Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens’ resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

BackgroundKlebsiella pneumoniae is a leading cause of hospital-acquired urinary tract infections and pneumonia worldwide, and is responsible for many cases of pyogenic liver abscess among diabetic patients in Asia. A defining characteristic of this pathogen is the presence of a thick, exterior capsule that has been reported to play a role in biofilm formation and to protect the organism from threats such antibiotics and host immune challenge.FindingsWe constructed two knockout mutants of K. pneumoniae to investigate how perturbations to capsule biosynthesis alter the cellular phenotype. In the first mutant, we deleted the entire gene cluster responsible for biosynthesis of the extracellular polysaccharide capsule. In the second mutant, we deleted the capsule export subsystem within this cluster. We find that both knockout mutants have lower amounts of capsule but produce greater amounts of biofilm. Moreover, one of the two mutants abolishes fimbriae expression as well.ConclusionsThese results are expected to provide insight into the interaction between capsule biosynthesis, biofilm formation, and fimbriae expression in this organism.

The in silico reconstruction of metabolic networks has become an effective and useful systems biology approach to predict and explain many different cellular phenotypes. When simulation outputs do not match experimental data, the source of the inconsistency can often be traced to incomplete biological information that is consequently not captured in the model. To address this problem, general approaches continue to be needed that can suggest experimentally-testable hypotheses to reconcile inconsistencies between simulation and experimental data. Here we present such an approach that focuses specifically on correcting cases in which experimental data show a particular gene to be essential but model simulations do not. We use metabolic models to predict efficient compensatory pathways, after which cloning and overexpression of these pathways are performed to investigate whether they restore growth and to help determine why these compensatory pathways are not active in mutant cells. We demonstrate this technique for a ppc knockout of Salmonella enterica serovar Typhimurium; the inability of cells to route flux through the glyoxylate shunt when ppc is removed was correctly identified by our approach as the cause of the discrepancy. These results demonstrate the feasibility of our approach to drive biological discovery while simultaneously refining metabolic network reconstructions.

Flax is an important oilseed crop with industrial, animal, and human nutrition uses. Breeding programs for linseed and fibre flax were initiated in Canada in the early 1900s. A total of 82 flax cultivars have been registered in Canada since 1910, including 24 cultivars introduced from foreign countries and 58 cultivars developed by Canadian breeders. This study collated pedigree data of Canadian flax cultivars and quantified their genetic base via pedigree analysis and coefficient of parentage (CP). A fairly high mean CP of 0.14 was observed between all registered cultivars; this value was even higher (0.23) when only the 46 cultivars released from 1981-2015 were considered. The registered cultivars traced back to 46 ancestors; 72% originated from foreign countries and contributed 83% of the genetic base of all cultivars, illustrating the dominant role played by foreign germplasm in the genetic improvement of Canadian flax. The top 11 ancestors contributed 70%-93% of the genetic base of modern flax cultivars released in the last three decades and formed the core gene pool of Canadian flax cultivars. The genetic base of Canadian cultivars is relatively narrow, although it has gradually expanded, especially in the last two decades. Broadening the genetic base through the introduction of new exotic germplasm is needed to invigorate the gene pool of Canadian flax breeding programs.Key words: flax, cultivar, pedigree, ancestor, genetic base, Canada.Résumé : Le lin est un important oléagineux utilisé à des fins industrielles ainsi que pour l'alimentation humaine et animale. Les premiers programmes d'hybridation visant à accroître la production de graines et de fibres de cette culture remontent au début du vingtième siècle. Quatre-vingt-deux variétés de lin ont été homologuées au Canada depuis 1910, ce qui comprend 24 cultivars de l'étranger et 58 créés par des améliorateurs canadiens. Cette étude rassemble les données généalogiques sur les variétés canadiennes et en quantifie la base génétique d'après leur ascendance et leur coefficient de parenté (CP). Les auteurs ont relevé un CP moyen relativement élevé (0,14) entre les variétés homologuées; le CP est encore plus élevé (0,23) quand on ne tient compte que des 46 cultivars homologués entre 1981 et 2015. Les variétés homologuées ont 46 ancêtres. Soixante-douze pour cent ont pour origine des pays étrangers et représentent 83 % de la base génétique des cultivars, signe du très grand rôle que le matériel génétique exotique a joué dans l'amélioration du lin canadien. Les onze principaux ancêtres ont fourni de 70 à 93 % de la base génétique des variétés de lin contemporaines, homologuées au cours des trois dernières décennies, et constituent le principal réservoir de gènes des cultivars canadiens. Les variétés canadiennes de lin se caractérisent par une base génétique assez étroite, bien que celle-ci se soit graduellement élargie, surtout au cours