Transcript profiling and expression level mapping.
Transcript abundance data from cRNA hybridizations to Affymetrix microarrays can potentially be used to identify genetic markers to facilitate high-throughput genotyping. We have shown that it is easily possible to use the information from Affymetrix expression arrays to accurately identify over 4,000 robust polymorphic transcript-derived markers (TDMs). We developed the method to identity TDM polymorphisms from experiments involving two tissues in two commercial varieties of barley and their doubled-haploid progeny. These TDMs represent ~18% of the total barley genes on the chip and can be used to predict the genotypes in an F(1)-derived, doubled-haploid population. According to our estimates, 35% of the TDMs reveal nucleotide polymorphism of the particular gene (single feature polymorphisms, SFPs) while 65% mark polymorphism resulting in extreme variation of gene expression (genetic expression markers, GEMs). These latter are probably mainly cis-acting regulators while a small proportion, approximately 5%, are loosely or un-linked transregulators.
Potokina
Elena
E
School of Biosciences, University of Birmingham, Birmingham, UK.
Druka
Arnis
A
Kearsey
Michael J
MJ
D002874:Chromosome Mapping; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers; D001467:Hordeum / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics
D005819:Genetic Markers; D012333:RNA, Messenger; D018749:RNA, Plant