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Rong J, Bowers JE, Schulze SR, Waghmare VN, Rogers CJ, Pierce GJ, Zhang H, Estill JC, Paterson AH. Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy. Genome Res 2005; 15:1198-210. [PMID: 16109973 PMCID: PMC1199534 DOI: 10.1101/gr.3907305] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons (Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (alpha) in Arabidopsis. At least 59% of the cotton map and 53% of the Arabidopsis transcriptome showed correspondence in multilocus gene arrangements based on one or both of two software packages (CrimeStatII, FISH). Genomic regions in which chromosome structural rearrangement has been rapid (obscuring gene order correspondence) have also been subject to greater divergence of individual gene sequences. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes.
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Morrell PL, Williams-Coplin TD, Lattu AL, Bowers JE, Chandler JM, Paterson AH. Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum. Mol Ecol 2005; 14:2143-54. [PMID: 15910333 DOI: 10.1111/j.1365-294x.2005.02579.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sorghum halepense L. (johnsongrass) is one of the world's most noxious weeds, and a paradigm for the potential dangers of crop-weed hybridization. Introduced into the southeastern United States about 200 years ago, S. halepense is a close relative of cultivated sorghum (Sorghum bicolor). Both artificial crossing and experimental field studies have demonstrated the potential for S. halepensex S. bicolor hybrid formation, but no prior study has addressed the long-term persistence of sorghum genes in johnsongrass populations. We surveyed 283 loci (on all 10 sorghum linkage groups) to identify 77 alleles at 69 loci that are found in US sorghum cultivars but are absent from a worldwide sampling of johnsongrass genotypes. These putatively cultivar-specific alleles were present in up to 32.3% of individuals in johnsongrass populations adjacent to long-term sorghum production fields in Texas and Nebraska. Lower frequencies of cultivar-specific alleles at smaller numbers of loci are found in johnsongrass populations from New Jersey and Georgia with no recent exposure to cultivated sorghum, suggesting that introgressed sorghum alleles may be dispersed across long distances. The number of cultivar-specific alleles and extensive multilocus patterns of cultivar-specific allelic composition observed at both linked and unlinked loci in the johnsongrass populations, are inconsistent with alternatives to introgression such as convergence, or joint retention of ancestral polymorphisms. Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated.
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Yüksel B, Bowers JE, Estill J, Goff L, Lemke C, Paterson AH. Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:87-94. [PMID: 15809848 DOI: 10.1007/s00122-005-1994-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 03/07/2005] [Indexed: 05/24/2023]
Abstract
Arachis hypogaea is a widely cultivated crop both as an oilseed and protein source. The genomic analysis of Arachis species hitherto has been limited to the construction of genetic maps; the most comprehensive one contains 370 loci over 2,210 cM in length. However, no attempt has been made to analyze the physical structure of the peanut genome. To investigate the practicality of physical mapping in peanut, we applied a total of 117 oligonucleotide-based probes ("overgos") derived from genetically mapped RFLP probes onto peanut BAC filters containing 182,784 peanut large-insert DNA clones in a multiplex experimental design; 91.5% of the overgos identified at least one BAC clone. In order to gain insights into the potential value of Arabidopsis genome sequence for studies in divergent species with complex genomes such as peanut, we employed 576 Arabidopsis-derived overgos selected on the basis of maximum homology to orthologous sequences in other plant taxa to screen the peanut BAC library. A total of 353 (61.3%) overgos detected at least one peanut BAC clone. This experiment represents the first steps toward the creation of a physical map in peanut and illustrates the potential value of leveraging information from distantly related species such as Arabidopsis for both practical applications such as comparative map-based cloning and shedding light on evolutionary relationships. We also evaluated the possible correlation between functional categories of Arabidopsis overgos and their success rates in hybridization to the peanut BAC library.
