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.