Browsing by Subject "Quantitative trait locus"

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    Genetic and Genomic Analysis of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon
    (2016-08) Della Coletta, Rafael
    Wheat stem rust, caused by the fungus Puccinia graminis f.sp. tritici (Pgt), is a devastating disease that has been under control for decades. However, new races of this pathogen have emerged that overcome many important wheat stem rust resistance genes, and their spread toward important areas of wheat production threatens global wheat production. Nonhost resistance in plants, which provides durable and broad-spectrum resistance to non-adapted pathogens, may hold great potential to help in the control of wheat stem rust, but the genetic and molecular basis of nonhost resistance is poorly understood. This research project employed the model plant Brachypodium distachyon (Brachypodium), a nonhost of Pgt, for genetic analysis to map loci associated with nonhost wheat stem rust resistance. Using bulked segregant analysis, next-generation sequencing, and bioinformatics approaches, seven quantitative trait loci were found to contribute to nonhost stem rust resistance in a recombinant inbred population derived from a cross between two Brachypodium genotypes with differing levels of resistance. In a second study, analysis of a Brachypodium recombinant inbred population segregating for an induced mutation that confers susceptibility to wheat stem rust led to the identification of a one base pair deletion in a gene that may be the cause of the mutant’s susceptibility. The gene is a homolog of the Arabidopsis gene TIME FOR COFFEE (TIC), which plays a role both in circadian clock regulation and jasmonate signaling. Collectively, the findings of this research project advance our understanding of the genetic basis of nonhost resistance to wheat stem rust, and will guide future research aiming to identify genes essential to the nonhost resistance response, as well as their mechanisms of action.
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    The genetic dissection of fruit texture traits in the apple cultivar honeycrisp.
    (2010-12) McKay, Steven John
    The commercially successful cultivar Honeycrisp, released by the University of Minnesota in 1991, is known for its high degrees of crispness and juiciness. This cultivar has been incorporated into numerous breeding programs in an effort to duplicate its desirable texture traits in conjunction with such other traits as disease resistance and improved tree vigor. This study characterizes several apple fruit texture traits within a large breeding population over several years, combining the established protocols of incomplete block design, sensory evaluation panels, and best linear unbiased prediction. Five full-sib families, all of which share `Honeycrisp' as a common parent, were assayed using a variety of molecular markers, and genetic maps were constructed for each of the five families. The five genetic maps were aligned to produce a consensus genetic map for `Honeycrisp'. Predicted genotype values from each of the five families were coupled with the corresponding molecular data and the genetic maps to identify quantitative trait loci (QTLs) for each family-by-year combination, which were compared relative to the consensus genetic map. Several intervals were identified within the map over which QTLs for multiple families and multiple years were collocated, reflecting consistent and robust QTLs. Results are largely in accordance with previous studies of other apple cultivars with notable exceptions, which are discussed in the context of the recently published apple genome sequence
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    Regions of the genome that affect agronomic performance in two-row barley
    (Crop Science, 1996) Steffenson, Brian; Tinker, N.A.; Mather, D.E.; Rossnagel, B.G.; Kasha, K.J.; Kleinhofs, A.; Hayes, P.M.; Falk, D.E.; Ferguson, T.; Shugar, L.P.; Legge, W.G.; Irvine, R.B.; Choo, T.M.; Briggs, K.G.; Ullrich, S.E.; Franckowiak, J.D.; Blake, T.K.; Graf, R.J.; Dofing, S.M.; Saghai Maroof, M.A.; Scoles, G.J.; Hoffman, D.; Dahleen, L.S.; Kilian, A.; Chen, F.; Biyashev, R.M.; Kudrna, D.A.
    Quantitative trait locus (QTL) main effects and QTL by environment (QTL × E) interactions for seven agronomic traits (grain yield, days to heading, days to maturity, plant height, lodging severity, kernel weight, and test weight) were investigated in a two-row barley (Hordeum vulgare L.) cross, Harrington/TR306. A 127-point base map was constructed from markers (mostly RFLP) scored in 146 random double-haploid (DH) lines from the Harrington/TR306 cross. Field experiments involving the two parents and 145 random DH lines were grown in 1992 and/or 1993 at 17 locations in North America. Analysis of QTL was based on simple and composite interval mapping. Primary QTL were declared at positions where both methods gave evidence for QTL. The number of primary QTL ranged from three to six per trait, collectively explaining 34 to 52% of the genetic variance. None of these primary QTL showed major effects, but many showed effects that were consistent across environments. The addition of secondary QTL gave models that explained 39 to 80% of the genetic variance. The QTL were dispersed throughout the barley genome and some were detected in regions where QTL have been found in previous studies. Eight chromosome regions contained pleiotropic loci and/or linked clusters of loci that affected multiple traits. One region on chromosome 7 affected all traits except days to heading. This study was an intensive effort to evaluate QTL in a narrow-base population grown in a large set of environments. The results reveal the types and distributions of QTL effects manipulated by plant breeders and provide opportunities for future testing of marker-assisted selection.