Markers, old and new, for examining Phytophthora infestans diversity

Late blight, caused by Phytophthora infestans , is an ongoing threat to potato and tomato crop production worldwide and considerable fundamental and applied research is conducted with the long-term aim of improved disease control. Understanding the mechanisms, processes and rates of P. infestans evolution is an important factor in predicting the effectiveness and durability of new management practices. A range of phenotypic and genotypic tests has been applied to achieve this goal, but each has limitations and new methods are sought. Recent progress in P. infestans genomics is providing the raw data for such methods and new high-throughput codominant biomolecular markers are currently being developed that have tremendous potential in the study of P. infestans population biology, epidemiology, ecology, genetics and evolution. This paper reviews some key applications, recommends some changes in approach and reports on the status and potential of new and existing methods for probing P. infestans genetic diversity.     

Resistance to yellow rust in Triticum dicoccoides. II. Crosses with resistant Triticum dicoccoides sel. G-25

A comparison was made between the genes in 29 new selections of wild emmer wheat resistant to yellow rust over wide geographic areas and the previously extensively studied selectionTriticum dicoccoides G-25. In 23 selections the resistance may be conferred by 1 dominant gene; these include 11 selections in which the gene is different from the dominant gene in sel. G-25 and two others in which the genes were closely linked or allelic to the gene in G-25, differing from sel. G-25 by race-specificity. Two dominant genes different from the gene in sel. G-25, seem to be present in one selection. In five selections the resistance may be conferred by one or two recessive genes, including three instances in which the recessive gene was associated with a dominat gene. Our findings show that at least 19 out of the 29 selections studied possess genes which are different from the gene inT. dicoccoides sel. G-25.Samenvatting In dit onderzoek werden 29 nieuwe resistente wilde-emmer selecties (Triticum dicoccoides) gekruist met de reeds uitvoerig bestudeerde resistente selectie G-25, om na te gaan of de resistentie van de nieuwe selecties wordt veroorzaakt door genen op dezelfde locus als het dominante gen in sel. G-25 of dat er andere loci bij zijn betrokken. De ouders, de F₁-en F₂-populaties van een bepaalade selectie werden in het kiemplantstadium getoetst met één Israëlisch gele-roest isolaat van fysio 2E0 of van fysio 2E18. In de uitsplitsende F₂-populaties werden de niet-sporulerende planten als resistent beschouwd en de sporulerende als vatbaar.In de F₂-populaties van 12 herkomsten werden geen vatbare planten gevonden, hetgeen er op duidt dat de resistentie wordt veroorzaakt door een gen op dezelfde locus als het gen in G-25 of door een gen dat neuw gekoppeld is aan het gen in G-25. Voor twee van deze herkomsten kan op basis van een fysio-specifieke interactie worden vastgesteld dat de resistentie berust op allelen die verschillen van het allel in sel. G-25. In 11 herkomsten werd een uitsplitsing voor twee dominante gene gevonden (RS=151), waarbij het tweede dominante gen uit de getoetste nieuwe selectie afkomstig is. De aanwezigheid van twee dominante genen verschillend van het gen in sel. G-25 werd gevonden in één herkomst (631). In de overige vijf selecties bleek de resistentie te worden veroorzaakt door één of twee recessieve genen waarnaast in drie gevallen ook nog een dominant gen werd gevonden.De resultaten tonen aan dat tenminste 19 van de 29 bestudeerde selecties resistentiegenen bezitten die verschillen van het gen inT. dicoccoides sel. G-25. Slechts in twee van deze selecties kan het gen allel zijn met het gen in sel. G-25.     

