A H Paterson

Summary

Affiliation: University of Georgia
Country: USA

Publications

  1. ncbi Leafing through the genomes of our major crop plants: strategies for capturing unique information
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nat Rev Genet 7:174-84. 2006
  2. ncbi Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench]
    Sankalp U Bhosale
    Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
    BMC Plant Biol 12:32. 2012
  3. ncbi Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Genome Biol 10:R68. 2009
  4. ncbi A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, 30602, USA
    BMC Genomics 12:470. 2011
  5. ncbi A draft physical map of a D-genome cotton species (Gossypium raimondii)
    Lifeng Lin
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
    BMC Genomics 11:395. 2010
  6. ncbi Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
    Jianping Wang
    Department of Plant Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Genomics 11:261. 2010
  7. ncbi Screening synteny blocks in pairwise genome comparisons through integer programming
    Haibao Tang
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 12:102. 2011
  8. ncbi Insights from the comparison of plant genome sequences
    Andrew H Paterson
    Department of Plant Biology, University of Georgia, Athens, Georgia
    Annu Rev Plant Biol 61:349-72. 2010
  9. ncbi A cornucopia of genomes
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Genome Biol 7:311. 2006
  10. ncbi Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
    A H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:9903-8. 2004

Detail Information

Publications92

  1. ncbi Leafing through the genomes of our major crop plants: strategies for capturing unique information
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nat Rev Genet 7:174-84. 2006
    ..Combining these methods with phylogenetically stratified sampling to allow comparative genomic approaches has the potential to further accelerate progress in angiosperm genomics...
  2. ncbi Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench]
    Sankalp U Bhosale
    Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
    BMC Plant Biol 12:32. 2012
    ..For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions...
  3. ncbi Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Genome Biol 10:R68. 2009
    ....
  4. ncbi A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, 30602, USA
    BMC Genomics 12:470. 2011
    ..Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity...
  5. ncbi A draft physical map of a D-genome cotton species (Gossypium raimondii)
    Lifeng Lin
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
    BMC Genomics 11:395. 2010
    ..Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing...
  6. ncbi Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
    Jianping Wang
    Department of Plant Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Genomics 11:261. 2010
    ..Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at approximately 12x. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level...
  7. ncbi Screening synteny blocks in pairwise genome comparisons through integer programming
    Haibao Tang
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 12:102. 2011
    ..We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events...
  8. ncbi Insights from the comparison of plant genome sequences
    Andrew H Paterson
    Department of Plant Biology, University of Georgia, Athens, Georgia
    Annu Rev Plant Biol 61:349-72. 2010
    ....
  9. ncbi A cornucopia of genomes
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Genome Biol 7:311. 2006
  10. ncbi Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
    A H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:9903-8. 2004
    ..Additional ancient duplication events probably remain to be discovered in other angiosperm lineages...
  11. ncbi Polyploidy, evolutionary opportunity, and crop adaptation
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Genetica 123:191-6. 2005
    ....
  12. ncbi QTL analysis of genotype x environment interactions affecting cotton fiber quality
    A H Paterson
    Center for Applied Genetic Technologies, Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 106:384-96. 2003
    ..These difficulties may be partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers, including those identified herein...
  13. ncbi Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence
    A H Paterson
    Center for Applied Genetic Technologies, Riverbend Research Lab, University of Georgia, Athens, GA 30602, USA
    Genome Biol 2:REVIEWS1011. 2001
    ..The remarkable morphological diversity of Brassica species and their relatives offers valuable opportunities to advance our knowledge of plant growth and development, and our understanding of rapid phenotypic evolution...
  14. ncbi Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
    Andrew H Paterson
    Plant Genome Mapping Laboratory and Department of Genetics, University of Georgia, Athens, GA 30602, USA
    Trends Genet 22:597-602. 2006
    ..Angiosperms show more frequent polyploidization and a higher degree of duplicate gene preservation than other paleopolyploids, making them well-suited to further study of duplication-resistant genes...
