The use of information from flanking markers to estimate the position and size of the effect of a quantitative trait locus (QTL) lying between two markers is shown to be affected by QTLs lying in neighbouring regions of the chromosome. In some situations the effects of two QTLs lying outside the flanked region are reinforced in such a way that a 'ghost' QTL may be mistakenly identified as a real QTL. These problems are discussed in the framework of a backcross using a regression model as the analytical tool to present the theoretical results. Regression models that use information obtained from three or more nearby markers are shown to be useful in separating the effects of QTLs in neighbouring regions. A simulated data set exemplifies the problem and is analysed by the interval mapping method as well as by the regression model.

Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation-responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.phosphate | epigenetics | abiotic stress | DNA methylation | methylome D uring evolution, plants have acquired a series of adaptive strategies that allow them to survive and complete their life cycles under adverse environmental conditions. Consequently, plants have evolved a myriad of physiological, cellular, and molecular mechanisms to cope with challenging environments. Plant responses to environmental stress include modifications in postembryonic development and metabolic reprogramming, which are highly dependent on the regulation of gene expression. It is well documented that gene regulation at the transcriptional and posttranscriptional levels plays an important role in plant stress responses; however, more recent evidence suggests that epigenetic mechanisms also play an important role in reprogramming gene expression in response to environmental cues and that epigenetic marks can serve as a priming mechanism to prepare future generations to better withstand biotic and abiotic stresses (1-3). These epigenetic marks include, but are not restricted to, posttranslational histone modifications and DNA methylation, a mechanism by which cytosine DNA methylation regulates the silencing and control of transposable elements (TEs) and repetitive sequences, genomic imprinting, and gene silencing. In plants, this DNA methylation modification is applied in three different sequence contexts (CG, CHG, and CHH, where H = A, C, or T), and the involvement of different pathways is necessary for the establishment, maintenance, and modification of DNA methylation patterns in these contexts (4, 5). These epigenetic processes can interact to orchestrate new heterochromatin states that modify gene expression [for re...

The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. In any case, it is difficult to completely comprehend the global changes that occur in the transcriptome, given that thousands of gene expression measurements are involved. We propose an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. We define transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. We introduce the formulae using a simple example and show their application in two datasets of gene expression in human tissues. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. The framework presented enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli.biological complexity ͉ gene expression ͉ microarrays ͉ serial analysis of gene expression (SAGE) ͉ Shannon entropy

BackgroundAnimal-derived elicitors can be used by plants to detect herbivory but they function only in specific insect–plant interactions. How can plants generally perceive damage caused by herbivores? Damaged-self recognition occurs when plants perceive molecular signals of damage: degraded plant molecules or molecules localized outside their original compartment.Methodology/Principal FindingsFlame wounding or applying leaf extract or solutions of sucrose or ATP to slightly wounded lima bean (Phaseolus lunatus) leaves induced the secretion of extrafloral nectar, an indirect defense mechanism. Chemically related molecules that would not be released in high concentrations from damaged plant cells (glucose, fructose, salt, and sorbitol) did not elicit a detectable response, excluding osmotic shock as an alternative explanation. Treatments inducing extrafloral nectar secretion also enhanced endogenous concentrations of the defense hormone jasmonic acid (JA). Endogenous JA was also induced by mechanically damaging leaves of lima bean, Arabidopsis, maize, strawberry, sesame and tomato. In lima bean, tomato and sesame, the application of leaf extract further increased endogenous JA content, indicating that damaged-self recognition is taxonomically widely distributed. Transcriptomic patterns obtained with untargeted 454 pyrosequencing of lima bean in response to flame wounding or the application of leaf extract or JA were highly similar to each other, but differed from the response to mere mechanical damage. We conclude that the amount or concentration of damaged-self signals can quantitatively determine the intensity of the wound response and that the full damaged-self response requires the disruption of many cells.Conclusions/SignificanceNumerous compounds function as JA-inducing elicitors in different plant species. Most of them are, contain, or release, plant-derived molecular motifs. Damaged-self recognition represents a taxonomically widespread mechanism that contributes to the perception of herbivore feeding by plants. This strategy is independent of insect-derived elicitors and, therefore, allows plants to maintain evolutionary control over their interaction with herbivores.

