Use of a reduced set of single nucleotide polymorphisms for genetic evaluation of resistance to Salmonella carrier state in laying hens

Chantier qualité GA; Salmonella propagation by apparently healthy chickens could be decreased by the selection and use of chicken lines that are more resistant to carrier state. Using a reduced set of markers, this study investigates, for the first time to the authors' knowledge, the feasibility of a genomic selection approach for resistance to carrier state in hen lines. In this study, commercial laying hen lines were divergently selected for resistance to Salmonella carrier state at 2 different ages: young chicks and adults at the peak of lay. A total of 600 birds were typed with 831 informative SNP markers and artificially infected with Salmonella Enteritidis. Phenotypes were collected 28 d (389 young animals) or 38 d (208 adults) after infection. Two types of variance component analyses, including SNP data or not, were performed and compared. The set of SNP used was efficient in capturing a large part of the genetic variation. Average accuracies from mixed model equations did not change between analyses, showing that using SNP data does not increase information in this data set. These results confirm that genomic selection for Salmonella carrier state resistance in laying hens is promising. Nevertheless, a denser SNP coverage of the genome on a greater number of animals is still needed to assess its feasibility and efficiency

Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review

<p>Abstract</p> <p>Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species <it>Salmonella enterica </it>and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of <it>S. enterica </it>serovar Enteritidis or <it>S. enterica </it>serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to <it>Salmonella </it>differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes <it>TLR4 </it>and <it>SLC11A1</it>, the Major Histocompatibility Complex (MHC) and the QTL <it>SAL1 </it>are interesting for more in-depth studies. This article reviews the main <it>Salmonella </it>infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.</p

Environmental drivers of distribution and reef development of the Mediterranean coral Cladocora caespitosa

Cladocora caespitosa is the only Mediterranean scleractinian similar to tropical reef-building corals. While this species is part of the recent fossil history of the Mediterranean Sea, it is currently considered endangered due to its decline during the last decades. Environmental factors affecting the distribution and persistence of extensive bank reefs of this endemic species across its whole geographic range are poorly understood. In this study, we examined the environmental response of C. caespitosa and its main types of assemblages using ecological niche modeling and ordination analysis. We also predicted other suitable areas for the occurrence of the species and assessed the conservation effectiveness of Mediterranean marine protected areas (MPAs) for this coral. We found that phosphate concentration and wave height were factors affecting both the occurrence of this versatile species and the distribution of its extensive bioconstructions in the Mediterranean Sea. A set of factors (diffuse attenuation coefficient, calcite and nitrate concentrations, mean wave height, sea surface temperature, and shape of the coast) likely act as environmental barriers preventing the species from expansion to the Atlantic Ocean and the Black Sea. Uncertainties in our large-scale statistical results and departures from previous physiological and ecological studies are also discussed under an integrative perspective. This study reveals that Mediterranean MPAs encompass eight of the ten banks and 16 of the 21 beds of C. caespitosa. Preservation of water clarity by avoiding phosphate discharges may improve the protection of this emblematic species.Spanish Ministry of Economy and Competitiveness [CTM2014-57949-R]info:eu-repo/semantics/publishedVersio

Automated data analysis to rapidly derive and communicate ecological insights from satellite-tag data: A case study of reintroduced red kites

Analysis of satellite-telemetry data mostly occurs long after it has been collected, due to the time and effort needed to collate and interpret such material. Such delayed reporting does reduce the usefulness of such data for nature conservation when timely information about animal movements is required. To counter this problem we present a novel approach which combines automated analysis of satellite-telemetry data with rapid communication of insights derived from such data. A relatively simple algorithm (comprising speed of movement and turning angle calculated from fixes), allowed instantaneous detection of excursions away from settlement areas and automated calculation of home ranges on the remaining data Automating the detection of both excursions and home range calculations enabled us to disseminate ecological insights from satellite-tag data instantaneously through a dedicated web portal to inform conservationists and wider audiences. We recommend automated analysis, interpretation and communication of satellite tag and other ecological data to advance nature conservation research and practice

Detection of two QTL on chicken chromosome 14 for keyhole lymphet heamocyanin

A keyhole lymphet heamocyanin is an antigen which triggers Th1 type of immune response. A QTL for a primary immune response towards keyhole lymphet heamocyanin has been detected on chicken chromosome 14 in three populations. The results from the most recent population were inconsistent and varied depending on the applied QTL detection model. The major goal of the current study was the reanalysis of this data using a 2 QTL model. Additionally, in order to provide more accurate estimates of QTL effects and positions, epistasis between the QTL was considered as a potential important contributor to quantitative traits. Four statistical models were assumed: M1: A model assuming marginal additive effects of two QTL; M2: A model assuming marginal and epistatic additive effects of two QTL; M3: A model assuming marginal additive and dominance effects of two QTL; M4: A model assuming marginal additive and dominance effects of two QTL and all possible pairwise epistases. Two QTL with significant additive and dominance effects were detected on chicken chromosome 14 using model M3. One QTL was detected at 63 cM between MCW0123 and ROS0005, another at 76 cM between ROS0005 and MCW0225/NTN2Lsts1 (FDR = 0.0051). Modelling only additive effects resulted in a significantly worse fit. On the other hand, including epistatic effects did not improve fit significantly. The current study confirms previous reports of the QTL location on GGA14. A notable finding of this study is recognition of two closely related QTL for a keyhole lymphet heamocyanin response at the distal part of chicken chromosome 14

Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies

Although fire blight, caused by the bacterium Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica) worldwide, no major, qualitative gene for resistance to this disease has been identified to date in apple. We conducted a quantitative trait locus (QTL) analysis in two F-1 progenies derived from crosses between the cultivars Fiesta and either Discovery or Prima. Both progenies were inoculated in the greenhouse with the same strain of E. amylovora, and the length of necrosis was scored 7 days and 14 days after inoculation. Additive QTLs were identified using the MAPQTL software, and digenic epistatic interactions, which are an indication of putative epistatic QTLs, were detected by two-way analyses of variance. A major QTL explaining 34.3-46.6% of the phenotypic variation was identified on linkage group (LG) 7 of Fiesta in both progenies at the same genetic position. Four minor QTLs were also identified on LGs 3, 12 and 13. In addition, several significant digenic interactions were identified in both progenies. These results confirm the complex polygenic nature of resistance to fire blight in the progenies studied and also reveal the existence of a major QTL on LG7 that is stable in two distinct genetic backgrounds. This QTL could be a valuable target in marker-assisted selection to obtain new, fire blight-resistant apple cultivars and forms a starting point for discovering the function of the genes underlying such QTLs involved in fire blight control

Dynamics of direct inter-pack encounters in endangered African wild dogs

Aggressive encounters may have important life history consequences due to the potential for injury and death, disease transmission, dispersal opportunities or exclusion from key areas of the home range. Despite this, little is known of their detailed dynamics, mainly due to the difficulties of directly observing encounters in detail. Here, we describe detailed spatial dynamics of inter-pack encounters in African wild dogs (Lycaon pictus), using data from custom-built high-resolution GPS collars in 11 free-ranging packs. On average, each pack encountered another pack approximately every 7 weeks and met each neighbour twice each year. Surprisingly, intruders were more likely to win encounters (winning 78.6% of encounters by remaining closer to the site in the short term). However, intruders did tend to move farther than residents toward their own range core in the short-term (1 h) post-encounter, and if this were used to indicate losing an encounter, then the majority (73.3%) of encounters were won by residents. Surprisingly, relative pack size had little effect on encounter outcome, and injuries were rare (<15% of encounters). These results highlight the difficulty of remotely scoring encounters involving mobile participants away from static defendable food resources. Although inter-pack range overlap was reduced following an encounter, encounter outcome did not seem to drive this, as both packs shifted their ranges post-encounter. Our results indicate that inter-pack encounters may be lower risk than previously suggested and do not appear to influence long-term movement and ranging

Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple

We used a new method called nucleotide-binding site (NBS) profiling to identify and map resistance gene analogues (RGAs) in apple. This method simultaneously allows the amplification and the mapping of genetic markers anchored in the conserved NBS-encoding domain of plant disease resistance genes. Ninety-four individuals belonging to an F1 progeny derived from a cross between the apple cultivars Discovery and TN10-8 were studied. Two degenerate primers designed from the highly conserved P-loop motif within the NBS domain were used together with adapter primers. Forty-three markers generated with NBS profiling could be mapped in this progeny. After sequencing, 23 markers were identified as RGAs, based on their homologies with known resistance genes or NBS/leucine-rich-repeat-like genes. Markers were mapped on 10 of the 17 linkage groups of the apple genetic map used. Most of these markers were organized in clusters. Twenty-five markers mapped close to major genes or quantitative trait loci for resistance to scab and mildew previously identified in different apple progenies. Several markers could become efficient tools for marker-assisted selection once converted into breeder-friendly markers. This study demonstrates the efficiency of the NBS-profiling method for generating RGA markers for resistance loci in appl

Delineation of a scab resistance gene cluster on linkage group 2 of apple

With the advent of genetic maps for apple that carry common transferable markers, it is possible to investigate genomic relationships between genes present in different accessions. Co-dominant markers, such as microsatellites, are particularly useful for this purpose. In recent years, genetic markers have been developed for a number of resistance genes for apple scab (Venturia inaequalis). In this paper, we present the discovery of a new scab resistance gene (Vh8) that maps to linkage group 2 (LG2). We then bring together the findings from different research groups on other scab resistance genes that also map to LG2 in an attempt to delineate their arrangement. These other genes comprise major genes (Vh2, Vr, Vbj and Vr2), as well as several race specific quantitative trait loci (QTLs) from `Discovery¿ and `TN10-8¿. Results indicate that Vh2 and Vr are probably identical, and that Vh2/Vr, Vh8, Vbj and at least one of the QTLs are closely linked to each other on the lower half of LG2. A putative map of this gene cluster is presented. The fourth major gene, Vr2, maps at a significant distance from this gene cluster at the top end of LG2. We discuss the consequences of resistance gene cluster arrangements on breeding strategies for durable resistance to apple scab and the use of marker-assisted selectio