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Develop and characterize immortal introgression populations, to reduce complex morphology into defined constituents amenable to functional genomic analyses.

To dissect the stages involved in transforming primitive trichomes to the economically important fibers of modern cotton cultivars, and provide for the identification of the associated transcriptome alterations, we will construct panels of near-isogenic lines (NILs), each containing one introgressed segment from a donor genotype but which collectively 'tile' the genome. NILs offer important advantages over traditional QTL mapping approaches, improving the ability to detect genes with small phenotypic effects and providing for testing of the main effects of small genomic regions in the absence of epistasis (though they provide for tests of epistasis). These genetic stocks will provide the complexity reduction that is important to our study and offer a valuable resource for identification of high-likelihood candidates for QTLs for virtually any trait, by identifying and characterizing additional recombinants in a region of interest. NILs may even be of interest as improved germplasm; this is beyond the scope of our studies, but collaborators who assist with field grow-outs may take advantage of this benefit.

The figure illustrates the construction and use of a near-isogenic line (NIL) panel for identification of high-likelihood candidates for QTLs. Initially, a donor and reference or recurrent parent are crossed and, subsequently, repeated back crosses to the reference parent lead to a reduction of the donor genome contribution. With marker assisted selection (MAS), a panel of NILs that tile the genome can be constructed. The resulting panel members can be tested for a range of phenotypic traits for the detection and locating of QTL candidates.

The NILs, each isolating about 0.5% of a donor genome in the background of a reference genotype, provide a powerful tool for genetically dissecting complex morphological and physiological differences, thereby increasing the precision with which phenotypic changes can be mapped to transcriptomic and genetic alterations. Using both G. hirsutum and G. barbadense, we will introgress primitive or wild accessions into advanced, modern cultivars, thereby creating two sets of NILs, in parallel, for evaluating the comparative genomics of cotton domestication. The primitive G. hirsutum accession selected for this purpose is a truly wild form (accession Tx2094), collected by J. McD. Stewart from the Yucatan Peninsula; molecular and morphological data justify its primitive position within the species. For G. barbadense we will use accession K101, a primitive form from Bolivia that either is wild or which has undergone little human selection; this choice too is justified by morphology and our earlier multilocus molecular analyses, which indicate that it harbors no evidence of introgression from G. hirsutum, an otherwise common phenomenon in G. barbadense.

In addition to the two sets of NILs between wild and domesticated cottons, we will create a reciprocal set of introgression lines between highly improved G. hirsutum and G. barbadense cultivars, permitting us to study the genes that contributed to species divergence, domestication, and breeding of these genotypes. We will use the elite G. hirsutum cultivar Acala Maxxa and the elite G. barbadense cultivar Pima S6. Selection of these two reference genotypes is based on multiple criteria, including elite fiber and agronomic phenotypes, availability of ESTs and BAC libraries that have been genetically-anchored (under prior NSF support) with ~2000 mapped sequence tagged sites, and their widespread historical importance in breeding and production. Thus, in total we will generate four sets of introgression lines, two representing intraspecific domestication and diversity and two representing not only speciation but the culmination of millennia of breeding efforts. Collectively these sets of NILs will provide an immortal resource for functional genomic analyses of virtually any trait of interest to breeders and biologists, including fiber and plant phenotypes, physiological characteristics, and responses to abiotic and biotic challenges.

We welcome your comments and suggestions.