Molecular genetics of behaviour: research strategies and perspectives for animal production

Genetic factors are undoubtedly involved in inter-individual variability of the behaviours that may be important for livestock production, as shown by pedigree studies, comparison of genetic stocks raised in the same environment, and selection experiments. The knowledge of gene polymorphisms responsible for genetic variability would increase the efficiency of selection, as shown for instance by the identification of the ryanodine receptor gene that harbours the mutations responsible for the porcine stress syndrome, that allows the eradication of the susceptibility allele. One strategy is to screen systematically the genes that are known to be involved in regulation of behaviour (functional candidate genes). This strategy is however very difficult for most behavioural traits, since behaviour is an emerging function from the whole brain/body and the molecular pathways involved in genetic variability are very poorly understood. Another strategy is to investigate linkage between trait variation and genetic markers in a segregating population (usually an intercross or backcross between two strains or breeds contrasting for the trait under study). It allows the detection of genomic regions influencing that trait (quantitative trait loci or QTL), and further investigation aims at the identification of the gene(s) located in each of these regions and the molecular polymorphisms involved in phenotypic variation. Although many QTL have been published for behavioural traits in experimental animals, very few examples are available where strong candidate genes have been identified. Further progress will be very much dependent upon the careful definition of behavioural traits to be studied (including their importance for animal production), on the reliability of their measurement in a large number of animals and on the efficient mastering of environmental factors of variability. The fast increase in the knowledge of genome sequence in several species will undoubtedly facilitate the application to farm animal species of the knowledge obtained in model organisms, as well as the use of model organisms to explore candidate genes detected by QTL studies in farm animals.     

猪水泡病病毒结构蛋白基因的克隆及其蛋白二级结构和淋巴细胞表位的预测

以免疫信息学和反向疫苗学为理论根据，利用RT-PCR法获得了猪水泡病病毒（SVDV）HK／70株的基因组序列并测序，应用生物信息学相关软件和方法，对SVDV结构蛋白的二级结构的不同方面及其抗原特异性淋巴细胞表位进行了预测，综合评价了SVDV结构蛋白的抗原特异性细胞表位，并计算出一些潜在的抗原位点。结果表明，VP1蛋白含有的细胞优势抗原表位最多，但其他结构蛋白也含有抗原特异性淋巴细胞表位，有的甚至有可能成为优势抗原表位或对优势抗原表位有协同作用。     

Modelling spatio-temporal dynamics of herbicide resistance

A mathematical model has been developed for the risk assessment of the spread of genes conferring herbicide resistance in plant populations. The model combines an age-and-stage-structured population dynamic model, a population genetic model and a model of spatial spread. This is achieved by embedding a local matrix population model into a cellular automaton model with raster cells as spatial units. The dynamics of each cell is determined by both its local dynamics and the interaction with neighbouring cells. The model is applied to the evaluation of management strategies to delay or even to prevent long-term evolution of resistance in an annual grass weed. The results show that the appearance and spread of resistant genes is a highly non-linear process exhibiting threshold phenomena, which occur for a wide range of parameters. The properties of the seed survival curve constitute the `genetic memory' of the system and thus determine its long-term dynamics. It is possible to delay the evolution of resistance by suspension of treatment, reduction in herbicide application rate and introducing fallow periods. Spatial spread from an infested plot is inhibited by leaving untreated strips between adjacent fields.     

Genetic diversity in populations of the fungi Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on grapevine in France

Isolates of Phaeomoniella chlamydospora ( Phc ) and Phaeoacremonium aleophilum ( Pha ), two haploid, deuteromycetous fungi, were obtained from vines showing symptoms of esca disease in different localities in two French regions, and within a single vineyard in one of these regions. The population genetic structure was determined in both fungi using random amplified polymorphic DNA (RAPD) analysis. Populations of Phc showed similar levels of diversity at local and regional levels. The most frequent Phc haplotypes were found in every population, and the frequencies of positive alleles of markers were similar across populations. The hypothesis that recombination had occurred was rejected for the full set of samples, but not for the samples reduced to haplotypes, indicating that Phc may be a recombining species. Different features were identified in Pha populations. First, the southern population of Pha appeared more diverse than the south-western populations. Second, genetic differentiation was identified between Pha populations from southern and south-western regions for several RAPDs. Finally, in the southern population of Pha no evidence for recombination was obtained, even by reducing the sample to haplotypes. Within the single vineyard surveyed, several haplotypes of both fungi were recovered and randomly distributed. Thus different infection events appeared to have occurred on a low spatial scale. Data from this study showed that haplotypes of both fungi were distributed over long distances geographically, and that most of the vineyards surveyed were infested by more than one haplotype of Phc and Pha .     

SSR-based genetic linkage analysis of resistance to crown rust (Puccinia coronata f. sp. lolii) in perennial ryegrass (Lolium perenne)

Crown rust (caused by Puccinia coronata f. sp. lolii) is a serious foliar disease of the pasture and turfgrass perennial ryegrass (Lolium perenne). Previous genetic studies have detected both qualitative and quantitative resistance mechanisms, and interpretation of the genetic system is complicated by variation within the sexually reproducing pathogen. Resistant and susceptible parental genotypes of ryegrass were identified using a composite urediniospore population collected from three geographically distinct locations. A two-way pseudo-testcross mapping population was obtained as the F₁ progeny of the pair-cross between ryegrass parental genotypes Vedette₆ and Victorian₉. Both parents showed intermediate resistance against a pathogen population collected in a single geographical zone (Hamilton, Victoria), but in the F₁ population, significant variation for a range of resistance-associated characters was detected. Statistical analysis of phenotypic data suggested a major gene effect, hence bulked segregant analysis with map-assigned simple sequence repeat (SSR) markers was used to scan the genome. A marker showing strong association with resistance was assigned to linkage group (LG) 2 of perennial ryegrass. Analysis of 11 LG2 SSR markers defined an interval between loci xlpssrh03f03 and xlpssrk02e02 as containing the gene or genes (LpPc1) conferring crown rust resistance. Resistance gene determinants were inherited from both parents, with up to 80% of the total phenotypic variation explained by markers segregating from Vedette₆ and up to 26% of the variation explained by markers segregating from Victorian₉. The two contributions together resulted in an additive increase in effect, with fully resistant individuals requiring determinants from both parents. A conserved syntenic relationship was observed with linkage group B of Avena strigosa, which is the location of a cluster of resistance genes to the oat form of crown rust. The implications of this study for marker-assisted selection of disease resistance in perennial ryegrass are discussed.     

Rapid detection of Phytophthora cinnamomi using PCR with primers derived from the Lpv putative storage protein genes

Phytophthora cinnamomi is an ecologically and economically important pathogen. In this study, PCR assays were developed with primer pair LPV2 or LPV3 for rapid detection and identification of this organism. Both primer pairs were selected from putative storage protein genes. The specificity of these primer pairs was evaluated against 49 isolates of P. cinnamomi , 102 isolates from 30 other Phytophthora spp., 17 isolates from nine Pythium spp. and 43 isolates of other water moulds, bacteria and true fungi. PCR with both primer pairs amplified the DNA from all isolates of P. cinnamomi regardless of origin. The LPV3 primers showed adequate specificity among all other species tested. The LPV2 primers cross-reacted with some species of Pythium and true fungi, but not with any other Phytophthora species. PCR with the LPV3 primers detected the pathogen at levels of a single chlamydospore or 10 zoospores in repeated tests. The PCR assay was at least 10 times more sensitive than the plating method for detection of the pathogen from artificially infested soilless medium, and, to a lesser extent, from naturally infected plants. PCR with LPV3 primers can be a useful tool for detecting P. cinnamomi from soilless media and plant tissues at ornamental nurseries, whereas the LPV2 primers can be an effective alternative for identification of this species from pure culture. Applications of these assays for detection of P. cinnamomi in other environments were also discussed.     

Genomics in equine veterinary medicine

Veterinary medicine is marching forward with genomics grasped firmly in one fist. Genomics has been part of our veterinary tool bag for some time in various guises, but the breadth and depth of its ramifications can be daunting. This article is designed to provide toe‐holds for veterinarians to enjoy a better understanding of genomics – a truly fascinating area of science.     

反向遗传技术在牛轮状病毒研究中的应用

本文综述了牛轮状病毒的生物学特性、反向遗传学系统的建立及其研究进展,并对反向遗传技术应用于牛轮状病毒进行展望。