  15. ncbi Ancient duplication of cereal genomes
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    New Phytol 165:658-61. 2005
  16. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  17. ncbi Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 107:472-7. 2010
    ..Although the exact timing of the sigma-duplication(s) is unclear because of uncertainties of the molecular clock assumption, our data suggest that it occurred early in the monocot lineage after its divergence from the eudicot clade...
  18. ncbi Leveraging the rice genome sequence for monocot comparative and translational genomics
    H C Lohithaswa
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
    Theor Appl Genet 115:237-43. 2007
    ....
  19. ncbi Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 19:1026-32. 2009
    ..The converted genes show no change in selection pressure. We also found no evidence that conversion contributed to guanine-cytosine (GC) content elevation...
  20. ncbi Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations
    F A Feltus
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
    Theor Appl Genet 112:1295-305. 2006
    ..bicolor)...
  21. ncbi Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 18:1944-54. 2008
    ..Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes...
  22. ncbi Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 422:433-8. 2003
    ....
  23. ncbi Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types
    J Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Heredity (Edinb) 108:500-6. 2012
    ..Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars...
  24. ncbi Synteny and collinearity in plant genomes
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Science 320:486-8. 2008
    ..Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character...
  25. ncbi Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy
    Junkang Rong
    Plant Genome Mapping Laboratory, Life Sciences Building, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 15:1198-210. 2005
    ..Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes...
  26. ncbi Patterns of tandem repetition in plant whole genome assemblies
    Rafael Navajas-Pérez
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Mol Genet Genomics 281:579-90. 2009
    ..A database including all tandem repeat sequences characterized here was created to benefit future comparative genomic analyses...
  27. ncbi A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genetics 166:389-417. 2004
    ..These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome...
  28. ncbi A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops
    F A Feltus
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Plant Physiol 140:1183-91. 2006
    ....
  29. ncbi QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane
    R Ming
    Plant Genome Mapping Laboratory, Department of Soil and Crop Sciences, Texas A and M University, College Station, Texas 77843, USA
    Genome Res 11:2075-84. 2001
    ..However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues...
  30. ncbi A framework linkage map of bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments
    C M Bethel
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
    Theor Appl Genet 112:727-37. 2006
    ..Using these maps we have estimated the recombinational length of the T89 and T574 genomes at 3,012 and 1,569 cM, respectively, which are 61 and 62% covered by our maps...
  31. ncbi Gene copy number evolution during tetraploid cotton radiation
    J Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Heredity (Edinb) 105:463-72. 2010
    ..Together with D subgenome-biased alterations in gene expression, perhaps gene loss may contribute to the relatively larger portion of quantitative trait variation attributable to D than A subgenome chromosomes of tetraploid cotton...
  32. ncbi Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype
    C S Jang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Heredity (Edinb) 102:266-73. 2009
    ..bicolor genes to rhizome-enriched expression in S. halepense, suggesting that polyploidy may have offered new evolutionary potential to S. halepense...
  33. ncbi A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats
    Thomas Wicker
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Plant J 41:184-94. 2005
    ....
  34. ncbi Extensive concerted evolution of rice paralogs and the road to regaining independence
    Xiyin Wang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genetics 177:1753-63. 2007
    ..The higher level of concerted evolution in the 5-7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization...
  35. ncbi Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation
    X Draye
    Applied Genetic Technology Center, Departments of Crop and Soil Science, Botany, and Genetics, University of Georgia, Athens, GA 30602, USA
    Plant Physiol 125:1325-41. 2001
    ....
  36. ncbi Evolutionary genetics of genome merger and doubling in plants
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, New York 14850, USA
    Annu Rev Genet 42:443-61. 2008
    ..Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages...
  37. ncbi Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
    Genetics 176:2577-88. 2007
    ..Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks...
  38. ncbi Crop-to-weed introgression has impacted allelic composition of johnsongrass populations with and without recent exposure to cultivated sorghum
    P L Morrell
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Mol Ecol 14:2143-54. 2005
    ..Naturalized johnsongrass populations appear to provide a conduit by which transgenes from sorghum could become widely disseminated...
