| Initially part of an international plan to sequence the sweet orange genome, this work has produced sweet orange (Citrus sinensis) and Poncirus trifoliata maps. These have at least doubled the density of existing maps. A custom Affymetrix microarray was produced toward this goal, integrating microarray expression and mapping technologies. The mapping portion of this chip was composed of highly redundant probe sets, which allowed for bi-allelic, co-dominant SNP (Single Nucleotide Polymorphism) markers to be mapped. The sequence source was an extensive EST (Expressed Sequence Tag) assembly from which SNP sequences were selected and a filtering methodology incorporating the known biological sequences of citrus ESTs and Arabidopsis genomic sequence were applied in an information-theory-based sieve (Chapter Two). A storage database ("LISA") handled SSR (Simple S equence Repeat) and microarray data and allowed for the mapping populations differing in parentage to be merged (Chapter Three). Quality control features built into the Affymetrix chip were utilized to maximize the quality of data from this platform in an unsupervised data re-characterization technique with a linear model at its core (Chapter Four). This provided SFP (Single Feature Polymorphism) markers derived from the expression probesets of the chip. Markers from GTYPE (Genotyping Analysis Software), an Affymetrix genotyping software product used to analyze tiled SNP markers, were also integrated into the fmal maps. In total, the fmal sweet orange map includes 988 markers in 972 loci of combined SSR, GTYPE, and SFP data and is shared on a website with hyperlinks to full gene annotation data. An analysis of the two maps is provided, relating the density and segregation distortion quantity amounts with each other and to established Aurantioideae maps (Chapter Five). Further, documentation describing the database backbone for the project exists in Appendix A, presented in the form of a brief user manual with figures. Also, a comprehensive re-annotation (full sequence search) of the Affymetrix expression and SNP chip content has been completed and stored in the LISA database (Appendix A). |
