that are disomic additions of individual maize chromosomes 1-9 and chromosome 10 as a short-arm telosome. The whole chromosome 10 addition is available only in haploid oat background. Most of the maize chromosome disomic addition lines have regular transmission; however, chromosome 5 showed diminished paternal transmission, and chromosome 10 is transmitted to offspring only as a short-arm telosome. To further dissect the maize genome, we irradiated monosomic additions with gamma rays and recovered radiation hybrid (RH) lines providing low- to medium-resolution mapping for most of the maize chromosomes. For maize chromosome 1, mapping 45 simple-sequence repeat markers delineated 10 groups of RH plants reflecting different chromosome breaks. The present chromosome 1 RH panel dissects this chromosome into eight physical segments defined by the 10 groups of RH lines. Genomic in situ hybridization revealed the physical size of a distal region, which is represented by six of the eight physical segments, as being approximately 20% of the length of the short arm, representing approximately one-third of the genetic chromosome 1 map. The distal approximately 20% of the physical length of the long arm of maize chromosome 1 is represented by a single group of RH lines that spans >23% of the total genetic map. These oat-maize RH lines provide valuable tools for physical mapping of the complex highly duplicated maize genome and for unique studies of inter-specific gene interactions.

Maize DNA-sequencing strategies and genome organization.

A large amount of repetitive DNA complicates the assembly of the maize genome sequence. Genome-filtration techniques, such as methylation-filtration and high-CoT separation, enrich gene sequences in genomic libraries. These methods may provide a low-cost alternative to whole-genome sequencing for maize and other complex genomes.

Transmission of maize chromosome 9 rearrangements in oat-maize radiation hybrids.

Oat-maize radiation hybrids are oat (Avena sativa L.) plants carrying radiation-induced subchromosome fragments of a given maize (Zea mays L.) chromosome. Since first-generation radiation hybrids contain various maize chromosome rearrangements in a hemizygous condition, variation might be expected in the transmission of these rearrangements to subsequent generations. The transmission and integrity of maize chromosome 9 rearrangements were evaluated in progenies of 30 oat-maize radiation hybrids by using a series of DNA-based markers and by genomic in situ hybridization. Maize chromosome 9 rearrangements were reisolated by self-fertilization in 24 of the 30 radiation hybrid lineages. Normal and deleted versions of maize chromosome 9 were transmitted at similar frequencies of 9.1% and 7.6%, respectively, while intergenomic translocations were transmitted at a significantly higher frequency of 47.6%. Most lines (93%) that inherited a rearrangement had it in the hemizygous condition. Lines with a rearrangement in the homozygous state (7%) were only identified in lineages with intergenomic translocations. Homozygous lines are more desirable from the perspective of stock maintenance, since they may stably transmit a given rearrangement to a subsequent generation. However, their isolation is not strictly required, since hemizygous lines can also be used for genome mapping studies.

A molecular marker map in 'Kanota' x 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota x Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.

Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize.

Vgt1 (Vegetative to generative transition 1) is a quantitative trait locus (QTL) for flowering time in maize (Zea mays L.). Vgt1 was initially mapped in a ca. 5-cM interval on chromosome bin 8.05, using a set of near-isogenic lines (NILs) in the genetic background of the late dent line N28, with the earliness allele introgressed from the early variety Gaspé Flint. A new large mapping population was produced by crossing N28 and one early NIL with a ca. 6-cM long Gaspé Flint introgression at the Vgt1 region. Using PCR-based assays at markers flanking Vgt1, 69 segmental NILs homozygous for independent crossovers near the QTL were developed. When the NILs were tested in replicated field trials for days to pollen shed (DPS) and plant node number (ND), the QTL followed a Mendelian segregation. Using bulk segregant analysis and AFLP profiling, 17 AFLP markers linked to the QTL region were identified. Statistical analysis indicated a substantial coincidence of the effects of Vgt1 on both DPS and ND. Vgt1 was mapped at ca. 0.3 cM from an AFLP marker. As compared to DPS, the higher heritability of ND allowed for a more accurate assessment of the effects of Vgt1. The feasibility of the positional cloning of Vgt1 is discussed.

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa.

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.

Sequence relationships, conserved domains, and expression patterns for maize homologs of the polycomb group genes E(z), esc, and E(Pc).

Polycomb group (PcG) proteins play an important role in developmental and epigenetic regulation of gene expression in fruit fly (Drosophila melanogaster) and mammals. Recent evidence has shown that Arabidopsis homologs of PcG proteins are also important for the regulation of plant development. The objective of this study was to characterize the PcG homologs in maize (Zea mays). The 11 cloned PcG proteins from fruit fly and the Enhancer of zeste [E(z)], extra sex combs (esc), and Enhancer of Polycomb [E(Pc)] homologs from Arabidopsis were used as queries to perform TBLASTN searches against the public maize expressed sequence tag database and the Pioneer Hi-Bred database. Maize homologs were found for E(z), esc, and E(Pc), but not for Polycomb, pleiohomeotic, Posterior sex combs, Polycomblike, Additional sex combs, Sex combs on midleg, polyhometoic, or multi sex combs. Transcripts of the three maize Enhancer of zeste-like genes, Mez1, Mez2, and Mez3, were detected in all tissues tested, and the Mez2 transcript is alternatively spliced in a tissue-dependent pattern. Zea mays fertilization independent endosperm1 (ZmFie1) expression was limited to developing embryos and endosperms, whereas ZmFie2 expression was found throughout plant development. The conservation of E(z) and esc homologs across kingdoms indicates that these genes likely play a conserved role in repressing gene expression.