Comprehensive diversity assessment of walnut-associated xanthomonads reveal the occurrence of distinct Xanthomonas arboricola lineages and of a new species (Xanthomonas euroxanthea) within the same tree

Xanthomonas arboricola pv. juglandis (Xaj) is the aetiological agent of walnut diseases causing economic losses on walnut production worldwide. This phytopathogen is spread around the world where walnuts are produced and has a considerable genetic diversity. Using a comprehensive sampling methodology, focusing on factors that could influence the diversity of walnut-colonizing Xaj in Portugal, this work provides new insights on xanthomonad populations on walnut. Genetic diversity was assessed by multilocus sequence analysis (MLSA) and dot blot hybridization patterns on 131 Xanthomonas isolates obtained from 64 walnut trees considering epidemiological metadata such as year of isolation, distinct bioclimatic regions, production regimes, and host-related features. The results showed that the majority of isolates were split into 17 lineages of Xaj, while the other isolates clustered in four MLSA groups that did not include Xaj strains. These four groups were represented by three lineages of X. arboricola, and 11 lineages of Xanthomonas spp., including strains assigned to the recently proposed new species Xanthomonas euroxanthea. Furthermore, distinct Xaj, X. arboricola, and Xanthomonas spp. were isolated from the same walnut tree, suggesting possible genetic admixture within the same host. Phylogenetic analysis through geoBurst revealed the high diversity of these Xanthomonas spp. populations. Assessment of type III effector genes gave the indication that some Xanthomonas spp. strains were nonpathogenic on walnut, with the exception for X. euroxanthea CPBF 424. Altogether, these findings add to the thorough characterization of walnut-associated xanthomonads in Portugal, providing a comprehensive snapshot of the current diversity that could contribute to risk assessment analysis and improve phytosanitary control.     

Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan

In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot^TM technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.     

Molecular epidemiology of clinical isolates of Pseudomonas aeruginosa isolated from horses in Ireland

Clinical isolates (n = 63) of Pseudomonas aeruginosa obtained from various sites in 63 horses were compared using ERIC2 RAPD PCR to determine their genetic relatedness. Resulting banding patterns (n = 24 genotypes) showed a high degree of genetic heterogeneity amongst all isolates examined, indicating a relative non-clonal relationship between isolates from these patients, employing this genotyping technique. This study characterised 63 clinical isolates into 24 distinct genotypes, with the largest cluster (genotype E) accounting for 10/63 (15.9%) of the isolates. ERIC2 RAPD PCR proved to be a highly discriminatory molecular typing tool of P. aeruginosa in isolates recovered from horses. With the adoption of several controls to aid reproducibility, this technique may be useful as an alternative to PFGE, particularly in epidemiological investigations of outbreaks where speed may be a significant parameter. This is the first report of clonal heterogeneity amongst P. aeruginosa from horses and demonstrated that ERIC RAPD PCR is a rapid method for the examination of this species in horses, which may be useful in outbreak analysis.     

四川58个小麦品种苗期抗条锈基因推导及成株期抗性表现

为了解四川小麦品种所含抗条锈基因及其在田间的抗性表现,将29个毒性谱各异的小麦条锈菌鉴别菌株于苗期接种35个已知抗条锈基因载体品系和58份四川小麦品种（系）,通过抗病谱对比分析和各品种（系）系谱分析,推导了四川小麦品种（系）的抗条锈基因型。在田间,选用中国小麦条锈菌优势小种CY32、CY33、Su-4和对Yr10、Yr24和Yr26致病的贵农22致病类型田间突变株进行混合接种,在乳熟期对各品种（系）的抗条锈性进行了鉴定。结果显示,Yr2、Yr5、Yr7、Yr9、Yr10、Yr24、Yr27、YrSpp、YrAlba等9个基因以单基因或基因组合的形式存在于44个四川小麦品种（系）中。有6个品种（系）含有Yr9基因,10个品种（系）含有Yr10基因,11个品种（系）含有Yr24基因,其中1个同时含有Yr10和Yr24基因。23个品种（系）含有未知基因及其组合。共有19个小麦品种（系）成株期对包含上述混合菌种在内的田间流行菌系表现抗病,其中5个品种抗性受成株抗性基因控制。     

Antimicrobial susceptibility and tetracycline resistance determinant genotyping of Gallibacterium anatis

The present investigation was undertaken to assess the antimicrobial susceptibility of a collection of 58 Gallibacterium isolates. All strains were tested by the broth dilution method using the veterinary fastidious medium. A total of 46 field strains were tested, whereof 23 were clinical isolates from 10 Mexican layer flocks and another 23 isolates originated from 13 clinically healthy poultry flocks in Denmark. In addition, 12 Gallibacterium reference strains that had been isolated some 30–40 years ago were included.     