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Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF, Kresovich S. Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:23-30. [PMID: 15864526 DOI: 10.1007/s00122-005-1952-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Accepted: 02/03/2005] [Indexed: 05/24/2023]
Abstract
Although molecular markers and DNA sequence data are now available for many crop species, our ability to identify genetic variation associated with functional or adaptive diversity is still limited. In this study, our aim was to quantify and characterize diversity in a panel of cultivated and wild sorghums (Sorghum bicolor), establish genetic relationships, and, simultaneously, identify selection signals that might be associated with sorghum domestication. We assayed 98 simple sequence repeat (SSR) loci distributed throughout the genome in a panel of 104 accessions comprising 73 landraces (i.e., cultivated lines) and 31 wild sorghums. Evaluation of SSR polymorphisms indicated that landraces retained 86% of the diversity observed in the wild sorghums. The landraces and wilds were moderately differentiated (F st=0.13), but there was little evidence of population differentiation among racial groups of cultivated sorghums (F st=0.06). Neighbor-joining analysis showed that wild sorghums generally formed a distinct group, and about half the landraces tended to cluster by race. Overall, bootstrap support was low, indicating a history of gene flow among the various cultivated types or recent common ancestry. Statistical methods (Ewens-Watterson test for allele excess, lnRH, and F st) for identifying genomic regions with patterns of variation consistent with selection gave significant results for 11 loci (approx. 15% of the SSRs used in the final analysis). Interestingly, seven of these loci mapped in or near genomic regions associated with domestication-related QTLs (i.e., shattering, seed weight, and rhizomatousness). We anticipate that such population genetics-based statistical approaches will be useful for re-evaluating extant SSR data for mining interesting genomic regions from germplasm collections.
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Paterson AH, Bowers JE, Van de Peer Y, Vandepoele K. Ancient duplication of cereal genomes. THE NEW PHYTOLOGIST 2005; 165:658-661. [PMID: 15720677 DOI: 10.1111/j.1469-8137.2005.01347.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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206
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Paterson AH, Bowers JE, Chapman BA, Peterson DG, Rong J, Wicker TM. Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity. Curr Opin Biotechnol 2004; 15:120-5. [PMID: 15081049 DOI: 10.1016/j.copbio.2004.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The importance of angiosperms to sustaining humanity by providing a wide range of 'ecosystem services' warrants increased exploration of their genomic diversity. The nearly completed sequences for two species representing the major angiosperm subclasses, specifically the dicot Arabidopsis thaliana and the monocot Oryza sativa, provide a foundation for comparative analysis across the angiosperms. The angiosperms also exemplify some challenges to be faced as genomics makes new inroads into describing biotic diversity, in particular polyploidy (genome-wide chromatin duplication), and much larger genome sizes than have been studied to date.
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Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 2004; 166:389-417. [PMID: 15020432 PMCID: PMC1470701 DOI: 10.1534/genetics.166.1.389] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.
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Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA. Structure and evolution of cereal genomes. Curr Opin Genet Dev 2004; 13:644-50. [PMID: 14638328 DOI: 10.1016/j.gde.2003.10.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cereal species, of central importance to our diet, began to diverge 50-70 million years ago. For the past few thousand years, these species have undergone largely parallel selection regimes associated with domestication and improvement. The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both the shared and the independent dimensions of cereal evolution. New data and population-based approaches are identifying genes that have been involved in cereal improvement. Reduced-representation sequencing promises to accelerate gene discovery in many large-genome cereals, and to better link the under-explored genomes of 'orphan' cereals with state-of-the-art knowledge.
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209
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Chapman BA, Bowers JE, Schulze SR, Paterson AH. A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics 2004; 20:180-5. [PMID: 14734308 DOI: 10.1093/bioinformatics/bth022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Whole genome duplications have played a major role in determining the structure of eukaryotic genomes. Current evidence revealing large blocks of duplicated chromatin yields new insights into the evolutionary history of species, but also presents a major challenge for researchers attempting to utilize comparative genomics techniques. Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons. RESULTS We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context. The methodology has been previously utilized for analysis of Arabidopsis and Saccharomyces duplication events. This new implementation provides a more flexible and reusable framework for these analyses. Scripts written in the Python programming language drive a number of freely available bioinformatics programs, creating a no-cost tool for researchers. The usefulness of the approach is demonstrated through genome-scale analysis of Arabidopsis and Oryza (rice) duplications. AVAILABILITY Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/
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210
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Paterson AH, Bowers JE, Chapman BA. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 2004; 101:9903-8. [PMID: 15161969 PMCID: PMC470771 DOI: 10.1073/pnas.0307901101] [Citation(s) in RCA: 656] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Integration of structural genomic data from a largely assembled rice genome sequence, with phylogenetic analysis of sequence samples for many other taxa, suggests that a polyploidization event occurred approximately 70 million years ago, before the divergence of the major cereals from one another but after the divergence of the Poales from the Liliales and Zingiberales. Ancient polyploidization and subsequent "diploidization" (loss) of many duplicated gene copies has thus shaped the genomes of all Poaceae cereal, forage, and biomass crops. The Poaceae appear to have evolved as separate lineages for approximately 50 million years, or two-thirds of the time since the duplication event. Chromosomes that are predicted to be homoeologs resulting from this ancient duplication event account for a disproportionate share of incongruent loci found by comparison of the rice sequence to a detailed sorghum sequence-tagged site-based genetic map. Differential gene loss during diploidization may have contributed many of these incongruities. Such predicted homoeologs also account for a disproportionate share of duplicated sorghum loci, further supporting the hypothesis that the polyploidization event was common to sorghum and rice. Comparative gene orders along paleo-homoeologous chromosomal segments provide a means to make phylogenetic inferences about chromosome structural rearrangements that differentiate among the grasses. Superimposition of the timing of major duplication events on taxonomic relationships leads to improved understanding of comparative gene orders, enhancing the value of data from botanical models for crop improvement and for further exploration of genomic biodiversity. Additional ancient duplication events probably remain to be discovered in other angiosperm lineages.
