Browsing by Subject "Linkage Disequilibrium"
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Item Comparative Genomics of Gossypium spp. through GBS and Candidate Genes ? Delving into the Controlling Factors behind Photoperiodic Flowering(2013-08-09) Young, Carla Jo LoganCotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton?s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity.Item Elucidating and Mapping Heat Tolerance in Wild Tetraploid Wheat (Triticum turgidum L.)(2012-02-14) Ali, Mohamed Badry MohamedIdentifying reliable screening tools and characterizing tolerant germplasm sources is essential for developing wheat (Triticum aestivum L.) varieties suited for the hot areas of the world. Our objective was to evaluate heat tolerance of promising wild tetraploid wheat (Triticum turgidum L.) accessions that could be used as sources of heat tolerance in common- and durum-wheat (Triticum durum) breeding programs. We screened 109 wild tetraploid wheat accessions collected by the International Center for Agriculture Research in the Dry Areas (ICARDA) from the hottest wheat growing areas in Africa and Asia, as well as, two common wheat checks for their response to heat stress by measuring damage to the thylakoid membranes, flag leaf temperature depression (FLTD), and spike temperature depression (STD) during exposure to heat stress for 16 beginning at anthesis. Measurements were taken on the day of anthesis then 4, 8, 12, and 16 days post anthesis (DPA) under controlled optimum and heat-stress conditions. Individual kernel weight (IKW) and heat susceptibility index (HSI) measurements were also obtained. Prolonged exposure to heat stress was associated with increased damage to thylakoid membranes, as indicated by the high ratio of constant fluorescence (O) to peak variable fluorescence (P). A positive and significant correlation was found between O/P ratio and both FLTD and STD under heat-stress conditions. A negative and significant correlation was found between FLTD and HSI and between STD and HSI based on the second and third measurements (4 and 8 DPA). Correlations obtained after the third measurement were not significant because heat-stress accelerated maturity and senescence. For a pedigree-based mapping strategy a family approach was then developed by crossing and back-crossing heat-tolerant and heat-susceptible germplasm. A set of 800 lines resulting from the pedigree-based family approach was phenotyped using FLTD, chlorophyll content and yield and its components under heat stress. Genotyping of these lines was accomplished using simple sequence repeat (SSRs) markers. Some QTLs associated with heat stress tolerance were identified. This study identified potential heat-tolerant wild tetraploid wheat germplasm and QTL conditioning heat tolerance that can be incorporated into wheat breeding programs to improve cultivated common and durum wheat.