The Cuatro Cié negas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 M). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a ''marine isolation origin hypothesis'' that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian.evolution ͉ genomic adaptation ͉ horizontal gene transfer ͉ phosphorus stress ͉ sulfolipids T he Cuatro Ciénegas Basin (CCB) is located in a valley Ϸ740 m above sea level in the state of Coahuila, Mexico, that measures Ϸ30 km by 40 km and is surrounded by high mountains (Ͼ3,000 m) (Fig. 1). CCB is an enclosed evaporitic basin that receives Ϸ150 mm of annual precipitation. Despite the dry climate of the valley, the CCB harbors an extensive system of springs, streams, and pools (1). The CCB ecosystem is not only characterized by a high endemism of macrooganisms and biodiversity of microorganisms (1, 2), but also by extremely oligotrophic waters that are unable to sustain algal growth, making microbial mats the base of the food web (3). In particular, phosphorus (P) levels in CCB appear to be rather low, because they were below the level of detection of several methods used (0.3 M) and the extremely high biomass C:P and N:P ratios (Ͼ100 by moles) previously reported for CCB stromatolites (3, 4). Unlike the present sea, the Churince spring water is poor in NaCl and carbonates, but it is rich in sulfates, magnesium, and calcium (4). Characterization of the microbiological diversity by sequencing 16S rRNA genes revealed that nearly half of the phylotypes from the CCB were closely related to bacteria from marine environments (2). Bacillus coahuilensis is a free-living, spore-forming bacteria isolated from the water column of a shallow desiccation lagoon in the Churince system at CCB (4) (Fig. 1 A and B). A molecular phylogenetic analysis of 16S rRNA sequences indicates that B. coahuilensis is closely ...

tannins and phytic acid) reduce the bioavailability of Ca, Fe, and Zn (Frossard et al., 2000). In common bean (Phaseolus vulgaris L.), some nutritional traitsDuring the past 25 yr, substantial progress has been such as proteins and mineral content are lower in the cultivated form as compared with the wild counterpart. To assess the feasibility of made on the clinical, biochemical, and immunological wild bean as the putative source of desirable traits such as minerals aspects of the role of Zn in humans (Ganapathy and or tannins, this study was performed to identify quantitative trait loci Volpe, 1999). Extensive research has shown that Zn is (QTL) associated with seed mass, Ca, Fe, Zn, and tannin content in involved in a myriad of critical reactions in the human bean seed. Two-hundred-ninety-one amplified fragment length polybody and is associated with cellular growth and repair, morphism (AFLP) markers were scored in 120 F 2:3 segregating individappetite, behavior, and susceptibility to infection. Reuals derived from a cross between cultivated 'Bayo Baranda' and cent studies have identified Zn deficiencies in children wild common bean accession G-22837. Seed weight and minerals and who consume diets high in cereals (Ranum, 1999). tannin contents were quantified on the seed harvested from the 120 individual plants. Significant transgressive segregation was observed Moreover, it is recognized that a nutritional deficiency among the F 2:3 individuals for some characteristics. A total of 57 AFLP in Zn is common throughout the world, including the markers were distributed among five linkage groups with a coverage USA. (Ganapathy and Volpe, 1999). of 497 centiMorgans (cM). Five putative QTL were significantly asso-Plant breeding has been mainly focused on increasing ciated with seed mass, two with Ca, two with Fe, one with Zn, and yield and disease resistance in crops, but not at improvfour with tannin content in the seed. These QTL explained ≈42, 25, ing the micronutrient concentration in grain (Frossard 25, 15, and 42% of the phenotypic variance, respectively. Due to et al., 2000). Developing cultivars with higher capacity known environmental effect on most nutritional traits, the use of QTL to accumulate Ca, Fe, and Zn could contribute signifiwith larger effects could be used to screen segregating populations cantly to the improvement of the micronutrient status that include wild genotypes, wild populations, and ancestral landraces from the region where outstanding wild populations are identified.

Differential cultivars and molecular markers were used to analyze 59 isolates of the bean anthracnose pathogen, Colletotrichum lindemuthianum, from different regions of Mexico. Ten distinct races were determined, three of which had not been reported previously in Mexico. Isolates were found to infect only a narrow range of the differential cultivars used and were restricted to cultivars of Middle American origin. A comparison of random amplified polymorphic DNA and amplified fragment length polymorphism (AFLP) analyses was carried out on a subset of the fungal isolates. Determination of genetic distances based on AFLP data and production of a dendrogram demonstrated two levels of association: i) isolates classified into two major groups according to the type of cultivar or system of cultivation from which they originated, and ii) isolates could be classified into smaller subgroups generally associated with the geographic location from which they were obtained. Bootstrap analysis and determination of confidence intervals showed these geographic groupings to be extremely robust.

BackgroundThe set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening.ResultsRNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; ‘Tampiqueño 74’) collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40–60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR.ConclusionsIn general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.