  39. ncbi 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
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genetics 165:367-86. 2003
    ..These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops...
  40. ncbi Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
    Brad A Chapman
    Plant Genome Mapping Laboratory and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 103:2730-5. 2006
    ....
  41. ncbi Organization and evolution of resistance gene analogs in peanut
    Bayram Yuksel
    Plant Genome Mapping Laboratory, The University of Georgia, Athens, 30605, USA
    Mol Genet Genomics 274:248-63. 2005
    ..The BACs isolated here will serve as a valuable resource for future applications, such as map-based cloning, and will help improve our understanding of the evolution and organization of these genes in the peanut genome...
  42. ncbi Chromosome structural changes in diploid and tetraploid A genomes of Gossypium
    Aparna Desai
    Coastal Plains Experiement Station, University of Georgia, Tifton, 31793, USA
    Genome 49:336-45. 2006
    ..Elevated recombination in the Dt genome was reported previously. These data on the At genome thus indicate that elevated recombination was a general property of allotetraploidy in cotton...
  43. ncbi Grains of knowledge: genomics of model cereals
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 15:1643-50. 2005
    ....
  44. ncbi Functional classification, genomic organization, putatively cis-acting regulatory elements, and relationship to quantitative trait loci, of sorghum genes with rhizome-enriched expression
    Cheol Seong Jang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Plant Physiol 142:1148-59. 2006
    ..Insight into genes and pathways that influence rhizome growth set the stage for genetic and/or exogenous manipulation of rhizomatousness, and for further dissection of the molecular evolution of rhizomatousness...
  45. ncbi Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts
    Lee H Pratt
    Department of Plant Biology, University of Georgia, Athens, 30602, USA
    Plant Physiol 139:869-84. 2005
    ..From these 775 TUs, signature genes were identified defining drought, Colletotrichum infection, skotomorphogenesis (etiolation), ovary, immature panicle, and embryo...
  46. ncbi Applied plant genomics: the secret is integration
    Mark T Osterlund
    Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602, USA
    Curr Opin Plant Biol 5:141-5. 2002
    ..In particular, whole-genome sequencing has provided opportunities for the broader application of reverse genetics, expression profiling, and molecular mapping in diverse species...
  47. ncbi Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery
    Daniel G Peterson
    Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 12:795-807. 2002
    ..High-throughput sequencing of Cot clones may be a means of "capturing" the sequence complexity of eukaryotic genomes at unprecedented efficiency...
  48. ncbi Structure and evolution of cereal genomes
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Curr Opin Genet Dev 13:644-50. 2003
    ..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...
  49. ncbi A comparative phylogenetic approach for dating whole genome duplication events
    Brad A Chapman
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Bioinformatics 20:180-5. 2004
    ..Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons...
  50. ncbi Comparative genome analysis of monocots and dicots, toward characterization of angiosperm diversity
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA
    Curr Opin Biotechnol 15:120-5. 2004
    ....
  51. ncbi An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments
    F Alex Feltus
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 14:1812-9. 2004
    ..The data set is freely available at http://www.plantgenome.uga.edu/snp...
  52. ncbi Emergence of a group 3 coronavirus through recombination
    Mark W Jackwood
    Department of Population Health, College of Veterinary Medicine, 953 College Station Road, University of Georgia, Athens, GA 30602, USA
    Virology 398:98-108. 2010
    ....
  53. ncbi Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
    John E Bowers
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 102:13206-11. 2005
    ..Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond...
  54. ncbi Construction and characterization of a peanut HindIII BAC library
    B Yuksel
    Plant Genome Mapping Lab, The University of Georgia, 111 Riverbend Road, Athens, GA 30605, USA
    Theor Appl Genet 111:630-9. 2005
    ..This BAC library has great potential to advance future research about the peanut genome...
  55. ncbi Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers
    A M Missaoui
    The Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602 6810, USA
    Theor Appl Genet 110:1372-83. 2005
    ..The information presented in this study establishes a foundation for extending genetic mapping in this crop and constitutes a framework for basic and applied genetic studies...
  56. ncbi Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis
    B Yuksel
    Plant Genome Mapping Laboratory, The University of Georgia, 111 Riverbend Road, Athens, GA 30605, USA
    Theor Appl Genet 111:87-94. 2005
    ..We also evaluated the possible correlation between functional categories of Arabidopsis overgos and their success rates in hybridization to the peanut BAC library...
  57. ncbi Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species
    M D Burow
    Department of Crop and Soil Science, University of Georgia, Athens, 30602, USA
    Genetics 159:823-37. 2001
    ..Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed...
  58. ncbi The repetitive landscape of the chicken genome
    Thomas Wicker
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 15:126-36. 2005
    ..This study also exemplifies the power of the CBCS method to create representative databases for the repetitive fractions of genomes for which only limited sequence data is available...
  59. ncbi Domestication and plant genomes
    Haibao Tang
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Curr Opin Plant Biol 13:160-6. 2010
    ....
  60. ncbi Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum
    Vijay N Waghmare
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:665-76. 2005
    ....
  61. ncbi Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length
    Peng W Chee
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:772-81. 2005
    ..The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development...
  62. ncbi EST derived PCR-based markers for functional gene homologues in cotton
    Peng W Chee
    University of Georgia, Coastal Plain Experimental Station, Tifton, GA 31793, USA
    Genome 47:449-62. 2004
    ..Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis...
  63. ncbi QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
    Guojun Li
    Department of Biochemistry and Molecular Biology, Computational Systems Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:e101. 2009
    ..QUBIC was written in ANSI C and tested using GCC (version 4.1.2) on Linux. Its source code is available at: http://csbl.bmb.uga.edu/ approximately maqin/bicluster. A server version of QUBIC is also available upon request...
  64. ncbi Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton
    Junkang Rong
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:1137-46. 2005
    ..Increasing knowledge of the correspondence of the cotton and Arabidopsis genomes provides several avenues by which genetic dissection of cotton fiber development may be accelerated...
  65. ncbi Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus
    J E Phillips
    Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
    Virus Genes 44:63-74. 2012
    ....
  66. ncbi Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation
    Peng Chee
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    Theor Appl Genet 111:757-63. 2005
    ....
  67. ncbi Correspondence of trichome mutations in diploid and tetraploid cottons
    Aparna Desai
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
    J Hered 99:182-6. 2008
    ..Studies of A genome diploids may help to clarify the genetic control of trichomes and fiber in both diploid and tetraploid cottons...
  68. ncbi Functional dissection of drought-responsive gene expression patterns in Cynodon dactylon L
    Changsoo Kim
    Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
    Plant Mol Biol 70:1-16. 2009
    ....
  69. ncbi Incongruent patterns of local and global genome size evolution in cotton
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 14:1474-82. 2004
    ....
  70. ncbi Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor
    Martha T Hamblin
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:471-83. 2004
    ..Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome...
  71. ncbi High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya
    Hao Ma
    Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
    Genetics 166:419-36. 2004
    ..This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya...
  72. ncbi Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 432:695-716. 2004
    ..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture...
  73. ncbi A primitive Y chromosome in papaya marks incipient sex chromosome evolution
    Zhiyong Liu
    Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
    Nature 427:348-52. 2004
    ..This finding provides direct evidence for the origin of sex chromosomes from autosomes...
  74. ncbi Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes
    Ray Ming
    Department of Soil and Crop Sciences, Texas A and M University, College Station 77843, USA
    Genome 45:794-803. 2002
    ....
  75. ncbi Rate variation among nuclear genes and the age of polyploidy in Gossypium
    David S Senchina
    Department of Botany, Iowa State University, USA
    Mol Biol Evol 20:633-43. 2003
    ..Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA...
