Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

Summary Selective breedings of mice were carried out for quantitative antibody responsiveness to flagellar Ag., f (Selection III) or somatic Ag., s (Selection IV) of two non cross‐reaction Salmonellae (Salm. tm., Salm. or.) alternated for immunization of consecutive generations. At the selection limit, these selections produced homozygous high (H) and low (L) responder lines for the character investigated: peak agglutinin response to optimal secondary immunization. The responsiveness to both f and s Ags. is submitted to polygenic regulation. The heritability (h2) realized during the selective breeding was 0.37 ± 0.07 for the response to f Ag. and 0.40 ± 0.1 for the response to s Ag. The respective part of genetic and environmental variance in F2 hybrids was 64% and 36% in selection III and 61% and 39% in selection IV. In the two selections, the dominance variance is negligible (<1%), therefore the genetic variance is essentially additive. The additive variance calculated as the heritable fraction of the F2 hybrid variance is somewhat lower, the reason for this difference is discussed. The quantitative antibody response to f Ag. in selection III is controlled by about seven independent loci. The antibody response to s Ag. in selection IV is controlled by about four independent loci. A possible association of relevant genes with the H‐2 locus was investigated. In selection III, no significant participation of H‐2 linked genes, in the regulation of responses to f and s Ags. of Salm, tm and Salm. or. could be demonstrated. In selection IV a partial contribution of H‐2 linked genes was observed concerning responsiveness to both f and s Ags. of Salm. tm.. but not to Salm. or. Ags. The H‐2 effect accounts for 25% of the total interline difference.

The objective of this study was to estimate genetic and nongenetic effects affecting survival in crossbred lambs during 3 time periods: through 1 d of age ( = 7,933), 2 to 30 d of age ( = 5,370), and 2 to 60 d of age ( = 5,216) in a population being upgraded to the dairy breeds of East Friesian and Lacaune in which lambs were artificially reared on milk replacer. Survival was analyzed for lambs born in 14 yr from 1998 to 2011 using pedigree information from 14,339 animals born in 23 yr from 1989 to 2011. Date of death, sex, age of the dam, birth type, month and year of birth, and breed composition were recorded, and the proportion of retained heterosis was calculated for each animal. Lambs were crossbreds of 2 or more breeds with 14 breeds represented in the population. Due to low mean genetic contribution of the 12 nondairy breeds, they were placed into 2 groups: meat breeds (Hampshire, Suffolk, and Texel) and maternal breeds (Romanov, Finnsheep, Dorset, Targhee, Rambouillet, Polypay, Katahdin, Arcott Rideau, and Commercial). The proportion of individual retained heterosis was positively associated ( < 0.05) with lamb survival from 2 to 30 and from 2 to 60 d of age. The predicted increase in survival of F lambs compared to purebred lambs was +8.8 and +14.6%, respectively. Predicted survival of meat breed lambs and maternal breed lambs was greater ( ≤ 0.01) than Lacaune lambs during all 3 periods. Predicted survival of East Friesian lambs was consistently lower ( ≤ 0.01) than meat breed and maternal breed lambs during all periods. The predicted survival of East Friesian lambs was numerically greater but not significantly different from Lacaune lambs. There was a lower ( < 0.01) survival of females compared to males through 1 d of age (-5.6%), but females had higher ( < 0.01) survival than males in the other 2 periods (2 to 30 d = +3.3% and 2 to 60 d = +6.0%). Through 1 d of age, lambs of triplet and greater birth types had lower ( < 0.01) survival than single lambs (-6.2%), and lambs from 1-yr-old dams had lower ( < 0.01) survival than lambs from 2-yr-old dams (+4.5%). Estimates of heritability of lamb survival were 0.14 (SE = 0.03), 0.03 (SE = 0.04), and 0.06 (SE = 0.03) for the 3 time periods, respectively. An increase in the proportion of individual retained heterosis was the most important genetic factor associated with increased lamb survival in this study.

Understanding causal mechanisms among variables is critical to efficient management of complex biological systems such as animal agriculture production. The increasing availability of data from commercial livestock operations offers unique opportunities for attaining causal insight, despite the inherently observational nature of these data. Causal claims based on observational data are substantiated by recent theoretical and methodological developments in the rapidly evolving field of causal inference. Thus, the objectives of this review are as follows: 1) to introduce a unifying conceptual framework for investigating causal effects from observational data in livestock, 2) to illustrate its implementation in the context of the animal sciences, and 3) to discuss opportunities and challenges associated with this framework. Foundational to the proposed conceptual framework are graphical objects known as directed acyclic graphs (DAGs). As mathematical constructs and practical tools, DAGs encode putative structural mechanisms underlying causal models together with their probabilistic implications. The process of DAG elicitation and causal identification is central to any causal claims based on observational data. We further discuss necessary causal assumptions and associated limitations to causal inference. Last, we provide practical recommendations to facilitate implementation of causal inference from observational data in the context of the animal sciences.

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