Fanny Calenge

Natural variation for sulfate content in Arabidopsis thaliana is highly controlled by APR2.

Most agronomic traits of importance, whether physiological (such as nutrient use efficiency) or developmental (such as flowering time), are controlled simultaneously by multiple genes and their interactions with the environment. Here, we show that variation in sulfate content between wild Arabidopsis thaliana accessions Bay-0 and Shahdara is controlled by a major quantitative trait locus that results in a strong interaction with nitrogen availability in the soil. Combining genetic and biochemical results and using a candidate gene approach, we have cloned the underlying gene, showing how a single–amino acid substitution in a key enzyme of the assimilatory sulfate reduction pathway, adenosine 5′-phosphosulfate reductase, is responsible for a decrease in enzyme activity, leading to sulfate accumulation in the plant. This work illustrates the potential of natural variation as a source of new alleles of known genes, which can aid in the study of gene function and metabolic pathway regulation. Our new insights on sulfate assimilation may have an impact on sulfur fertilizer use and stress defense improvement.

Leaf Fructose Content Is Controlled by the Vacuolar Transporter SWEET17 in Arabidopsis

In higher plants, soluble sugars are mainly present as sucrose, glucose, and fructose. Sugar allocation is based on both source-to-sink transport and intracellular transport between the different organelles and depends on actual plant requirements. Under abiotic stress conditions, such as nitrogen limitation, carbohydrates accumulate in plant cells. Despite an increasing number of genetic studies, the genetic architecture determining carbohydrate composition is poorly known. Using a quantitative genetics approach, we determined that the carrier protein SWEET17 is a major factor controlling fructose content in Arabidopsis leaves. We observed that when SWEET17 expression is reduced, either by induced or natural variation, fructose accumulates in leaves, suggesting an enhanced storage capacity. Subcellular localization of SWEET17-GFP to the tonoplast and functional expression in Xenopus oocytes showed that SWEET17 is the first vacuolar fructose transporter to be characterized in plants. Physiological studies in planta provide evidence that SWEET17 acts to export fructose out of the vacuole. Overall, our results suggest that natural variation in leaf fructose levels is controlled by the vacuolar fructose transporter SWEET17. SWEET17 is highly conserved across the plant kingdom; thus, these findings offer future possibilities to modify carbohydrate partitioning in crops.

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

Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species Salmonella enterica 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 S. enterica serovar Enteritidis or S. enterica 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 Salmonella differ according to the chicken line studied, the trait assessed and the chickens 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 TLR4 and SLC11A1, the Major Histocompatibility Complex (MHC) and the QTL SAL1 are interesting for more in-depth studies. This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.

Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics.

Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 × Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes.

QTL for resistance to Salmonella carrier state confirmed in both experimental and commercial chicken lines

The ability of chickens to carry Salmonella without displaying disease symptoms is responsible for Salmonella propagation in poultry stocks and for subsequent human contamination through the consumption of contaminated eggs or meat. The selection of animals more resistant to carrier state might be a way to decrease the propagation of Salmonella in poultry stocks and its transmission to humans. Five QTL controlling variation for resistance to carrier state in a chicken F(2) progeny derived from the White Leghorn inbred lines N and 6(1) had been previously identified using a selective genotyping approach. Here, a second analysis on the whole progeny was performed, which led to the confirmation of two QTL on chromosomes 2 and 16. To assess the utility of these genomic regions for selection in commercial lines, we tested them together with other QTL identified in an [Nx6(1)] x N backcross progeny and with the candidate genes SLC11A1 and TLR4. We used a commercial line divergently selected for either low or high carrier-state resistance both in young chicks and in adult hens. In divergent chick lines, one QTL on chromosome 1 and one in the SLC11A1 region were significantly associated with carrier-state resistance variations; in divergent adult lines, one QTL located in the major histocompatibility complex on chromosome 16 and one in the SLC11A1 region were involved in these variations. Genetic studies conducted on experimental lines can therefore be of potential interest for marker-assisted selection in commercial lines.

Toward integrative genomics study of genetic resistance to Salmonella and Campylobacter intestinal colonization in fowl

Salmonella enterica serotypes Enteritidis and Typhimurium and Campylobacter jejuni are responsible for most cases of food poisoning in Europe. These bacteria do not cause severe disease symptoms in chicken, but they are easily propagated by symptomless chicken carriers which cannot be easily isolated. This animal tolerance is detrimental to food safety. In this particular case, increasing animals resistance is not sufficient, since some animals considered as resistant are able to carry bacteria during several weeks without displaying disease symptoms. We review studies aimed at evaluating the resistance of chicken to Salmonella and Campylobacter intestinal colonization, either a few days or several weeks after infection. While studies of the genetic control of Campylobacter colonization are only beginning, mostly due to technical difficulties in infection protocols, genetic studies of Salmonella colonization have been conducted for now more than 20 years. They have initially reported an estimation of the genetic parameters associated with resistance to Salmonella colonization and are now aimed at identifying the genomic regions controlling variation of this trait in experimental lines and commercial populations. With the advent of high-throughput genomics, we are closer than ever to identify the true genes controlling resistance to Enterobacteria colonization in chicken. The comparison of genes involved in early resistance to intestinal colonization with genes controlling resistance to bacteria persistence several weeks after infection (i.e., carrier-state) should soon highlight the differences between the molecular mechanisms underlying those two distinct phenotypes. It will also be highly interesting to compare the genes or genomic regions controlling Campylobacter and Salmonella, in order to evaluate the feasibility of a selection conducted on both bacteria simultaneously.

