Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection.
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.
Quraishi
Umar Masood
UM
Génétique, Diversité et Ecophysiologie des Céréales (GDEC), UMR 1095 INRA/Université Blaise Pascal, Domaine de Crouelle, 234 avenue du Brézet, 63100, Clermont-Ferrand, France.
Abrouk
Michael
M
Bolot
Stéphanie
S
Pont
Caroline
C
Throude
Mickael
M
Guilhot
Nicolas
N
Confolent
Carole
C
Bortolini
Fernanda
F
Praud
Sébastien
S
Murigneux
Alain
A
Charmet
Gilles
G
Salse
Jerome
J
D001483:Base Sequence; D002523:Edible Grain / Q000235:genetics*; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D005838:Genotype; D012275:Oryza / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software; D014908:Triticum / Q000235:genetics
D005819:Genetic Markers