Iowa State University Brigham Young University University of Georgia







Overview
Phylogeny
Fiber Evolution


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

Genetic and Physical mapping resources
Comparative BAC Sequencing
Genome Sequence Resources
EST D-genome map
EST Resources
Microarray

Web Database
Education and Outreach
Significance for cotton industry
Cotton Literature
Cotton Links
Events
Wendel Lab
PGML (Paterson Lab)
Udall Lab

Lists & protocols
Publications
How to
CEGC Site Search

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
turn explanations on/off

Understanding the Effects of Selection on Genetic Diversity


Overview | Selection and Sequencing | Analysis | People | Publications

Analysis

Raw sequences will be trimmed, aligned, and subjected to phenetic and phylogeographic analysis (using, for example, PAUP and Phylip), as well as diversity and divergence estimation using DNAsp (http://www.ub.es/dnasp/). This will shed light on levels of nucleotide variation throughout the genome and as well as the portion and proportion that has been captured in modern cultivars. Diversity for this quasi-randomly selected set of genes will be normalized against genomic context and GC content (among other confounding factors) by calculating the fractional diversity in cultivars relative to total diversity. Based on our previous analysis of variation for 48 genes among species, we anticipate an approximately normal distribution of diversity estimates for these mostly neutral or near-neutral genes. This analysis will serve as the context for evaluating the same estimates obtained for stage 2 sequencing, i.e., for the set of genes putatively subjected to human selection, either directly or through their linkage to selected genes. A comparison of these two curves (Figure) will provide important information about the nature of the cotton genome under selection. We emphasize that our aim is not to prove selection, and in fact population genetic screens may fail for several reasons, but the data will provide an important framework in this regard. We argue that multiple sources of evidence will bear on the question of domestication, i.e., introgressed segments, expression analyses, homoeolog-specificity, and population genetic bottlenecks. This confluence or melding of approaches will likely be especially powerful. Moreover, the data will provide estimates of linkage disequilibrium (LD) in Gossypium, employing TASSEL at various scales (e.g., within the species, within modern cultivars), with an eye toward future appropriate design of association mapping experiments.

Nucleotide diversity among 50 genes is expected to be quasi-normal, ranging from low (left) to high (right). Randomly sampled genes (black) will contain more diversity than those subject to selection (red). The most likely candidates for genes experiencing selection/hitchhiking are in the blue region.

Finally, the data will be partitioned by homoeolog to test the previous mysterious observation that the D genome of allopolyploid cotton accumulates diversity at a higher rate than does the A-genome. This observation is especially intriguing in that these two co-resident genomes, which vary two-fold in genome size but which essentially are collinear, are housed in a common nucleus and hence subjected to the same ecological, mating system and population-level processes, features that otherwise are often invoked to account for variation in diversity among genes and organisms.


We welcome your comments and suggestions.