New QTL for resistance to Salmonella carrier-state identified on fowl microchromosomes

Chicken’s ability to carry Salmonella without displaying disease symptoms leads to an invisible propagation of Salmonella in poultry stocks. Using chicken lines more resistant to carrier state could improve both animal health and food safety. Previous studies identified several QTL for resistance to carrier state. To improve genome coverage and QTL detection power we produced a new set of 480 informative SNP markers and genotyped a larger number of animals. Ten additional microchromosomes could be covered when compared with previous studies. These new data led to the identification of 18 QTL significant at the chromosome-wide level. The only QTL significant at the genome-wide level were identified on microchromosomes 14 and 22 and have never been identified previously. Using a higher number of animals improved the power and the precision of QTL detection. Some of the QTL newly identified are located close to candidate genes or microsatellite markers previously identified for their involvement in the genetic control of resistance to Salmonella, which confirms their interest for selection purposes.

Genomic selection for carrier-state resistance in chicken commercial lines

BackgroundSalmonella propagation by apparently healthy chicken and subsequent food security concerns could be decreased by the selection and use of chicken lines more resistant to carrier-state. In the present study we applied the first steps of the genomic selection methodology to assess the interest of including genetic markers for the genetic evaluation of hen lines infected with Salmonella Enteritidis.MethodsWe studied commercial laying hen lines divergently selected for resistance to Salmonella carrier-state at two different ages. A total of 600 animals were typed with 1536 SNP markers and artificially infected with S. Enteritidis. Phenotypes were collected four weeks (young animals) or five weeks (adults) later. Two types of variance component analyses, including or not including SNP data, were performed and compared. All variance components were estimated by Bayesian methods and Gibbs sampling.ResultsThe comparison of both genetic analyses shows that SNP are efficient in capturing genetic variation, although none of them captures a large affect on the traits studied. Average accuracies do not change between analyses, showing that using SNP data does not really increase information.ConclusionsThese preliminary results show that genomic selection for Salmonella carrier-state resistance in laying hens is promising, although a denser SNP coverage of the genome on a higher number of animals is needed to assess its feasibility and efficiency compared to classical pedigree evaluation.

Selection for increased resistance to Salmonella carrier-state.

Improving the fowls natural ability to clear Salmonella from their body is important in reducing disease prevalence in poultry flocks, as recommended by a recent regulation of the European Commission. It may be efficient, as expected from estimation of heritability coefficients : 0.16 in chicks and 0.18 for global contamination of hens. The animals age has to be considered since the genetic correlation between resistances at the two ages is negative. Selecting two series of divergent lines for increased or decreased resistance, after inoculation at one week of age (chick resistance) or at the peak of lay (adult resistance) confirmed the efficiency at least of selection for the adult resistance. In parallel, genes controlling variations to Salmonella resistance were researched and several QTLs identified in crosses between experimental lines and, for some of them, confirmed in commercial lines. Thanks to the derivation of a model of Salmonella propagation within a flock, it has been shown that a combination of vaccination and genetic selection can result in very low percentage of contamination.

Broiler lines divergently selected for digestive efficiency also differ in their susceptibility to colibacillosis

Increasing feed efficiency of broiler chickens by selective breeding could lead to decreased feed cost and reduced environmental impact of poultry production. At INRA, two broiler chicken lines (D+/D−) were divergently selected for their digestive efficiency. Strong differences were shown between both lines for the anatomy and histology of the digestive tract, and for the intestinal microbiota composition. In the present study, we investigated whether this selection also had an effect on susceptibility to colibacillosis, which is one of the main causes of economic losses in poultry production. The broiler lines D+/D− were challenged with an avian pathogenic Escherichia coli strain. A first experiment was conducted to assess the 50% lethal dose by subcutaneous infection of hatchlings, whereas a second experiment reproduced colibacillosis by infecting air sacs of 23-day-old chicks. The 50% lethal dose was very low for both lines. However, the line with the higher digestive efficiency (D+) was the less susceptible to colibacillosis. This result is interesting for selection purposes and opens the way to integrative genetic studies of the interactions between digestion efficiency and resistance to colibacillosis.