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Abstract
Interspecific hybridization is an important potential source of genetic variation for crop improvement and provides the opportunity to study gene flow between species. Plant architecture, defined as resource allocation to different organs such as branches, flowers, and fruits, necessitates crop specific agronomic practices and its component traits affect cotton fiber quality and yield. Most of mapping populations used previously segregated for many loci, and the large amount of genetic variation often masks small-effect QTLs that may be important to practical crop improvement. This problem can be solved by development of experimental populations with only a subset of chromosome segments segregating. This dissertation reports progress toward development and characterization of reciprocal advanced backcross populations between GH cultivar Acala Maxxa and GB cultivar Pima S6 to study comparative genetic variation and molecular dissection of fiber quality and plant architectural traits. Different levels of variation among genotypes for the same traits in the respective backgrounds suggest different levels of epistatic interactions, a hypothesis supported by significant differencesin abundance of transgressive segregants for such traits. The magnitude of correlations involving ELO, UHM and UI differed significantly in both backgrounds which shows background specific nature of correlations among traits. For fiber quality, 53 QTLs in GH background and 50 QTLs in GB background were identified. Despite GB having superior fiber quality, 32% of QTLs identified in this background had favorable alleles from GH. Totals of 27 and 22 QTLs were identified for plant architectural traits in GH and GB backgrounds, respectively. More than 90% of QTLs for fiber quality and architectural traits had small effect (i.e. explaining less than 10% of phenotypic variance), exemplifying the merit of the advanced backcross approach. Comparative study showed differential permeability for introgression and retention for some genomic regions in the reciprocal backgrounds, suggesting background specific meiotic drive or positive selection of donor alleles at these regions or loci. Significantly higher number of distorted markers originated from different subgenomes in the reciprocal backgrounds, consistent with previous reports that suggest different role of subgenomes in the evolution of tetraploid cotton.