Transcript profiling and expression level mapping.

Methods Mol Biol. 2009;513:81-92

Authors: Potokina E, Druka A, Kearsey MJ

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.

PMID: 19347647 [PubMed - indexed for MEDLINE]

High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley.

Theor Appl Genet. 2009 Sep;119(5):851-65

Authors: Hofinger BJ, Jing HC, Hammond-Kosack KE, Kanyuka K

An original method has been established for the identification of novel alleles of eukaryotic translation initiation factor 4E (eIF4E) gene, which is required for resistance to agronomically important bymoviruses, in barley germplasm. This method involves scanning for sequence variations in cDNA-derived PCR amplicons using High-resolution melting (HRM) followed by direct Sanger sequencing of only those amplicons which were predicted to carry nucleotide changes. HRM is a simple, cost-effective, rapid and high-throughput assay, which so far has only been widely used in clinical pathology for molecular diagnostic of diseases and patient genotyping. Application of HRM allowed significant reduction in the amount of expensive Sanger sequencing required for allele mining in plants. The method described here involved an investigation of total cDNA rather than genomic DNA, thus permitting the analyses of shorter (up to 300-bp) and fewer overlapping amplicons to cover the coding sequence. This strategy further reduced the allele mining costs. The sensitivity and accuracy of HRM for predicting genotypes carrying a wide range of nucleotide polymorphisms in eIF4E approached 100%. Results of the current study are promising and suggest that this method could also potentially be applied to the discovery of superior alleles controlling other important traits in barley as well in other model and crop plant species.

PMID: 19578831 [PubMed - indexed for MEDLINE]

Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility.

BMC Plant Biol. 2009;9:118

Authors: Raji AA, Anderson JV, Kolade OA, Ugwu CD, Dixon AG, Ingelbrecht IL

Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications.

PMID: 19747391 [PubMed - indexed for MEDLINE]

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits.

BMC Plant Biol. 2010;10:5

Authors: Haseneyer G, Stracke S, Piepho HP, Sauer S, Geiger HH, Graner A

Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach.

PMID: 20064201 [PubMed - indexed for MEDLINE]