Correction to: Genetic characterization of Addison’s disease in Bearded Collies

Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes. We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs. We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats. This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.     

Hereditary evaluation of multiple developmental abnormalities in the Havanese dog breed

The Havanese is a toy breed that presents with a wide range of developmental abnormalities. Skeletal defects, particularly osteochondrodysplasia (OCD), are the most frequently observed anomalies. Cataracts, liver shunts, heart murmurs, and missing incisors are also common in this breed. Estimates of heritability and complex segregation analyses were carried out to evaluate modes of transmission for these abnormalities. A moderate heritability was identified and evidence for a single major locus was found. Novel statistical analysis methods were used to identify four traits that co-segregate: cataracts, hepatic abnormalities, OCD, and cardiac abnormalities. A canine-specific microarray was used to identify changes in gene expression in the liver that accompany the aforementioned developmental problems. One hundred and thirteen genes were found to be differentially regulated in the Havanese.     

Perinatal physiology in cloned and normal calves: hematologic and biochemical profiles

Although a majority of clones are born normal and apparently healthy, mortality rates of nearly 30% are described in many reports. Such losses are a major limitation of cloning technology and represent substantial economic investment as well as justifiable animal health and welfare concerns. Prospective, controlled studies are needed to understand fully the causes of neonatal mortality in clones and to develop preventive and therapeutic strategies to minimize losses. We report here the findings of studies on the hematologic and biochemical profiles of cloned and control calves in the immediate 48-h postpartum period. Cloned calves were similar to control calves for a majority of parameters studied including blood gases, concentrations of plasma proteins, minerals and electrolytes, and white blood cell, neutrophil, lymphocyte, and platelet counts. The most notable differences between clones and controls in this study were reduced red- and white-blood cell counts in clones at birth and 1 h of age. As a group, plasma electrolyte concentrations were more variable in clones, and the variability tended to be shifted either higher (sodium, chloride) or lower (potassium, bicarbonate) than in controls. Previously, we noted differences in carbohydrate parameters, the length of time required for clones to make the neonatal adaptation to life ex utero, and morphology of the cloned placenta. Taken together, our findings suggest that cloned calves experience greater difficulty adjusting to life ex utero and that further research is warranted to determine the nature of the relationship between the physiological differences noted here in clones at birth and concomitant abnormal placental morphology.     

Morphology and morphometry of in vivo- and in vitro-produced bovine concepti from early pregnancy to term and association with high birth weights

This study was designed to characterize conceptus development based on pre- and postnatal measurements of in vivo- and in vitro-derived bovine pregnancies. In vivo-produced embryos were obtained after superovulation, whereas in vitro-produced embryos were derived from established procedures for bovine IVM, IVF and IVC. Blastocysts were transferred to recipients to obtain pregnancies of single (in vivo/singleton or in vitro/singleton groups) or twin fetuses (in vitro/twins group). Ultrasonographic examinations were performed weekly, from Day 30 of gestation through term. Videotaped images were digitized, and still-frames were used for the measurement of conceptus traits. Calves and fetal membranes (FM) were examined and measured upon delivery. In vitro-produced fetuses were smaller than in vivo controls (P < 0.05) during early pregnancy (Day 37 to Day 58), but in vitro/singletons presented significantly higher weights at birth than in vivo/control and in vitro/twin calves (P < 0.05). From late first trimester of pregnancy (Day 72 to Day 93), placentomes surrounding in vitro-derived singleton fetuses were longer and thinner than controls (P < 0.05). At term, the presence of giant cotyledons in the fetal membranes in the in vitro group was associated with a larger cotyledonary surface area in the fetal horn (P < 0.05). The biphasic growth pattern seen in in vitro-produced pregnancies was characterized by conceptus growth retardation during early pregnancy, followed by changes in the development of the placental tissue. Resulting high birth weights may be a consequence of aberrant placental development due to the disruption of the placental restraint on fetal growth toward the end of pregnancy.     

The genetics of epilepsy in the Belgian tervuren and sheepdog

Idiopathic epilepsy is characterized by recurrent seizure activity without an identifiable underlying anatomic defect. Dogs experiencing repeated bouts of severe seizures are given therapeutic medication to control their frequency and severity. Idiopathic epilepsy has been reported in many dog breeds and was identified as the predominant health issue facing dog breeds in a recent survey by the American Kennel Club. A growing body of evidence supports a hereditary basis for idiopathic epilepsy, with a variety of genetic inheritance models proposed. In the Belgian tervuren and sheepdog, epilepsy is highly heritable with a polygenic mode of inheritance, though apparently influenced by a single autosomal recessive locus of large effect. In an effort to establish molecular linkage between the epileptic phenotype and the locus of large effect, we have screened genomic DNA from families of affected tervuren and sheepdogs with 100 widely dispersed, polymorphic canine microsatellite markers (0.595 average PIC value). Although not significant (LOD scores <3.0), three genomic regions have shown nominal linkage between markers and the epileptic phenotype. Additional related dogs are being screened with these and additional markers to increase the power to detect the presence of a linked locus.     

