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Fiber Evolution

Introgression Populations
Homoeolog-specific Profiling
Genetic Networks & Phenotype
Effects of Selection
Sequence Capture

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Comparative BAC Sequencing
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EST D-genome map
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Perturbations in Genetic Networks and Gene Expression

Overview | Procedures | Genetic Networks | cis and trans effects | People | Publications

cis and trans effects

Genes may be differentially expressed because they are located on the introgressed chromosome segment and are regulated in cis differentially in the donor and recipient genomes. Alternatively, a differentially expressed gene may be localized outside of the introgressed segment, elsewhere in the genome, with its altered expression reflecting the downstream consequences (in trans) of genes on the introgressed segment. To take advantage of this novel opportunity to quantify the nature of the cis and trans effects on phenotype, and in the process uncover details of the gene network underlying cotton fiber development, we will map a subset of the differentially expressed genes, using NILs from the wild vs. domesticated G. hirsutum cross. In selecting this particular cross, we seek to elucidate the footprints of selection caused by domestication. Following expression profiling of these 10-15 NILs, we will select approximately 20 genes from each NIL that are most differentially expressed. Using procedures outlined below, we will amplify and sequence (from clones) each selected gene from the relevant NIL, and look for heterozygosity in the resulting amplicon pool. Our expectation is that all genes in the NILs will be homozygous except those residing on the introgressed segment; sequencing a 800-1000 bp fragment, at least half of which is intron, is expected to reveal at least one polymorphism for most genes. This approach has a double payoff in that it sets the stage for round 2 sequencing in component 4, as described below. As an alternative protocol, we will evaluate a heteroduplex cleavage method, by treating amplicons with Cel1 endonuclease, followed by detection on denaturing PAGE gels.

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