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211
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Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li Z, Lin YR, Liu SC, Luo L, Marler BS, Ming R, Mitchell SE, Qiang D, Reischmann K, Schulze SR, Skinner DN, Wang YW, Kresovich S, Schertz KF, Paterson AH. A High-Density Genetic Recombination Map of Sequence-Tagged Sites for Sorghum, as a Framework for Comparative Structural and Evolutionary Genomics of Tropical Grains and Grasses. Genetics 2003; 165:367-86. [PMID: 14504243 PMCID: PMC1462765 DOI: 10.1093/genetics/165.1.367] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM (∼300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of ≤50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny—in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.
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212
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Bowers JE, Chapman BA, Rong J, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003; 422:433-8. [PMID: 12660784 DOI: 10.1038/nature01521] [Citation(s) in RCA: 1021] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 02/05/2003] [Indexed: 11/09/2022]
Abstract
Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ancestry approximately 170-235 million years ago yield conflicting results. This difference may be largely due to the propensity of angiosperms to undergo chromosomal duplication ('polyploidization') and subsequent gene loss ('diploidization'); these evolutionary mechanisms have profound consequences for comparative biology. Here we integrate a phylogenetic approach (relating chromosomal duplications to the tree of life) with a genomic approach (mitigating information lost to diploidization) to show that a genome-wide duplication post-dates the divergence of Arabidopsis from most dicots. We also show that an inferred ancestral gene order for Arabidopsis reveals more synteny with other dicots (exemplified by cotton), and that additional, more ancient duplication events affect more distant taxonomic comparisons. By using partial sequence data for many diverse taxa to better relate the evolutionary history of completely sequenced genomes to the tree of life, we foster comparative approaches to the study of genome organization, consequences of polyploidy, and the molecular basis of quantitative traits.
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213
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Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH. Genetic, physical, and informatics resources for maize. On the road to an integrated map. PLANT PHYSIOLOGY 2002; 130:1598-605. [PMID: 12481043 PMCID: PMC1540265 DOI: 10.1104/pp.012245] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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214
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Bailey DM, Bowers JE, Gutsche CD. Ring Enlargements. X. The Reactions of Cycloalkanones Carrying Two-carbon and Four-carbon Side Chains Containing Potential Diazoalkyl Moieties1. J Org Chem 2002. [DOI: 10.1021/jo01038a002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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215
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Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 2002; 12:795-807. [PMID: 11997346 PMCID: PMC186575 DOI: 10.1101/gr.226102] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cot-based sequence discovery represents a powerful means by which both low-copy and repetitive sequences can be selectively and efficiently fractionated, cloned, and characterized. Based upon the results of a Cot analysis, hydroxyapatite chromatography was used to fractionate sorghum (Sorghum bicolor) genomic DNA into highly repetitive (HR), moderately repetitive (MR), and single/low-copy (SL) sequence components that were consequently cloned to produce HRCot, MRCot, and SLCot genomic libraries. Filter hybridization (blotting) and sequence analysis both show that the HRCot library is enriched in sequences traditionally found in high-copy number (e.g., retroelements, rDNA, centromeric repeats), the SLCot library is enriched in low-copy sequences (e.g., genes and "nonrepetitive ESTs"), and the MRCot library contains sequences of moderate redundancy. The Cot analysis suggests that the sorghum genome is approximately 700 Mb (in agreement with previous estimates) and that HR, MR, and SL components comprise 15%, 41%, and 24% of sorghum DNA, respectively. Unlike previously described techniques to sequence the low-copy components of genomes, sequencing of Cot components is independent of expression and methylation patterns that vary widely among DNA elements, developmental stages, and taxa. High-throughput sequencing of Cot clones may be a means of "capturing" the sequence complexity of eukaryotic genomes at unprecedented efficiency.