  76. ncbi Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives
    Tae Jin Yang
    Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151 921, South Korea
    Theor Appl Genet 114:627-36. 2007
    ..Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome...
  77. ncbi Integrative mapping of Gossypium hirsutum L. by meiotic fluorescent in situ hybridization of a tandemly repetitive sequence (B77)
    Yuanfu Ji
    Department of Soil and Crop Sciences, Texas A and M University, College Station, Texas 77843, USA
    Genetics 176:115-23. 2007
    ..However, additional codominant DNA marker information in the affected region excluded the B77 polymorphism detected by Southern blot hybridization from chromosome 20 and, indeed, from the remainder of the genome...
  78. ncbi Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
    Plant J 50:995-1006. 2007
    ..In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions...
  79. ncbi Chromosomal location and gene paucity of the male specific region on papaya Y chromosome
    Qingyi Yu
    Hawaii Agriculture Research Center, Aiea, HI 96701, USA
    Mol Genet Genomics 278:177-85. 2007
    ..Our findings provide critical information for deciphering the sex chromosomes in papaya and reference information for comparative studies of other sex chromosomes in animals and plants...
  80. ncbi Restriction landmark genome scanning method using isoschizomers (MspI/HpaII) for DNA methylation analysis
    Tomoko Takamiya
    Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
    Electrophoresis 27:2846-56. 2006
    ..Therefore, this result strongly indicates that the improved RLGS method is readily applicable to practical analyses of methylation dynamics, and provides clues to the relationship between methylation and gene expression...
  81. ncbi Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor
    Martha T Hamblin
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Genetics 173:953-64. 2006
    ..Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model...
  82. ncbi Physical and genetic structure of the maize genome reflects its complex evolutionary history
    Fusheng Wei
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 3:e123. 2007
    ..Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes...
  83. ncbi The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
    Ray Ming
    Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
    Nature 452:991-6. 2008
    ....
  84. ncbi A global assembly of cotton ESTs
    Joshua A Udall
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    Genome Res 16:441-50. 2006
    ..The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics...
  85. ncbi Toward sequencing cotton (Gossypium) genomes
    Z Jeffrey Chen
    Plant Physiol 145:1303-10. 2007
  86. ncbi A phylogenetic analysis of indel dynamics in the cotton genus
    Corrinne E Grover
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, USA
    Mol Biol Evol 25:1415-28. 2008
    ..Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing...
  87. ncbi Chromosome evolution in eukaryotes: a multi-kingdom perspective
    Avril Coghlan
    Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Trends Genet 21:673-82. 2005
    ..There is little evidence that chromosomal rearrangements cause speciation, but they probably intensify reproductive isolation between species that have formed by another route...
  88. ncbi Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness
    Xavier Draye
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843, USA
    Theor Appl Genet 111:764-71. 2005
    ..barbadense in conventional breeding programs to improve upland cotton...
  89. ncbi Efficient capture of unique sequences from eukaryotic genomes
    Daniel G Peterson
    Dept of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA
    Trends Genet 18:547-50. 2002
    ..CBCS should accelerate comparative genomics research, especially in large genomes such as those of many crops...
  90. ncbi Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor
    Martha T Hamblin
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Genetics 171:1247-56. 2005
    ..From a practical standpoint, these results suggest that S. bicolor is well suited for association studies using reasonable numbers of markers, since LD typically extends at least several kilobases but has largely decayed by 15 kb...
  91. ncbi Genetic, physical, and informatics resources for maize. On the road to an integrated map
    Karen C Cone
    Division of Biological Sciences, University of Missouri, Columbia 65211, USA
    Plant Physiol 130:1598-605. 2002
  92. ncbi Low X/Y divergence in four pairs of papaya sex-linked genes
    Qingyi Yu
    Hawaii Agriculture Research Center, Aiea, HI 96701, USA
    Plant J 53:124-32. 2008
    ..Our findings indicate that sex chromosomes did not evolve at the family level in Caricaceae, and reinforce the theory that sex chromosomes evolve at the species level in some lineages...