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Additional file 3: Flanking 50-bp sequences for the top associated SNPs in LG12_QTL_2. Genomic sequences flanking the IFI6/IFI27-like and ZDHHC14 SNPs computed from Dicentrarchus labrax genome (seabass_V1.0).

Additional file 1: Figure S1. PCA on genotypes of commercial populations (pop A and pop B) and wild populations in the Atlantic (Atl) and Eastern Mediterranean (East-Med). Principal component analysis (PCA) using genotypic data from two commercial populations and two wild populations, one from the Atlantic strain (Atl) and the other from the West Mediterranean strain (East-Med).

International audience; Hypoxia is one of the major threats to the aquaculture sector resulting in substantial economic losses to the fish farmers. Thus, tolerance to hypoxia is of high economic interest to be genetically improved by breeding programs. Rainbow trout (Oncorhynchus mykiss) is one of the most cultured salmonid species worldwide, with welldeveloped breeding programs. Still, studies of genetic potential to improve hypoxia tolerance in this species are rare. In the present study, 1320 individuals of rainbow trout were used for a genome-wide association study of acute hypoxia tolerance based on imputed high-density genotypes to explore the genetic architecture and related candidate genes affecting hypoxia response. Three significant (Omy31_1, Omy31_2, Omy20) and two putative (Omy15, Omy28) quantitative trait loci (QTLs) were detected, but each of them only explained between 0.2% and 0.8% of the genetic variance of acute hypoxia tolerance. However, heritability was estimated at a moderate value of 0.24-0.28, that suggests a solid potential to improve hypoxia tolerance in the studied rainbow trout population by genetic selection. Moreover, it was shown that genomic prediction for hypoxia tolerance would lead to a relative increase of ~11% for genomic selection (GS) accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. Finally, fifteen genes (ids, fmr1, arx, lonrf3, commd5, map4k4, smu1, b4galt1, re1, abca1, noa1, igfbp7, noxo1, bcl2a, mylk3) were proposed as potential functional candidates involved in hypoxia tolerance. Taking all proposed candidate genes (6 out of 15 genes) and high linkage disequilibrium (r 2) values within the main QTL (Omy31_1), we may hypothesize that the complex response to acute hypoxia in rainbow trout, i.e., the interplay between behavioural, morphological, and physiological responses, is primarily encoded by a supergene. However, further functional validation of their effects may help to specify the biological mechanisms triggering a response to acute hypoxia in rainbow trout.

Ce volume regroupe les textes issus du programme Casdar « Semence et Sélection Variétale » finalisés en 2015, 2017 et 2019. Le numéro a été coordonné par le Comité Scientifique du Comité Technique Permanent de la Sélection des plantes cultivées (CTPS).; International audience; This program aimed at characterizing oat varieties (Avena sativaL.) originating from INRAE Clermont-Ferrand collection as well as from main oat-producing countries. These varieties and some of their progenies (F6) were evaluated for their crown rust tolerance. Simultaneously, these lines were molecularlyassessed for their allelic composition for known resistance genes. A consensus map of 178 SNP markers covering 26 linkage groups was established. An association study between rust-resistance phenotype and molecular markers willbe conducted which should result in the identification of linkage between some SNPs and resistance loci. The most relevant markers will further be used in marker-assisted selection programs. Moreover, several experimentations were conducted to develop a protocol for doubled-haploid (DH) line production. The most promising technique was the one involving anther culture.; Ce programme porte sur la caractérisation de variétés d’avoine (Avena sativaL.) provenant de diverses origines et notamment de la collectionINRAE de Clermont-Ferrand mais également de variétés provenant des principaux pays producteurs. Ces différentes variétés collectées, ainsi que certains de leurs croisements (F6), ont été caractérisés aux champs pour leur tolérance à la rouille par les partenaires privés. Parallèlement, ces lignées ont été évaluées au laboratoire pour leur composition allélique au niveau des principaux gènes de résistance connus et marqués. Une carte génétiqueconsensus a été établie, elle comporte 178 marqueurs SNP répartis en 26 groupes de liaison. Au final, une étude d’association entre phénotypes résistants ou sensibles et diversité allélique aux gènes a permis d’identifier des marqueurs pertinents utilisables en sélection assistée. Dans le même temps, un ensemble d’expérimentations a été mené pour mettre au point une méthode de production de plantes haploïdesdoublées(HD). La technique la plus prometteuse est la culture d’anthères.