High-throughput approach to detection of knockdown resistance (kdr) mutation in mosquitoes, Culex quinquefasciatus, based on real-time PCR using single-labelled hybridisation probe/melting curve analysis

BACKGROUND: Knockdown resistance (kdr) mutation (L1014F) is a well‐defined mechanism of resistance to pyrethroids and DDT in many insect species. Sensitive detection of the mutations associated with resistance is a prerequisite for resistance management strategies. The authors have developed a new real‐time molecular diagnostic assay based on SimpleProbe^®/melting curve analysis for large‐scale kdr genotyping in the wild population of Culex quinquefasciatus Say, the principal vector of bancroftian filariasis. Melting curve analysis is based on the thermal stability difference between matched and mismatched DNA duplexes. The application of SimpleProbe^® chemistry in insects described here is novel in entomology research. RESULTS: The mosquitoes homozygous for knockdown‐resistant and knockdown‐susceptible allele showed melting peaks at 60.45 °C ( ± 0.25) and 64.09 °C ( ± 0.24) respectively. The heterozygous mosquitoes yielded both peaks at approximately 60.5 °C ( ± 0.2) and 64.20 °C ( ± 0.23). Among the 92 samples genotyped, 16 were found to be homozygous resistant, 44 homozygous susceptible and 32 heterozygous. Comparative assessments were made of all the reported methods for kdr genotyping. CONCLUSION: The present method is cheaper, faster, more reliable and versatile than other alternatives proposed in detecting correct kdr genotypes in mosquitoes. This is the first report using a single‐labelled hybridisation probe to detect point mutations in insect populations. Copyright © 2010 Society of Chemical Industry     

Field studies with in‐feed medication of pigs in the Netherlands using the anthelmintic thiophanate with particular reference to efficacy against Ascaris suum

Summary

Studies on the efficacy in pigs of low level in‐feed medication with the anthelmintic thiophanate at a minimum intake of 6 mg/kg/day for fourteen days are reported. A trial was conducted to compare a group of medicated fattening pigs with a similar unmedicated group on premises known to have a high challenge of Ascaris spp. Daily growth rate was improved whilst feed conversion ratio and the liver condemnation rate were reduced in the treatment group.

Routine medication of a whole herd using this regime contributed to a great improvement of the herd production when assessed by the above criteria. User studies in various geographical areas of the Netherlands involving 1500 adult pigs and 1200 fattening pigs medicated with thiophanate in‐feed for fourteen days demonstrated that the compound eliminated the faecal worm egg output and was readily accepted and tolerated by pigs.     

Impact of inclusion rates of crossbred phenotypes and genotypes in nucleus selection programs

Numerous methods have been suggested to incorporate crossbred (CB) phenotypes and genotypes into swine selection programs, yet little research has focused on the implicit trade-off decisions between generating data at the nucleus or commercial level. The aim of this study was to investigate the impact of altering the proportion of purebred (PB) and CB phenotypes and genotypes in genetic evaluations on the response to selection of CB performance. Assuming CB and PB performance with moderate heritabilities (h2=0.4), a three-breed swine crossbreeding scheme was simulated and selection was practiced for six generations, where the goal was to increase CB performance. Phenotypes, genotypes, and pedigrees for three PB breeds (25 and 175 mating males and females for each breed, respectively), F₁ crosses (400 mating females), and terminal cross progeny (2,500) were simulated. The genome consisted of 18 chromosomes with 1,800 quantitative trait loci and 72k single nucleotide polymorphism (SNP) markers. Selection was performed in PB breeds using estimated breeding value for each phenotyping/genotyping strategy. Strategies investigated were: 1) increasing the proportion of CB with genotypes, phenotypes, and sire pedigree relationships, 2) decreasing the proportion of PB phenotypes and genotypes, and 3) altering the genetic correlation between PB and CB performance (rpc). Each unique rpc scenario and data collection strategy was replicated 10 times. Results showed that including CB data improved the CB performance regardless of rpc or data collection strategy compared with when no CB data were included. Compared with using only PB information, including 10% of CB progeny per generation with sire pedigrees and phenotypes increased the response in CB phenotype by 134%, 55%, 33%, 23%, and 21% when rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively. When the same 10% of CB progeny were also genotyped, CB performance increased by 243%, 54%, 38%, 23%, and 20% when the rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively, compared with when no CB data were utilized. Minimal change was observed in the average CB phenotype when PB phenotypes were included or proportionally removed when CB were genotyped. Removal of both PB phenotypes and genotypes when CB were genotyped greatly reduced the response in CB performance. In practice, the optimal inclusion rate of CB and PB data depends upon the genetic correlation between CB and PB animals and the expense of additional CB data collection compared with the economic benefit associated with increased CB performance.