Jerome Salse

Summary

Affiliation: Institut National de la Recherche Agronomique
Country: France

Publications

  1. ncbi request reprint Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis
    Etienne Paux
    INRA, UMR 1095, ASP, 234, avenue du Brézet, 63100, Clermont Ferrand, France
    Funct Integr Genomics 8:29-32. 2008
  2. pmc Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution
    Jerome Salse
    Institut National de la Recherche Agronomique Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont Ferrand, France
    Plant Cell 20:11-24. 2008
  3. doi request reprint Palaeogenomics of plants: synteny-based modelling of extinct ancestors
    Michael Abrouk
    INRA, UMR 1095, Laboratoire Genetique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Trends Plant Sci 15:479-87. 2010
  4. doi request reprint Paleo-evolutionary plasticity of plant disease resistance genes
    Rongzhi Zhang
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
    BMC Genomics 15:187. 2014
  5. doi request reprint In silico archeogenomics unveils modern plant genome organisation, regulation and evolution
    Jerome Salse
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Group PPAV Paléogénomique des Plantes pour l Amélioration Variétale, Domaine de Crouelle, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Curr Opin Plant Biol 15:122-30. 2012
  6. doi request reprint Palaeogenomics in cereals: modeling of ancestors for modern species improvement
    Jerome Salse
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Research group PPAV Paleogénomique des Plantes pour l Amélioration Variétale, 234 avenue du Brezet, Clermont Ferrand, France
    C R Biol 334:205-11. 2011
  7. pmc New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides
    Jerome Salse
    UMR INRA 1165 CNRS 8114 UEVE Unité de Recherche en Génomique Végétale, 2, rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
    BMC Genomics 9:555. 2008
  8. doi request reprint Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
    Jerome Salse
    INRA Université Blaise Pascal UMR 1095, Genetique, Diversité et Ecophysiologie des Céréales, Domaine de Crouelle, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Brief Bioinform 10:619-30. 2009
  9. pmc Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals
    Jerome Salse
    Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1095, Genetique, Diversité et Ecophysiologie des Céréales, Universite Blaise Pascal, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Proc Natl Acad Sci U S A 106:14908-13. 2009
  10. doi request reprint Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.)
    Umar Masood Quraishi
    INRA University Blaise Pascal, UMR1095 Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brezet, 63100, Clermont Ferrand, France
    Funct Integr Genomics 11:71-83. 2011