Rapid appearance of epistasis during adaptive divergence following colonization

Theory predicts that short-term adaptation within populations depends on additive (A) genetic effects, while gene-gene interactions 'epistasis (E)' are important only in long-term evolution. However, few data exist on the genetic architecture of adaptive variation, and the relative importance of A versus non-additive genetic effects continues to be a central controversy of evolutionary biology after more than 70 years of debate. To examine this issue directly, we conducted hybridization experiments between two populations of wild soapberry bugs that have strongly differentiated in 100 or fewer generations following a host plant shift. Contrary to expectation, we found that between-population E and dominance (D) have appeared quickly in the evolution of new phenotypes. Rather than thousands of generations, adaptive gene differences between populations have evolved in tens. Such complex genetic variation could underlie the seemingly extreme rates of evolution that are increasingly reported in many taxa. In the case of the soapberry bug, extraordinary ecological opportunity, rather than mortality, may have created hard selection for genetic variants. Because ultimate division of populations into genetic species depends on epistatic loss of hybrid compatibility, local adaptation based on E may accelerate macro-evolutionary diversification.     

And the beak shall inherit – evolution in response to invasion

The increased demographic performance of biological invaders may often depend on their escape from specifically adapted enemies. Here we report that native taxa in colonized regions may swiftly evolve to exploit such emancipated exotic species because of selection caused by invaders. A native Australian true bug has expanded it host range to include a vine imported from tropical America that has become a serious environmental weed. Based on field comparisons and historical museum specimens, we show that over the past 30–40 years, seed feeding soapberry bugs have evolved 5–10% longer mouthparts, better suited to attack the forest‐invading balloon vines, which have large fruits. Laboratory experiments show that these differences are genetically based, and result in a near‐doubling of the rate at which seeds are attacked. Thus a native biota that initially permits invasion may rapidly respond in ways that ultimately facilitate control.     

Inheritance of resistance to Xylella fastidiosa within a Vitis rupestris × Vitis arizonica hybrid population

The inheritance of resistance to Xylella fastidiosa (Xf), the bacterium which causes Pierces disease (PD) in grapevines, was evaluated within a factorial mating design consisting of 16 full-sib families with resistance derived from Vitis arizonica interspecific hybrids. Measurements of disease progression under greenhouse conditions were based on quantitative assessment of Xf populations in stem tissues and on three phenotypic scores: leaf scorch, a cane maturation index (CMI) and an index that incorporated shoot stunting into the cane maturation index (CMSSI). Measurement of bacterial populations yielded the highest broad-sense heritability for resistance on a genotype mean basis (0.97), indicating that this measure of resistance was the least effected by environmental variation. Narrow-sense heritability of PD resistance was moderately high and measured 0.52, 0.60, 0.63 and 0.37 for Xf populations, CMI scores, CMSSI scores and leaf scorch values, respectively. Complex segregation analysis using the computer program Statistical Analysis for Genetic Epidemiology (sage) strongly indicated the existence of a major gene for PD resistance, which accounted for 91% of the total genetic variance. Conversion of the quantitative data into qualitative resistance levels and evaluation via a chi-square analysis showed that 15 of the 16 families segregated in accordance with a single gene hypothesis with a dominant allele controlling PD resistance. These data indicate that the trait should be relatively easy to pass on from parents to progeny in a breeding program for the development of PD-resistant grape cultivars, particularly when selection is based on cane maturation scores or stem Xf populations.     

The effects of selection for gain in mice on the direct-maternal genetic correlation

Components of genetic variation for postweaning growth traits were estimated for both control and growth stocks of mice. The effect of phenotypic selection for gain, which genetically combines selection for additive direct and maternal effects, on additive genetic variance components, heritability, and additive genetic correlationsis discussed. Quantitative genetic theory predicts that simultaneous selection for two metric traits in the same direction will cause the genetic correlation between the two traits to become more negative. The results presented in this paper conflict with this theory. The direct-maternal additive genetic correlation was more negative in the control line (with 356 mice) than in the growth-selected line (with 320 mice) for the three traits analyzed (0.310 vs 0.999 for 21-day weight, 0.316 vs 1.000 for 42-day weight, and 0.506 vs 1.000 for gain from 21–42 days). Estimates were obtained by restricted maximum likelihood (REML) computed under a derivative free algorithm (DFREML).