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Understanding the Effects of Selection on Genetic Diversity

Overview | Selection and Sequencing | Analysis | People | Publications


Provide the foundation for understanding the effects of selection on genetic diversity in cotton.

To begin to connect the phenotypic and genetic data to the process of domestication, we will employ a population genetic approach. An important goal for crop plants and their wild relatives is to understand the patterning of overall genetic diversity with a species (see special issue of Annals of Botany, 10/07). Molecular data provide the necessary context for key aspects of a species’ history and genetic structure, including:

  1. inferring crop origins and their subsequent diffusion pathways;
  2. quantifying levels and apportionment of genetic variation within modern cultivars and the myriad landraces and populations comprising the wild-to-domesticated continuum;
  3. elucidating the phylogeographic history of divergence and recombination;
  4. assessing the severity of genetic bottlenecks and gene pool relationships;
  5. determining the history of intraspecific and interspecific gene flow;
  6. assessing the nature and genomic location of selection; and
  7. revealing genome wide patterns of recombination and linkage disequilibrium.

Here we propose to generate the first genome-wide DNA sequence-based analysis of nucleotide diversity for G. hirsutum, building on a wealth of previously generated data and taking advantage of the genomic tools that we and others have produced. In doing so we hope to fulfill or set the stage for the promises enumerated above. In addition, this work, with its experimental design, will:

  1. provide a context for population genetic-based inferences regarding the targets of artificial selection.
  2. quantify the genome-wide patterns of nucleotide diversity for 50 homoeologous gene pairs, thereby testing our previously published but hitherto mysterious observation of unequal mutation rates in the two co-resident genomes of allopolyploid cotton.

Specifically, we propose here to generate sequence data in two stages: first, for 50 pairs of homoeologs (100 genes total), distributed broadly throughout the genome, for each of a carefully selected set of 40 accessions (or cultivars) spanning the wild-to-domesticated continuum; and second, for an additional 50 genes implicated by comparative expression profiling and phenotypic variation as possibly being targets of human selection. This impressive data set will permit us to address the nine objectives enumerated above, in the process enabling future investigations (not proposed here) of association mapping and the effects of selection.

Plant material.

Modern Upland cotton cultivars are day-length neutral annuals developed following thousands of years of selection from perennial antecedents with shorter, sparser fiber. As often is the case with crop plants, this history was accompanied by extreme reductions in genetic diversity. As a species, G. hirsutum encompasses a wealth of morphological and ecological diversity, as underscored by a taxonomic and nomenclatural history that includes ~30 specific epithets; most of this diversity has not been captured in modern breeding lines. Our earlier allozyme and RFLP analyses of circa 250 nuclear loci provide an assessment of relationships among landraces, wild forms, and cultivars; this will guide our selection of material to include here. In addition to including approximately 15 cultivars representing the primary gene pool of modern cotton commerce, we will include 25 accessions from the Mesoamerican center of diversity, including wild and primitively domesticated forms. All accessions either are in Wendel’s collection or are readily available from the US National Cotton Germplasm Center in College Station. Plants will be grown in the greenhouse in Ames.

We welcome your comments and suggestions.