FPC Web Tools for Rice, Maize, and Distribution

Pampanwar, Vishal; Engler, Friedrich; Hatfield, James; Blundy, Steve; Gupta, Gaurav; Soderlund, Carol

doi:10.1104/pp.104.056291

Cited by 26 publications

(19 citation statements)

References 25 publications

(23 reference statements)

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“…The development of linkage and FPC-type physical maps of maize has led to a good understanding of the distribution of genes along the chromosomes (Davis et al 1999;Lee et al 2002;Sharopova et al 2002) and the physical distances between genes that reside within single FPC contigs (Nelson et al 2005;Pampanwar et al 2005;Yim et al 2007). Even so, the linkage maps are based on recombination frequencies that vary widely in relation to physical distances (Anderson et al , 2004Wang et al 2006), and the FPC physical maps may not accurately predict the physical distance between the ends of adjacent contigs.…”

Section: Discussionmentioning

confidence: 99%

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Amarillo

Bass

2007

Genetics

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A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize markerselected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC-FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.

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Section: Discussionmentioning

confidence: 99%

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Amarillo

Bass

2007

Genetics

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“…Any sequences that are located on the map can then be used to anchor additional sequences, such as sequenced markers, cDNAs, or genomic survey sequence. This procedure has been used extensively in the maize and rice agarose maps Engler et al, 2003;Pampanwar et al, 2005).…”

Section: Placing Sequence Onto An Hicf Physical Mapmentioning

confidence: 99%

Whole-Genome Validation of High-Information-Content Fingerprinting

Bharti²,

et al. 2005

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Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.

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“…ESTs and conceptual translation were used to distinguish gene paralogs. Chromosomal positions of genes in the maize B73 inbred line were mapped either by utilizing tools available in the WebAGCoL package (Pampanwar et al, 2005) or at Maize GDB (www.maizegdb.org). Prediction of the chloroplast targeting site was made using ChloroP software (Emanuelsson et al, 1999).…”

Section: Sequence Analysis and Chromosome Mappingmentioning

confidence: 99%

Timing and Biosynthetic Potential for Carotenoid Accumulation in Genetically Diverse Germplasm of Maize

2009

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Enhancement of the carotenoid biosynthetic pathway in food crops benefits human health and adds commercial value of natural food colorants. However, predictable metabolic engineering or breeding is limited by the incomplete understanding of endogenous pathway regulation, including rate-controlling steps and timing of expression in carotenogenic tissues. The grass family (Poaceae) contains major crop staples, including maize (Zea mays), wheat (Triticum aestivum), rice (Oryza sativa), sorghum (Sorghum bicolor), and millet (Pennisetum glaucum). Maize carotenogenesis was investigated using a novel approach to discover genes encoding limiting biosynthetic steps in the nutritionally targeted seed endosperm. A combination of bioinformatics and cloning were first used to identify and map gene families encoding enzymes in maize and other grasses. These enzymes represented upstream pathways for isopentenyl diphosphate and geranylgeranyl diphosphate synthesis and the downstream carotenoid biosynthetic pathway, including conversion to abscisic acid. A maize germplasm collection was used for statistical testing of the correlation between carotenoid content and candidate gene transcript levels. Multiple pathway bottlenecks for isoprenoid biosynthesis and carotenoid biosynthesis were discovered in specific temporal windows of endosperm development. Transcript levels of paralogs encoding isoprenoid isopentenyl diphosphate and geranylgeranyl diphosphate-producing enzymes, DXS3, DXR, HDR, and GGPPS1, were found to positively correlate with endosperm carotenoid content. For carotenoid pathway enzymes, transcript levels for CrtISO inversely correlated with seed carotenoid content, as compared with positive correlation of PSY1 transcripts. Since zeaxanthin epoxidase (ZEP) depletes the carotenoid pool in subsequent conversion to abscisic acid, ZEP transcripts were examined. Carotenoid accumulation was found to be inversely associated with ZEP1 and ZEP2 transcript levels. Extension of the maize results using phylogenetic analysis identified orthologs in other grass species that may serve as potential metabolic engineering targets.

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FPC Web Tools for Rice, Maize, and Distribution

Cited by 26 publications

References 25 publications

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescencein SituHybridization Map of Maize (Zea maysL.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

Whole-Genome Validation of High-Information-Content Fingerprinting

Timing and Biosynthetic Potential for Carotenoid Accumulation in Genetically Diverse Germplasm of Maize

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