Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection

  • Umar Masood Quraishi
  • Michael Abrouk
  • Stéphanie Bolot
  • Caroline Pont
  • Mickael Throude
  • Nicolas Guilhot
  • Carole Confolent
  • Fernanda Bortolini
  • Sébastien Praud
  • Alain Murigneux
  • Gilles Charmet
  • Jerome Salse
Original Paper

Abstract

Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice–wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. 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.

Keywords

Synteny SNP Viscosity QTL Candidate genes Comparative genomics Genome mapping Quantitative trait loci 

Supplementary material

10142_2009_129_MOESM1_ESM.xls (622 kb)
Supplementary material S1List of 827 orthologous gene pairs between rice and wheat. Detailed features for the 13 orthologous regions identified between rice and wheat. For each of the 827 orthologous wheat and rice gene pairs are mentioned the GenBank accession name, position, chromosome number, sequence, as well as the sequence alignment criterion (CIP, CALP). (XLS 619 kb)
10142_2009_129_MOESM2_ESM.xls (594 kb)
Supplementary material S2List of 695 COS markers. Detailed features for the 695 orthologous wheat and rice gene pairs associated with COS primers. For each COS marker are mentioned wheat and rice orthologous genes with their Genbank accession name, position, chromosome number, sequence, the sequence alignment criterion (CIP, CALP); as well as the intron-spanning primers (number of intron, forward and reverse primer, amplicon size). (XLS 591 kb)
10142_2009_129_MOESM3_ESM.xls (40 kb)
Supplementary material S3List of 31 COS markers for fine mapping of PV QTL in Renan × Recital. Detailed features for the 31 orthologous wheat and rice gene pairs associated with COS primers involved in PV QTL fine mapping. For each COS marker are mentioned the wheat and rice orthologous genes with their GenBank accession name, position, chromosome number, sequence, the intron-spanning primers (number of intron, forward and reverse primer, amplicon size); as well as the polymorphism data (NP for No Polymorphism; P for Polymorphism) and mapping data (chromosome 7A, 7B or NA when the mapping information is not available). (XLS 40.5 kb)
10142_2009_129_MOESM4_ESM.xls (81 kb)
Supplementary material S4List of 124 rice candidate genes for PV QTL in Renan × Recital. The rice annotated gene within the orthologous region of the PV QTL are detailed through the chromosome number, LOC name, gene start/end positions, GenBank accession number, function. (XLS 81 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Umar Masood Quraishi
    • 1
  • Michael Abrouk
    • 1
  • Stéphanie Bolot
    • 1
  • Caroline Pont
    • 1
  • Mickael Throude
    • 2
  • Nicolas Guilhot
    • 1
  • Carole Confolent
    • 1
  • Fernanda Bortolini
    • 1
  • Sébastien Praud
    • 2
  • Alain Murigneux
    • 3
  • Gilles Charmet
    • 1
  • Jerome Salse
    • 1
  1. 1.Génétique, Diversité et Ecophysiologie des Céréales (GDEC)UMR 1095 INRA/Université Blaise PascalClermont-FerrandFrance
  2. 2.BiogemmaRiomFrance
  3. 3.Limagrain Verneuil HoldingRiomFrance

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