Abstract
BackgroundWheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.ResultsSix wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.ConclusionThe Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.
Highlights
Wheat (Triticum aestivum L.) is a staple food crop worldwide
There were 396 probe sets with overall R-square (Rsq) ratio > 4 and minimum count > 1, where Rsq = proportion of the variability explained by the clusters, Rsq_ratio equals to Rsq/(1-Rsq), and minimum count is the number of varieties in the smallest cluster
Sequence Variation of Selected Single feature polymorphism (SFP) For designing primers, the Rsq_ratios for the individual probes within a probe set were considered and focus was on probes with the highest values of Rsq_ratios because those were driving the cluster formation most strongly and, were most likely to be polymorphic between varieties (Figure 1)
Summary
Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (~17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. High-resolution mapping of genes is limited by lack of sufficient DNA markers. This limitation is especially significant when quantitative trait loci (QTLs) control a trait because QTLs may remain undetected or their effects may be underestimated when marker density is low. Linkage disequilibrium (LD) maps and association mapping require the identification of many markers at very high resolution from many different individuals. If cRNA is used for hybridization, gene expression markers (GEMs) that reflect expression level differences may be detected [12,13]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