International audience

Les inhibiteurs de l’ALS en échec face à l’ambroisie à feuilles d’armoiseEn France, la résistance aux herbicides inhibiteurs de l’acétolactate-synthase (ALS) émerge chez l’ambroisie. Très utilisés car applicables sur la majorité des grandes cultures, ces produits phytosanitaires généralistes inhibent l’ALS, une enzyme clé des végétaux dans la synthèse d’acides aminés essentiels. Ils constituent la deuxième famille de désherbants la plus employée, et en paient le tribut : la résistance à cette classe d’herbicides a été identifiée dans plus de 160 espèces d’adventices, ou « mauvaises herbes ». Récemment rajoutée à cette liste, l’ambroisie à feuilles d’armoise (Ambrosia artemisiifolia) est une plante envahissante et allergène originaire d’Amérique du Nord introduite en Europe au XIXème siècle.Solidement implantée en France métropolitaine, elle s’est lentement étendue depuis son foyer dans la vallée du Rhône dans les années 1880, jusqu’à atteindre aujourd’hui la quasi-totalité des départements de l’hexagone. Plante pionnière tout-terrain, l’ambroisie peut aussi bien coloniser les cultures que les chantiers, les abords des routes ou les friches. Menaçante pour l’équilibre des écosystèmes locaux et les agriculteurs, elle l’est aussi pour nombre de personnes allergiques, puisque le pollen qu’elle relâche massivement entre août et octobre peut provoquer des réactions particulièrement violentes chez les individus sensibles.Trouver l’aiguille dans la botte de foin.Pour limiter la propagation de la résistance aux inhibiteurs de l’ALS, des chercheurs INRAE ont développé, avec l’ambroisie comme modèle, une procédure permettant la détection massive des mutations causant une résistance et la quantification de leurs fréquences. Pour ce faire, les chercheurs ont génotypé par séquençage à très haut débit des portions codantes du gène de l’ALS de 10950 plantes, collectées dans 219 parcelles sélectionnées au hasard sur la base de la présence de fortes infestations d’ambroisie. C’est dans les 40 millions de séquences obtenues que les scientifiques ont cherché des mutations du gène de l’ALS connues pour conférer une résistance aux herbicides, grâce à un programme informatique de leur conception capable de reconnaître ces infimes altérations génétiques dans un océan de données.Résultat : cinq mutations différentes ont été détectées dans 15 parcelles groupées en quatre foyers de résistance, dont le plus important dans le Tarn-et-Garonne, le département où a eu lieu le premier signalement de résistance de l’ambroisie aux inhibiteurs de l’ALS. Ce travail valide le concept de diagnostic massif des résistances aux produits phytosanitaires par séquençage à très haut débit, et permet d’établir une première cartographie des foyers de résistance de l’ambroisie, pouvant mener à l’avenir à des campagnes d’arrachage ciblé. L’équipe travaille désormais à étendre et systématiser ce type d’analyses à d’autres adventices.

International audience; Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need to be investigated to adapt control measures in livestock farms.

Additional file 1. Table S1: Number of SNPs per minimum allele frequency (MAF) category in each line. Table S2: Average r2 ± SD between SNPs according to different distances. Table S3: Sensitivity analysis of ROH estimates to MAF and maximal distance gap between two SNPs and derived inbreeding coefficient. Table S4: Estimates of effective population size (standard errors in brackets) for each line with or without Omy5 and Omy20.

Background: Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a signifcant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fxation index (FST), linkage disequilibrium (LD), efective population size (Ne) and inbreeding coefcient derived from runs of homozygosity (ROH). Results: Our results showed a moderate level of genetic diferentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the frst 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to diferences in local rates of recombination or due to key genes that tended to have fxed favorable alleles for domestication or production. Conclusions: This is the frst report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder efects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efcient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fsh genome.

Additional file 2. Figure S1: Line mean linkage disequilibrium at 50Â kb for each chromosome. Figure S2: Proportion of individuals per line with a SNP in a ROH along the genome. Figure S3: Proportion of individuals per line with a SNP in a ROH along chromosome 10.

International audience

Book of abstracts, ISBN: 978-2-9563873-0-5, EAN: 9782956387305Book of abstracts, ISBN: 978-2-9563873-0-5, EAN: 9782956387305; Rapid identification of high-molecular-weight glutenin subunits by SNP markers to breed for high quality. Eucarpia Cereal Section - Breeding cereals for sustainable agriculture

International audience; Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms(SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research.

La pasteurellose est la première cause de mortalité des femelles en élevage cunicole. Le projet RELAPA (Génomique pour la REsistance génétique des LApins à la PAsteurellose) a pour objectif de mettre en évidence des régions du génome associées à la réponse à la pasteurellose. Pour ce faire, 955 lapins ont été inoculés à 6 semaines d’âge avec une souche de Pasteurella multocida pyogène et suivis pendant 14 jours. La réponse des animaux était très variable, avec 7% de lapins résistants (sans aucun symptôme de pasteurellose et sans Pasteurella multocida détectée dans les organes) et 11% d’animaux très sensibles (morts ou euthanasiés pendant l’essai avec des Pasteurella multocida détectées). L’effet du père sur les caractères mesurés est très significatif, ce qui laisse présager l’existence d’une variabilité génétique importante dans la résistance à la pasteurellose.