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216
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Gutsche CD, Bowers JE. Ring enlargements. XI. Structural influences on the course of the intramolecular diazo alkane-carbonyl reaction. J Org Chem 2002. [DOI: 10.1021/jo01279a078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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217
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Draye X, Lin YR, Qian XY, Bowers JE, Burow GB, Morrell PL, Peterson DG, Presting GG, Ren SX, Wing RA, Paterson AH. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. PLANT PHYSIOLOGY 2001; 125:1325-41. [PMID: 11244113 PMCID: PMC65612 DOI: 10.1104/pp.125.3.1325] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2000] [Accepted: 12/20/2000] [Indexed: 05/18/2023]
Abstract
The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a "grass genome model." Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. "Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis.
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218
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Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming R, Wright RJ. Comparative genomics of plant chromosomes. THE PLANT CELL 2000; 12:1523-40. [PMID: 11006329 PMCID: PMC149067 DOI: 10.1105/tpc.12.9.1523] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2000] [Accepted: 08/14/2000] [Indexed: 05/18/2023]
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219
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Uskov AV, McInerney J, Karin JR, Bowers JE. Intraband carrier kinetics and picosecond pulse shaping in field-enhanced bulk semiconductor absorbers. OPTICS LETTERS 1998; 23:376-378. [PMID: 18084517 DOI: 10.1364/ol.23.000376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Picosecond pulse propagation through a field-enhanced waveguide bulk semiconductor saturable absorber is studied numerically. Fast switching from unsaturated absorption to delayed strong saturation and gain, as well as the predicted dependence of saturation energy on electric field, is based on intraband carrier kinetics and electric-field dynamics in the absorber and can lead to improved, controllable pulse shaping.
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220
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Wu W, Hawkins AR, Bowers JE. Analysis of the effect of an electric-field profile on the gain bandwidth product of avalanche photodetectors. OPTICS LETTERS 1997; 22:1183-1185. [PMID: 18185789 DOI: 10.1364/ol.22.001183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We investigate the effect of the electric-field profile on the gain-bandwidth product of avalanche photodetectors with separate absorption and multiplication. We show that for a given multiplication layer thickness the electric-field profile plays an important role in determining the gain-bandwidth product. The calculation results show that an increasing triangular electric-field profile yields a larger gain-bandwidth product than most other profiles for Si/InGaAs avalanche photodetectors.
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Abstract
The world's great wines are produced from a relatively small number of classic European cultivars of Vitis vinifera L Most are thought to be centuries old and their origins have long been the subject of speculation. Among the most prominent of these cultivars is Cabernet Sauvignon, described as "the world's most renowned grape variety for the production of fine red wine". Although now grown in many countries, Cabernet Sauvignon derives its fame from its long association with the Bordeaux region of France, where it has been grown at least since the 17th century. We present microsatellite DNA evidence for the hypothesis that Cabernet Sauvignon is the progeny of two other Bordeaux cultivars, Cabernet franc and Sauvignon blanc. Likelihood ratios support this hypothesis to a very high degree of probability. A close relationship between Cabernet Sauvignon and Cabernet franc has been suspected but the genetic contribution of Sauvignon blanc, despite its similar name, is a surprise.
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222
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Bowers JE. A survey of RN-MS degree programs in Illinois. CHART 1994; 91:3-4. [PMID: 8025963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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223
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Jiang W, Shimizu M, Mirin RP, Reynolds TE, Bowers JE. Electrically pumped mode-locked vertical-cavity semiconductor lasers. OPTICS LETTERS 1993; 18:1937-1939. [PMID: 19829453 DOI: 10.1364/ol.18.001937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate what is to our knowledge the first electrically pumped mode-locked vertical-cavity surfaceemitting laser. The lasing threshold current is 15 mA with a 1% output coupler. The output pulse width is 80 ps at a repetition rate of 1 GHz.
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224
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Morton PA, Crawford DL, Bowers JE. Design of 1.3-microm GaInAsP surface-emitting lasers for high-bandwidth operation. OPTICS LETTERS 1990; 15:679-681. [PMID: 19768045 DOI: 10.1364/ol.15.000679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Important design considerations for high-speed GaInAsP 1.3-microm surface-emitting lasers are described. Modified rate equations for surface-emitting lasers and a small-signal analysis are used to calculate the frequency response versus the mirror reflectivity. For the structure analyzed, the results predict optimum reflectivities of 98% for highfrequency operation and maximum quantum efficiency. Strong gain-saturation effects are predicted owing to the high photon densities that occur in these devices. As the mirror thickness increases, the frequency response of the laser reduces greatly. The effect of heating is found to be important and is included in the analysis.
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Helkey RJ, Morton PA, Bowers JE. Partial-integration method for analysis of mode-locked semiconductor lasers. OPTICS LETTERS 1990; 15:112. [PMID: 19759728 DOI: 10.1364/ol.15.000112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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