Collaborators

Detail Information

Publications25

  1. ncbi request reprint Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis
    Etienne Paux
    INRA, UMR 1095, ASP, 234, avenue du Brézet, 63100, Clermont Ferrand, France
    Funct Integr Genomics 8:29-32. 2008
    ....
  2. pmc Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution
    Jerome Salse
    Institut National de la Recherche Agronomique Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont Ferrand, France
    Plant Cell 20:11-24. 2008
    ....
  3. doi request reprint Palaeogenomics of plants: synteny-based modelling of extinct ancestors
    Michael Abrouk
    INRA, UMR 1095, Laboratoire Genetique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Trends Plant Sci 15:479-87. 2010
    ..Recent palaeogenomic data demonstrate that whole-genome duplications have provided a motor for the evolutionary success of flowering plants over the last 50-70 million years...
  4. doi request reprint Paleo-evolutionary plasticity of plant disease resistance genes
    Rongzhi Zhang
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
    BMC Genomics 15:187. 2014
    ..e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the opportunity to gain insights into disease resistance genes (R-genes) evolutionary plasticity...
  5. doi request reprint In silico archeogenomics unveils modern plant genome organisation, regulation and evolution
    Jerome Salse
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Group PPAV Paléogénomique des Plantes pour l Amélioration Variétale, Domaine de Crouelle, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Curr Opin Plant Biol 15:122-30. 2012
    ..In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today...
  6. doi request reprint Palaeogenomics in cereals: modeling of ancestors for modern species improvement
    Jerome Salse
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Research group PPAV Paleogénomique des Plantes pour l Amélioration Variétale, 234 avenue du Brezet, Clermont Ferrand, France
    C R Biol 334:205-11. 2011
    ..Finally, detailed synteny and duplication relationships led to an improved representation of cereal genomes in concentric circles, thus providing a new reference tool for improved gene annotation and cross-genome markers development...
  7. pmc New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides
    Jerome Salse
    UMR INRA 1165 CNRS 8114 UEVE Unité de Recherche en Génomique Végétale, 2, rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
    BMC Genomics 9:555. 2008
    ..speltoides (2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42)...
  8. doi request reprint Improved criteria and comparative genomics tool provide new insights into grass paleogenomics
    Jerome Salse
    INRA Université Blaise Pascal UMR 1095, Genetique, Diversité et Ecophysiologie des Céréales, Domaine de Crouelle, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Brief Bioinform 10:619-30. 2009
    ..Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits...
  9. pmc Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals
    Jerome Salse
    Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1095, Genetique, Diversité et Ecophysiologie des Céréales, Universite Blaise Pascal, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Proc Natl Acad Sci U S A 106:14908-13. 2009
    ..If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants...
  10. doi request reprint Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.)
    Umar Masood Quraishi
    INRA University Blaise Pascal, UMR1095 Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brezet, 63100, Clermont Ferrand, France
    Funct Integr Genomics 11:71-83. 2011
    ....
  11. doi request reprint Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection
    Umar Masood Quraishi
    Genetique, Diversité et Ecophysiologie des Céréales GDEC, UMR 1095 INRA Université Blaise Pascal, Domaine de Crouelle, 234 avenue du Brezet, 63100, Clermont Ferrand, France
    Funct Integr Genomics 9:473-84. 2009
    ..Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region...
  12. pmc Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
    Frédéric Choulet
    Institut National de la Recherche Agronomique, Universite Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F 63100 Clermont Ferrand, France
    Plant Cell 22:1686-701. 2010
    ....
  13. pmc Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak
    Saneyoshi Ueno
    INRA, UMR 1202 BIOGECO, 69 route d Arcachon, F 33612 Cestas, France
    BMC Genomics 11:650. 2010
    ....
  14. doi request reprint The 'inner circle' of the cereal genomes
    Stéphanie Bolot
    INRA UBP UMR 1095, Domaine de Crouelle, 234 avenue du Brézet 63100 Clermont Ferrand, France
    Curr Opin Plant Biol 12:119-25. 2009
    ....
  15. doi request reprint A physical map of the 1-gigabase bread wheat chromosome 3B
    Etienne Paux
    Institut National de la Recherche Agronomique, Université Blaise Pascal INRA UBP, UMR 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Ferrand, France
    Science 322:101-4. 2008
    ..This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach...
  16. pmc Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
    Florent Murat
    INRA, UMR 1095, Laboratoire Genetique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
    Genome Res 20:1545-57. 2010
    ....
  17. pmc Structure and expression analysis of rice paleo duplications
    Mickael Throude
    UMR 1095 INRA UBP, Genetique, Diversité et Ecophysiologie des Céréales GDEC, Domaine de Crouelle, 234, 63100 Clermont Ferrand, France
    Nucleic Acids Res 37:1248-59. 2009
    ....
  18. doi request reprint Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution
    Umar Masood Quraishi
    INRA Université Blaise Pascal UMR 1095 GDEC, Domaine de Crouelle, 234 avenue du Brezet, 63100 Clermont Ferrand, France
    Plant J 65:745-56. 2011
    ..We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements...
  19. pmc RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)
    Caroline Pont
    INRA, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, 234 avenue du Brezet, Clermont Ferrand, France
    Genome Biol 12:R119. 2011
    ..Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes...
  20. doi request reprint Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes
    Florent Murat
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Clermont Ferrand, France
    Genome Biol Evol 6:12-33. 2014
    ..e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data. ..
  21. pmc Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication
    Michael Abrouk
    Institut National de la Recherche Agronomique Université Blaise Pascal, Unité Mixte de Recherche 1095, Genetique, Diversité et Ecophysiologie des Céréales, Clermont Ferrand, France
    Plant Cell 24:1776-92. 2012
    ..Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation...
  22. pmc Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses
    Bianca Dibari
    INRA UMR 1095 Génétique Diversité Ecophysiologie des Céréales GDEC, Clermont Ferrand, France
    BMC Genomics 13:221. 2012
    ..PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum...
  23. doi request reprint Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes
    Caroline Pont
    INRA UBP UMR 1095, Centre de Clermont Ferrand Theix, 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
    Plant J 76:1030-44. 2013
    ..Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat. ..
  24. doi request reprint Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species
    Nathalie Chantret
    Domaine de Melgueil, INRA UMR DIAPC, 34130 Mauguio, France
    J Mol Evol 66:138-50. 2008
    ..The coding sequence evolution appeared to be submitted to heterogeneous selective pressure and intronic sequences analysis revealed that the molecular clock hypothesis is violated in most cases...
  25. pmc Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes
    Florent Murat
    INRA UBP UMR 1095 GDEC génétique, Diversité et Ecophysiologie des Céréales, Clermont Ferrand, France
    Genome Biol Evol 4:805-16. 2012
    ..This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes...