No abstract

In one of the longest-running experiments in biology, researchers at the University of Illinois have selected for altered composition of the maize kernel since 1896. Here we use an association study to infer the genetic basis of dramatic changes that occurred in response to selection for changes in oil concentration. The study population was produced by a cross between the high-and low-selection lines at generation 70, followed by 10 generations of random mating and the derivation of 500 lines by selfing. These lines were genotyped for 488 genetic markers and the oil concentration was evaluated in replicated field trials.Three methods of analysis were tested in simulations for ability to detect quantitative trait loci (QTL). The most effective method was model selection in multiple regression. This method detected ‫05ف‬ QTL accounting for ‫%05ف‬ of the genetic variance, suggesting that Ͼ50 QTL are involved. The QTL effect estimates are small and largely additive. About 20% of the QTL have negative effects (i.e., not predicted by the parental difference), which is consistent with hitchhiking and small population size during selection. The large number of QTL detected accounts for the smooth and sustained response to selection throughout the twentieth century. T HE genetic architecture of a quantitative trait con-tries. An objective of our study is to identify genes that sists of a set of parameters that explain the genetic may be used to increase the oil concentration of maize component of trait variation within or among populakernels through plant breeding or genetic engineering. tions. These parameters include the number of quanti-The experiment reported here originated in 1896 tative trait loci (QTL) affecting the trait, their locations when C. G. Hopkins began the Illinois long-term selecin the genome, the frequencies of alternative genotypes tion lines, which have become a "textbook" example of segregating at the QTL, the pattern of linkage disequithe power of artificial selection (see review by Dudley libria among QTL, and the magnitudes of additive, and Lambert 2004). From an open-pollinated variety dominance, and epistatic effects. Knowledge of genetic of maize, Hopkins started two populations that were architecture has applications in two areas: (1) the identiselected divergently for the percentage of kernel dry fication of genes with utility in agriculture and/or treatweight that consists of oil ("oil concentration" or "perment of disease and (2) making inferences about the centage of oil"). These populations are called Illinois evolutionary processes that maintain genetic variation high oil (IHO) and Illinois low oil (ILO). In each generand those that cause divergence between populations.ation and each population, bulked kernels from each Here we report a study of oil variation in maize that has of a number of ears (half-sib families) were analyzed both types of application. and the highest (or lowest) 20% of ears were selected to The kernels of a modern maize (Zea mays L.) hybrid be parents o...

Phosphorylation of the transcription factor encoded by spo0A is required for the initiation of sporulation in Bacillus subtilis. Production and accumulation of Spo0AϳP is controlled by histidine protein kinases and the spo0 gene products. To identify additional genes that might be involved in the initiation of sporulation and production of Spo0AϳP, we isolated genes which when present on a multicopy plasmid could suppress the sporulation defect of a spo0K mutant. kinC was one gene isolated in this way. A multicopy plasmid containing kinC completely or partially suppressed the sporulation defect caused by mutations in spo0K, kinA, spo0F, and spo0B, indicating that at least when overexpressed, KinC is capable of stimulating phosphorylation of Spo0A independently of the normal phosphorylation pathway. The predicted product of kinC is 428 amino acids long and is most similar to KinA and KinB, the histidine protein kinases involved in the initiation of sporulation. In otherwise wild-type strains, kinC null mutations caused little or no defect in sporulation under the conditions tested. However, in the absence of a functional phosphorelay (spo0F or spo0B), KinC appears to be the kinase responsible for phosphorylation of the sof-1 and rvtA11 forms of Spo0A.Cells of the gram-positive soil bacterium Bacillus subtilis differentiate to form heat-resistant metabolically dormant spores under appropriate conditions. The initiation of sporulation depends upon activation of the Spo0A transcription factor by phosphorylation (20), and a threshold concentration of Spo0AϳP appears to be required (11). Spo0AϳP is involved in the transcriptional regulation of many sporulation genes. It directly activates transcription of spoIIA, spoIIE, and spoIIG, which are necessary for sporulation (4,6,48,49,57,62). Also, Spo0AϳP represses transcription of abrB (56), which encodes a repressor of several genes involved in sporulation (44,55,59,64).Spo0A receives phosphate, albeit indirectly, from KinA (2, 38) and KinB (58), histidine protein kinases that belong to a conserved family of proteins known as sensor kinases. Sensor kinases are generally involved in signal transduction; they autophosphorylate and donate phosphate to particular proteins in response to changes in the environment, modifying the activity of those proteins. The proteins that receive phosphate from sensor kinases belong to a conserved family of proteins known as response regulators, which are often involved in transcriptional regulation. Together, a sensor protein and its cognate response regulator form a two-component system. There are many examples of two-component systems involved in signal transduction in bacteria (1, 37), and similar systems in plants (10) and yeasts (36) have recently been identified.Although Spo0A belongs to the response regulator family of proteins, it does not normally obtain phosphate directly from a histidine protein kinase. Rather, Spo0A receives phosphate through a multicomponent phosphorelay (9). KinA (and other kinases) first donates phosphate to...

Activation (phosphorylation) of the transcription factor encoded by spo0A is essential for the initiation of sporulation in Bacillus subtilis. At least three histidine protein kinases are involved in the phosphorylation of Spo0A. Under some growth conditions, KinA was the primary kinase, but under other conditions, KinB had the more critical role. KinC was required for the initial activation of Spo0A, even in the presence of KinA and KinB.Under appropriate conditions, cells of the gram-positive soil bacterium Bacillus subtilis differentiate to form dormant heatresistant endospores. One of the key factors determining whether cells initiate sporulation is the accumulation of the active phosphorylated form of the transcription factor encoded by spo0A (reviewed in reference 7). Spo0A belongs to the response regulator family of transcription factors (1, 20) which usually receive phosphate on an aspartate residue from histidine protein kinases known as sensor kinases (1,20). The histidine protein kinases autophosphorylate on a histidine residue and then serve as a phosphate donor to a cognate response regulator. Unlike most response regulators, Spo0A does not receive phosphate directly from a histidine protein kinase. Rather, phosphorylation of Spo0A requires the transfer of phosphate through the phosphorelay (5). The sporulation kinases first serve as phosphate donors to the response regulator encoded by spo0F. Phosphate is then transferred from Spo0F to Spo0B and finally to Spo0A (5, 7). The physiological function of the phosphorelay seems to be to integrate the many signals that regulate the initiation of sporulation (8, 10-13) and to generate a threshold concentration of Spo0AϳP necessary for the initiation of sporulation (6).Spo0AϳP is a transcriptional activator and repressor, depending on the location of the target binding site. Spo0AϳP represses transcription of abrB (22, 27) and activates transcription of several sporulation genes, including spoIIA (28), spoIIE (32), and spoIIG (3, 4). The abrB gene product is a transcriptional repressor, and repression of abrB by Spo0AϳP causes activation of genes that are normally repressed by AbrB (31,34). Less Spo0AϳP is needed for repression of abrB than for activation of the spoII genes, since several mutations that decrease activation of Spo0A have little or no effect on abrB expression while causing a decrease in expression of spoII genes (6,19,21,26,29).Three histidine protein kinases are involved in the initiation of sporulation: KinA (2, 21), KinB (29), and KinC (15,16). Under most sporulation conditions tested, kinA null mutations cause a small reduction in the sporulation frequency while null mutations in either kinB or kinC cause little or no decrease in sporulation frequency (15,16,29). The experiments described

A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0-15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists.