Exploring the assumptions underlying genetic variation in host nematode resistance (Open Access publication)

The wide range of genetic parameter estimates for production traits and nematode resistance in sheep obtained from field studies gives rise to much speculation. Using a mathematical model describing host – parasite interactions in a genetically heterogeneous lamb population, we investigated the consequence of: (i) genetic relationships between underlying growth and immunological traits on estimated genetic parameters for performance and nematode resistance, and (ii) alterations in resource allocation on these parameter estimates. Altering genetic correlations between underlying growth and immunological traits had large impacts on estimated genetic parameters for production and resistance traits. Extreme parameter values observed from field studies could only be reproduced by assuming genetic relationships between the underlying input traits. Altering preferences in the resource allocation had less pronounced effects on the genetic parameters for the same traits. Effects were stronger when allocation shifted towards growth, in which case worm burden and faecal egg counts increased and genetic correlations between these resistance traits and body weight became stronger. Our study has implications for the biological interpretation of field data, and for the prediction of selection response from breeding for nematode resistance. It demonstrates the profound impact that moderate levels of pleiotropy and linkage may have on observed genetic parameters, and hence on outcomes of selection for nematode resistance.     

Advances in QTL mapping in pigs

Over the past 15 years advances in the porcine genetic linkage map and discovery of useful candidate genes have led to valuable gene and trait information being discovered. Early use of exotic breed crosses and now commercial breed crosses for quantitative trait loci (QTL) scans and candidate gene analyses have led to 110 publications which have identified 1,675 QTL. Additionally, these studies continue to identify genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. A well developed QTL database called PigQTLdb is now as a valuable tool for summarizing and pinpointing in silico regions of interest to researchers. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve traits of economic performance. The long awaited sequencing efforts are also now beginning to provide sequence available for both comparative genomics and large scale single nucleotide polymorphism (SNP) association studies. While these advances are all positive, development of useful new trait families and measurement of new or underlying traits still limits future discoveries. A review of these developments is presented.     

A changing climate for grassland research

Here, we review the current genetic approaches for grass improvement and their potential for the enhanced breeding of new varieties appropriate for a sustainable agriculture in a changing global climate. These generally out-breeding, perennial, self-incompatible species present unique challenges and opportunities for genetic analysis. We emphasise their distinctiveness from model species and from the in-breeding, annual cereals. We describe the modern genetic approaches appropriate for their analysis, including association mapping. Sustainability traits discussed here include stress resistance (drought, cold and pathogeneses) and favourable agronomic characters (nutrient use efficiency, carbohydrate content, fatty acid content, winter survival, flowering time and biomass yield). Global warming will predictably affect temperature-sensitive traits such as vernalisation, and these traits are under investigation. Grass biomass utilisation for carbon-neutral energy generation may contribute to reduced atmospheric carbon emissions. Because the wider potential outcomes of climate change are unpredictable, breeders must be reactive to events and have a range of well-characterised germplasm available for new applications.     

The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

Background  

Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface.     

The design and implementation of insect resistance management programs for Bt crops

Cotton and corn plants with insect resistance traits introduced through biotechnological methods and derived from the bacterium Bacillus thuringiensis (Bt) have been widely adopted since they were first introduced in 1996. Because of concerns about resistance evolving to these Bt crops, they have been released with associated IRM programs that employ multiple components and reflect the input of academic, industrial and regulatory experts. This paper summarizes the current status of Bt crop technologies in cotton and corn, the principles of IRM for Bt crops and what they mean for the design of IRM programs. It describes how these IRM programs have been implemented and some of the key factors affecting successful implementation. Finally, it suggests how they may evolve to properly steward these traits in different geographies around the world. The limited number of reported cases of resistance after more than 15 years of intensive global use of Bt crops suggest that this exercise has been broadly successful. Where resistance issues have been observed, they have been associated with first generation technologies and incomplete or compromised IRM programs (i.e., inadequate structured refuge). Next generation technologies with multiple pyramided modes of action, together with the implementation of IRM strategies that are more dependent upon manufacturing and less dependent upon grower behavior, such as seed mixes, should further enhance IRM programs for Bt crops.     

An EM algorithm for mapping quantitative resistance loci

Many disease resistance traits in plants have a polygenic background and the disease phenotypes are modified by environmental factors. As a consequence, the phenotypic values usually show a quantitative variation. The phenotypes of such disease traits, however, are often measured in discrete but ordered categories. These traits are called ordinal traits. In terms of disease resistance, they are called quantitative resistance traits, as opposed to qualitative resistance traits, and are controlled by the quantitative resistance loci (QRL). Classical quantitative trait locus mapping methods are not optimal for ordinal trait analysis because the assumption of normal distribution is violated. Methods for mapping binary trait loci are not suitable either because there are more than two categories in ordinal traits. We developed a maximum likelihood method to map these QRL. The method is implemented via a multicycle expectation-conditional-maximization (ECM) algorithm under the threshold model, where we can estimate both the QRL effects and the thresholds that link the disease liability and the categorical phenotype. The method is verified in simulated data under various combinations of the parameters. An SAS program is available to implement the multicycle ECM algorithm. The program can be downloaded from our website at www.statgen.ucr.edu.     

The inheritance of the traits of resistance to fungal diseases by distant hybrids of wheat with amphiploids

The inheritance of resistance to powdery mildew, leaf rust and septorios of hybrids from crosses of wheat--rye and two wheat--Elymus amphiploids with durum and bread wheat was studied. Spontaneous hybridization was revealed to be a determining factor of the new available trait formation in the wide crosses. Control of the leaf rust and heary leaf traits by the same alien chromosome of Elytricum fertile is confirmed. While in the wheat--Aegilops amphiploid H74/90-258 these traits are not linked and controlled by one and two genes, respectively. The alien resistance is easier introgessed into wheat genome in the cross of 8x-amphiploid with durum wheat, than with bread wheat. Constant homozygous strains with group resistance to the studied diseases have been revealed.     

Incidence of antibiotic resistance and sex pheromone response among enterococci isolated from clinical human samples and from municipal waste water

The incidence of resistance to various antibiotics as well as the capacity to elicit aggregation response to sex pheromones have been investigated in strains of Enterococcus faecalis isolated from clinical and municipal waste waters (MWW). While clinical isolates showed a high incidence of antibiotic resistance (87%) and sex pheromone response (33%), these traits appeared with a much lower frequency in MWW isolates (12% and 4% respectively). The simultaneous incidence of both traits was of 52% and 0% for clinical and MWW isolates, respectively. The capacity to elicit a positive pheromone response as well as antibiotic resistance traits seemed to be strongly correlated with the presence of gelatinase activity among clinical isolates. Among MWW isolates, only sex pheromone response seemed to correlate with the presence of gelatinase activity.     

Expression of phenotypic traits following modulation of colchicine resistance in J774.2 cells

Development of resistance to colchicine in the mouse macrophage-like cell line J774.2 coincides with the expression of a variety of phenotypic traits. A cloned subline (J7/CLC-20), maintained in 20 microM colchicine, exhibits reduced steady-state association with drug, increased presence of a 140,000-145,000 dalton (140-145 kD) phosphoglycoprotein associated with the plasma membrane, double minute chromosomes and cross-resistance to other drugs. While similar phenotypic traits are observed in J774.2 cells resistant to taxol and vinblastine, differences in the electrophoretic mobilities of the resistance-specific glycoproteins in each of the three sublines suggest that multi-drug resistant sublines exhibit specificity for individual drugs. In an attempt to elucidate the relationships between the phenotypic traits associated with colchicine resistance, the degree of colchicine resistance in J7/CLC-20 cells was modulated and the levels of expression of the phenotypic traits were quantitated. In the absence of colchicine in the growth medium, J7/CLC-20 cells reverted to drug sensitivity within 35 days. A decrease in the level of resistance coincided with coordinate changes in both the quantity of the resistance-specific glycoprotein and the average number of double minute chromosomes. We propose that the emergence and disappearance of the resistance-specific glycoprotein and double minute chromosomes may be closely linked. However, J7/CLC-20 cells which had regained their drug sensitivity after growth in drug-free medium maintained a reduced level of steady-state drug association. The persistence of reduced drug association in cells that have reverted to a drug-sensitive state suggests that this phenomenon, although related to colchicine resistance, need not be the primary or only mechanism of drug resistance.     

植物类过敏反应介导的抗病研究进展

很多植物通过过敏反应产生广谱抗病性,类过敏反应发生机制的解析以及相关基因的研究对培育广谱抗病品种、提高作物的适应性和稳产性具有重要意义。植物类过敏反应介导的抗病性可大致分为活性氧迸发、信号分子的传递以及抗病系统的激活三个阶段,对这三个阶段的最新研究进展进行了综述,以期为植物抗病相关研究提供参考。     

A QTL resource and comparison tool for pigs: PigQTLDB

During the past decade, efforts to map quantitative trait loci (QTL) in pigs have resulted in hundreds of QTL being reported for growth, meat quality, reproduction, disease resistance, and other traits. It is a challenge to locate, interpret, and compare QTL results from different studies. We have developed a pig QTL database (PigQTLdb) that integrates available pig QTL data in the public domain, thus, facilitating the use of this QTL data in future studies. We also developed a pig trait classification system to standardize names of traits and to simplify organization and searching of the trait data. These steps made it possible to compare primary data from diverse sources and methods. We used existing pig map databases and other publicly available data resources (such as PubMed) to avoid redundant developmental work. The PigQTLdb was also designed to include data representing major genes and markers associated with a large effect on economically important traits. To date, over 790 QTL from 73 publications have been curated into the database. Those QTL cover more than 300 different traits. The data have been submitted to the Entrez Gene and the Map Viewer resources at NCBI, where the information about markers was matched to marker records in NCBI’s UniSTS database. Having these data in a public resource like NCBI allows regularly updated automatic matching of markers to public sequence data by e-PCR. The submitted data, and the results of these calculations, are retrievable from NCBI via Entrez Gene, Map Viewer, and UniSTS. Efforts were undertaken to improve the integrated functional genomics resources for pigs.     

Updating the 'crop circle'

Comparative analyses unravel the relationships between genomes of related species. The most comprehensive comparative dataset obtained to date is from the grass family, which contains all of the major cereals. Early studies aimed to identify chromosomal regions that have remained conserved over long evolutionary time periods, but in recent years, researchers have focused more on the extent of colinearity at the DNA-sequence level. The latter studies have uncovered many small rearrangements that disturb colinearity in orthologous chromosome regions. In part, genomes derive their plasticity from genome- and gene-amplification processes. Duplicated gene copies are more likely to escape selective constraints and thus move to other regions of the genome, where they might acquire new functions or become deleted. These rearrangements will affect map applications. The most popular applications, especially since the complete rice genomic sequence has been available, are the use of comparative data in the generation of new markers to tag traits in other species and to identify candidate genes for these traits. The isolation of genes underlying orthologous traits is the first step in conducting comparative functional studies.     

Investigating latitudinal clines for life history and stress resistance traits in Drosophila simulans from eastern Australia

Latitudinal clines have been demonstrated for many quantitative traits in Drosophila and are assumed to be due to climatic selection. However, clinal studies are often performed in species of Drosophila that contain common cosmopolitan inversion polymorphisms that also show clinal patterns. These inversion polymorphisms may be responsible for much of the observed clinal variation. Here, we consider latitudinal clines for quantitative traits in Drosophila simulans from eastern Australia. Drosophila simulans does not contain cosmopolitan inversion polymorphisms, so allows the study of clinal selection on quantitative traits that are not confounded by associations with inversions. Body size showed a strong linear cline for both females and males. Starvation resistance exhibited a weak linear cline in females, whereas chill-coma recovery exhibited a significant nonlinear cline in females only. No clinal pattern was evident for development time, male chill-coma recovery, desiccation or heat resistance. We discuss these results with reference to the role inversion polymorphisms play in generating clines in quantitative traits of Drosophila.     

Double stranded RNA expression and its topical application for non-transgenic resistance to plant viruses

The discovery of RNA silencing has heralded a new phase in the understanding of nucleic acid metabolism and has provided researchers with alternative methods to define the biochemical, developmental and self-protection pathways in plants. Manipulation of these pathways to ultimately modify, induce or enhance favorable traits and repress or completely eliminate unfavorable qualities including disease susceptibility can be achieved by insertion or infiltration of transgenes encoding appropriate effectors. Remarkably, in contrast to transgene derived viral resistance, the RNA silencing mechanism can be readily induced by the topical application of dsRNA effector molecules. The current review summarises the various dsRNA production systems available for producing the large amounts of dsRNA required for topical application onto field grown crops. Also discussed are several investigations utilising a topical application of exogenous, sequence-specific dsRNA to induce the RNA silencing mechanism for viral resistance in plants. Currently, there are limitations for the spray-on application of dsRNA for field use. Further research to define a new phase in the non-transgenic delivery of RNA silencing for complete management of plant pathogens is crucial for its commercial application.     

How to approach the study of syndromes in macroevolution and ecology

Syndromes, wherein multiple traits evolve convergently in response to a shared selective driver, form a central concept in ecology and evolution. Recent work has questioned the existence of some classic syndromes, such as pollination and seed dispersal syndromes. Here, we discuss some of the major issues that have afflicted research into syndromes in macroevolution and ecology. First, correlated evolution of traits and hypothesized selective drivers is often relied on as the only evidence for adaptation of those traits to those hypothesized drivers, without supporting evidence. Second, the selective driver is often inferred from a combination of traits without explicit testing. Third, researchers often measure traits that are easy for humans to observe rather than measuring traits that are suited to testing the hypothesis of adaptation. Finally, species are often chosen for study because of their striking phenotypes, which leads to the illusion of syndromes and divergence. We argue that these issues can be avoided by combining studies of trait variation across entire clades or communities with explicit tests of adaptive hypotheses and that taking this approach will lead to a better understanding of syndrome‐like evolution and its drivers.     

Morphological and physiological traits of three major Arabidopsis thaliana accessions

Arabidopsis is currently the most studied organism in plant biology. Its short life cycle and small genome size have rendered it one of the principal model systems. Additionally, numerous large T-DNA insertion mutant collections are available. The advent of molecular biology and the completion of the Arabidopsis genome sequence have contributed to helping researchers discover a large variety of mutants identified for their phenotypes. Yet, it is important to consider that natural phenotypic variations exist and appear in natural ecotypes, differing greatly in several traits. Although there are a vast number of ecotypes available, only a few have been extensively studied, and some have been created in laboratories. In order to identify new phenotypic differences, we chose to study the differences observed between three ecotypes: Columbia (Col-0), Landsberg erecta (Laer-0) and Wassilewskija (Ws-0). Our research focuses on observable morphological traits throughout plant growth and development along the entire plant life cycle. We then attempted to shed some light on phenotypic discrepancies through the study of the class III peroxidase protein family, which is involved in many aspects of plant growth and tissue differentiation. Both morphological and molecular aspects reveal that there are major variations between ecotypes, hence indicating a possibly interesting heterotic effect in the F1 from crosses between different Arabidopsis ecotypes.     

Patterns of intraspecific trait variation along an aridity gradient suggest both drought escape and drought tolerance strategies in an invasive herb

Background and AimsIn water-limited landscapes, some plants build structures that enable them to survive with minimal water (drought resistance). Instead of making structures that allow survival through times of water limitation, annual plants may invoke a drought escape strategy where they complete growth and reproduction when water is available. Drought escape and resistance each require a unique combination of traits and therefore plants are likely to have a suite of trait values that are consistent with a single drought response strategy. In environments where conditions are variable, plants may additionally evolve phenotypically plastic trait responses to water availability. Invasive annual species commonly occur in arid and semi-arid environments and many will be subject to reduced water availability associated with climate change. Assessing intraspecific trait variation across environmental gradients is a valuable tool for understanding how invasive plants establish and persist in arid environments.MethodsIn this study, we used a common garden experiment with two levels of water availability to determine how traits related to carbon assimilation, water use, biomass allocation and flowering phenology vary in California wild radish populations across an aridity gradient.Key ResultsWe found that populations from arid environments have rapid flowering and increased allocation to root biomass, traits associated with both drought escape and tolerance. Early flowering was associated with higher leaf nitrogen concentration and lower leaf mass per area, traits associated with high resource acquisition. While trait values varied across low- and high-water treatments, these shifts were consistent across populations, indicating no differential plasticity across the aridity gradient.ConclusionsWhile previous studies have suggested that drought escape and drought resistance are mutually exclusive drought response strategies, our findings suggest that invasive annuals may employ both strategies to succeed in novel semi-arid environments. As many regions are expected to become more arid in the future, investigations of intraspecific trait variation within low water environments help to inform our understanding of potential evolutionary responses to increased aridity in invasive species.     

Modifying glucosinolates in oilseed rape – Giamoustaris & Mithen (1995): a top‐twenty paper in the Annals of Applied Biology

Part of the reason for the under‐exploitation of physical resistance traits in plant breeding is that the genetic basis and heritability of these traits is poorly characterised, and any associations of particular traits with pest and disease resistances have yet to be determined. In raspberry, some associations between architectural traits and disease resistances have been demonstrated, for example cane hairs and resistance to cane diseases. The aim of this work is to examine a range of traits, including leaf trichomes, leaf density, cane density, bush density, lateral length and lateral numbers, to determine the heritability and therefore breeding potential of these traits. The effect of these traits against aphids and spider mites, two important pests in raspberry, was examined. Chromosomal regions with candidate genes regulating these traits were identified as the first step to understanding the genetic control.