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Experimental Plan

Our experimental approach is multifaceted and synergistic, relying on the complementary expertise of the PIs and their collaborators and the wealth of background data and resources generated in previous funding periods and elsewhere. We anticipate that our work will yield physical resources and tools that will enable opportunities in Gossypium genomics, while also answering fundamental questions about phenotypic evolution, the domestication process, polyploidy, and the developmental genetic network responsible for the world’s most important textile fiber plant. Here we describe four interrelated experimental components. This work builds on our present efforts and is focused on elucidating the key genes and biological processes involved in transforming wild cotton into modern, high-yielding forms. We will enhance innovative expression profiling approaches to identify gene expression patterns and co-expression networks correlated with phylogenetic and morphological variation in Gossypium, by using genetic substitutions of small chromosomal regions that contribute to phenotypic variation between species and genotypes. While our efforts are focused on fiber development, the tools and approaches will be broadly applicable to a wide range of traits and questions.

Overview of experimental plan, showing interrelationships of major components (1 through 4, circled) and outcomes (boxes, below). Near-isogenic introgression lines (1) will be constructed and phenotypically evaluated. Selected lines will be studied using homoeolog-specific microarrays (3), developed following deep EST sequencing, assembly, and design (2). Genomic diversity and potential bottlenecks will be evaluated (4) using a diverse assemblage of G. hirsutum accessions spanning the wild-to-domesticated continuum.

Our experimental design is molded by two key considerations: (1) a single polyploidization led to multiple Gossypium species with divergent fiber phenotypes; and (2) each of two polyploid Gossypium species were independently domesticated. To dissect this naturally-occurring phenotypic variation into small components amenable to functional genomics, we will develop panels of near-isogenic lines (NILs), each containing substitutions of single chromosomal segments that collectively ‘tile’ the genome(s) of a series of carefully-selected Gossypium genotypes. Such stocks are powerful resources for identifying both obvious and subtle phenotypes resulting from with naturally-occurring genetic variation, also facilitating the identification of high-likelihood candidates for genes for any measurable trait. Our goal is to use these stocks to examine the effect(s) on the fiber transcriptome network of small chromosomal substitutions, in regions that have known phenotypic effects on fiber development. These data will be dovetailed with follow-up analyses of genetic diversity, to gather additional evidence relevant to natural and/or human selection.


We welcome your comments and suggestions.