To increase genetic diversity with elite upland cotton, introgression populations with wild species of cotton, Gossypium mustelinum and G. tomentosum, were created. To accomplish this objective, F1, F2, BC1F1, and BC1F2 generations were developed along with random mating populations (BC1rm1 and BC1rm2) and grown in a randomized complete block design with four replications in College Station, Texas during 2003 and 2004, and in Mexico during 2005 for G. mustelinum introgression populations. These generations were tested with microsatellite markers from chromosome 11 in order to measure the effects of selection and recombination. Later generations (BC2F1, BC2rm1, BC2F2, BC3F1, BC3rm1 and BC3F2) and composite generations were evaluated in a randomized complete block design with four replications during 2004 and 2005 for agronomic properties. Introgression barriers for G. mustelinum were found to include daylength sensitivity and hybrid breakdown, which was only apparent in Mexico. Backcross generations had improved fiber quality. Random mating populations did not have increased variance and means differed little from BC1F1 levels. Microsatellite markers showed decreased frequency of G. mustelinum alleles and decreasing heterozygosity, but no increase in map distances in random mating populations. Upper-half mean length and upper quartile length by weight were highly heritable, as measured with parent-offspring regression. Most other agronomic traits had moderate heritabilities. Composite generations were found to be favorable for selection and breeding. For G. tomentosum populations, hybrid breakdown was also a problem with low yields for F2 and BC1F2 generations, but day length sensitivity was not. Little or no increase in variance was found in random mating populations when compared to BC1F1 levels. G. tomentosum populations did not show improvements in fiber length as seen in G. mustelinum populations, but did have increased strength in BC1F1 and F1 generations over TM-1. Mapping distances increased in the random mating populations for G. tomentosum, and the frequency of alien alleles did not decrease in random mating populations. Generation means approached recurrent parental values for most traits within three backcrosses. Composite generations were found to be the most useful for breeding and selection.

The first part of this research focused on wide-cross whole-genome radiation hybrid (WWRH) mapping of the cotton (Gossypium) genome. Radiation hybrid mapping has been used extensively to map the genomes of human and certain animal species, but not plant species. In lieu of in vitro hybrid cell line technologies for plants, we developed a novel approach for radiation hybrid mapping based on wide-cross in vivo hybridization. Flowers from one species of cotton, either G. hirsutum or G. barbadense, were -irradiated and then used to pollinate the other species. The resulting hybrid plants were assessed as a mapping tool. Two WWRH mapping panels were constructed from 5- and 8-krad -irradiation treatments. Both panels demonstrated that the WWRH mapping method can be used to map the cotton genome, and that this method complements traditional linkage mapping approaches. The second part of this research focused on the identification of cold-responsive genes using spotted oligo-gene microarray analysis. Increased cold-tolerance in cotton would promote early and uniform seedling establishment, expand the growing season, decrease susceptibility to fungal infections and certain diseases, and increase fiber yield and quality. BLAST searches of the cotton database using amino acid sequences of 93 drought/cold-related genes from Arabidopsis and several other plant species led to 806 cotton orthologous cDNAs and expressed sequence tags (ESTs). Eight hundred and six cotton 70-mer oligos were designed and included in an oligo-gene microarray containing 1,536 70-mer oligos, each representing a cDNA or EST from cotton, or one of 121 chloroplast genes or 66 mitochondrial genes from Arabidopsis. Thirty-eight cotton cDNAs and ESTs were identified as cold-responsive genes based on experimental treatment and oligo-gene microarray analysis. Expression was up-regulated for 36 genes and down-regulated for two genes by cold treatment. Results from microarray analysis were tested and confirmed by northern blot analysis for 16 genes. Our data suggest that Arabidopsis orthologous genes can be used to identify homologous cotton genes. The oligo-gene microarray is a valid approach to study transcriptional changes in cotton.

The first part of this research focused on wide-cross whole-genome radiation hybrid (WWRH) mapping of the cotton (Gossypium) genome. Radiation hybrid mapping has been used extensively to map the genomes of human and certain animal species, but not plant species. In lieu of in vitro hybrid cell line technologies for plants, we developed a novel approach for radiation hybrid mapping based on wide-cross in vivo hybridization. Flowers from one species of cotton, either G. hirsutum or G. barbadense, were -irradiated and then used to pollinate the other species. The resulting hybrid plants were assessed as a mapping tool. Two WWRH mapping panels were constructed from 5- and 8-krad -irradiation treatments. Both panels demonstrated that the WWRH mapping method can be used to map the cotton genome, and that this method complements traditional linkage mapping approaches. The second part of this research focused on the identification of cold-responsive genes using spotted oligo-gene microarray analysis. Increased cold-tolerance in cotton would promote early and uniform seedling establishment, expand the growing season, decrease susceptibility to fungal infections and certain diseases, and increase fiber yield and quality. BLAST searches of the cotton database using amino acid sequences of 93 drought/cold-related genes from Arabidopsis and several other plant species led to 806 cotton orthologous cDNAs and expressed sequence tags (ESTs). Eight hundred and six cotton 70-mer oligos were designed and included in an oligo-gene microarray containing 1,536 70-mer oligos, each representing a cDNA or EST from cotton, or one of 121 chloroplast genes or 66 mitochondrial genes from Arabidopsis. Thirty-eight cotton cDNAs and ESTs were identified as cold-responsive genes based on experimental treatment and oligo-gene microarray analysis. Expression was up-regulated for 36 genes and down-regulated for two genes by cold treatment. Results from microarray analysis were tested and confirmed by northern blot analysis for 16 genes. Our data suggest that Arabidopsis orthologous genes can be used to identify homologous cotton genes. The oligo-gene microarray is a valid approach to study transcriptional changes in cotton.