Identification of QTLs controlling seed dormancy in peach (Prunus persica)

Dormancy is a condition that delays or inhibits growth in seed, vegetative buds, and floral buds. In peach, seed germination occurs when seed accumulate sufficient stratification and growing degree hours to break dormancy and begin growing. Correlations have been reported between mean seed stratification requirements and mean bud chilling requirements among Prunus families, but an individual seed’s germination date and subsequent vegetative and floral bud break date are not correlated. Prior to this study, the genetic factors involved in regulating seed dormancy and their location on the peach genomic map were unknown. Segregating F₂ seed were collected from a high?×?low chill F₁ peach hybrid in 2005, 2006, and 2008. Germination date and growth habit was measured after the stratification requirement of the 2005 seed was fully met. The seed collected in 2006 and 2008 received varying amounts of stratification, which enabled data on stratification requirement, heat requirement, and growth habit to be collected. Genomic DNA was extracted from seedling leaf tissue and screened with SSR markers selected from the Prunus reference map at an average resolution of 20 cM. Seed dormancy quantitative trait loci (QTLs) were detected on G1, G4, G6/8, and G7. The QTLs detected on G6/8 and G7 were discovered in the same region as QTLs associated with floral bud chilling requirement and bloom time in peach.     

Identification of a regulatory cascade controlling Type III Secretion System 3 gene expression in Burkholderia pseudomallei

A major and critical virulence determinant of many Gram‐negative bacterial pathogens is the Type III Secretion Systems (T3SS). T3SS3 in Burkholderia pseudomallei is critical for bacterial virulence in mammalian infection models but its regulation is unknown. B. pseudomallei is the causative agent of melioidosis, a potentially fatal disease endemic in Southeast Asia and northern Australia. While screening for bacterial transposon mutants with a defective T3SS function, we discovered a TetR family regulator (bspR) responsible for the control of T3SS3 gene expression. The bspR mutant exhibited significant virulence attenuation in mice. BspR acts through BprP, a novel transmembrane regulator located adjacent to the currently delineated T3SS3 region. BprP in turn regulates the expression of structural and secretion components of T3SS3 and the AraC family regulator bsaN. BsaN and BicA likely form a complex to regulate the expression of T3SS3 effectors and other regulators which in turn affect the expression of Type VI Secretion Systems (T6SS). The complete delineation of the bspR initiated T3SS regulatory cascade not only contributes to the understanding of B. pseudomallei pathogenesis but also provides an important example of how bacterial pathogens could co‐opt and integrate various regulatory motifs to form a new regulatory network adapted for its own purposes.     

Identification of QTLs controlling tissue-culture traits in barley ( Hordeum vulgare L.)

Quantitative trait loci (QTLs) controlling callus growth (CG), subsequent shoot differentiation ratio (SD) and green shoot ratio (GS) in immature embryo culture were identified in barley. A base map was developed from 99 recombinant inbred lines (RILs) of 'Azumamugi' 2 'Kanto Nakate Gold'. The tissue-culture traits were evaluated at the F₇ and F₁₀ generations of the RILs. The RILs showed wide and continuous variations in each of the three tissue-culture traits. Three QTLs for CG, three QTLs for SD and two QTLs for GS were detected by using composite interval mapping. A QTL for SD on chromosome 3H had a large effect, and 'Kanto Nakate Gold', which has a high differentiation ability, contributed to this QTL. The location of this QTL is identical to, or very close to, the uzu locus. We discuss the relationships between tissue-culture loci in 'Azumamugi' 2 'Kanto Nakate Gold' and those in other mapping populations.     

Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene

New genes originate frequently across diverse taxa. Given that genetic networks are typically comprised of robust, co-evolved interactions, the emergence of new genes raises an intriguing question: how do new genes interact with pre-existing genes? Here, we show that a recently originated gene rapidly evolved new gene networks and impacted sex-biased gene expression in Drosophila. This 4–6 million-year-old factor, named Zeus for its role in male fecundity, originated through retroposition of a highly conserved housekeeping gene, Caf40. Zeus acquired male reproductive organ expression patterns and phenotypes. Comparative expression profiling of mutants and closely related species revealed that Zeus has recruited a new set of downstream genes, and shaped the evolution of gene expression in germline. Comparative ChIP-chip revealed that the genomic binding profile of Zeus diverged rapidly from Caf40. These data demonstrate, for the first time, how a new gene quickly evolved novel networks governing essential biological processes at the genomic level.     

On parametric stability of gene networks controlling ontogenetic processes

The problem of evaluating the parametric stability of three models of pro- and eukaryotic gene networks controlling ontogenetic processes has been defined and solved. Experimental plans of testing gene networks for parametric stability based on the method of generalized threshold models were developed and realized as a software application. We examined the "sensitivity" of the functioning modes to random variations of the parameters in the three model systems: the system of developmental control of phage lambda, the subsystem of morphogenetic control of Arabidopsis thaliana flower, and the gene subnetwork controlling early ontogeny in Drosophila melanogaster. The parametric stability was quantitatively assessed for these models.     

Evolution of gene regulatory networks controlling body plan development

Evolutionary change in animal morphology results from alteration of the functional organization of the gene regulatory networks (GRNs) that control development of the body plan. A major mechanism of evolutionary change in GRN structure is alteration of cis-regulatory modules that determine regulatory gene expression. Here we consider the causes and consequences of GRN evolution. Although some GRN subcircuits are of great antiquity, other aspects are highly flexible and thus in any given genome more recent. This mosaic view of the evolution of GRN structure explains major aspects of evolutionary process, such as hierarchical phylogeny and discontinuities of paleontological change.     

Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean

Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we report on variation in both the microbe-associated molecular pattern-triggered oxidative burst and gene expression across four soybean (Glycine max) genotypes. Variation in MTI correlated with the level of pathogen resistance for each genotype. A quantitative trait locus analysis on these traits identified four loci that appeared to regulate gene expression during MTI in soybean. Likewise, we observed that both MTI variation and pathogen resistance were quantitatively inherited. The approach utilized in this study may have utility for identifying key resistance loci useful for developing improved soybean cultivars.