Thomas R. Famula

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.

Estimation of parentage and relatedness in the polyploid white sturgeon (Acipenser transmontanus) using a dominant marker approach for duplicated microsatellite loci

We investigated the usefulness of microsatellite loci in the white sturgeon, Acipenser transmontanus, for estimating parentage and relatedness using algorithms developed for dominant markers. Microsatellite alleles were scored as independent dominant markers, and the resultant data were used with likelihood ratio statistics to estimate parentage. We tested three parentage scenarios: (1) assignment to parent pairs, (2) assignment to sires and dams independently when all possible parents were included (three sires and three dams), and (3) assignment to sires and dams when the true sires and dams were combined with a broodstock of 157 fish. Accuracy of assignment to parent-pairs exceeded 99% (scenario 1). Assignment accuracy to sires and dams independently was lower (scenario 2) but we present methods to improve this accuracy even when the number of possible sires and dams is large (scenario 3). Using LOD scores in conjunction with δ values, a statistic quantifying confidence in the LOD scores, accuracy was maintained at a high level even when the number of sires and dams is large (n=90 and 73, respectively). Pairwise relatedness estimates were also made for fish from known sib groups to test if the correct sib groups could be identified using the dominant marker approach. The use of unweighted pair-group method using arithmetic mean (UPGMA) clustering algorithm to identify sib groups from a matrix of relatedness values proved to be successful for identifying all full-sib groups. The results suggest our approach of scoring microsatellite alleles as dominant markers can be used to accurately estimate parentage and relatedness.

Evaluation of allele frequencies of inherited disease genes in subgroups of American Quarter Horses

OBJECTIVE To estimate allele frequencies of the hyperkalaemic periodic paralysis (HYPP), lethal white foal syndrome (LWFS), glycogen branching enzyme deficiency (GBED), hereditary equine regional dermal asthenia (HERDA), and type 1 polysaccharide storage myopathy (PSSM) genes in elite performance subgroups of American Quarter Horses (AQHs). DESIGN Prospective genetic survey. ANIMALS 651 elite performance AQHs, 200 control AQHs, and 180 control American Paint Horses (APHs). PROCEDURES Elite performance AQHs successful in 7 competitive disciplines (barrel racing, cutting, halter, racing, reining, western pleasure, and working cow horse) were geno- typed for 5 disease-causing alleles. Age-matched control AQHs and APHs were used to establish comparative whole-breed estimates of allele frequencies. RESULTS Highest allele frequencies among control AQHs were for type 1 PSSM (0.055) and GBED (0.054), whereas HERDA (0.021) and HYPP (0.008) were less prevalent. Control APHs uniquely harbored LWFS (0.107) and had high prevalence of HYPP (0.025), relative to AQHs. Halter horse subgroups had significantly greater allele frequencies for HYPP (0.299) and PSSM (0.155). Glycogen branching enzyme deficiency, HERDA, and PSSM were found broadly throughout subgroups; cutting subgroups were distinct for HERDA (0.142), and western pleasure subgroups were distinct for GBED (0.132). Racing and barrel racing subgroups had the lowest frequencies of the 5 disease genes. CONCLUSIONS AND CLINICAL RELEVANCE Accurate estimates of disease-causing alleles in AQHs and APHs may guide use of diagnostic genetic testing, aid management of genetic diseases, and help minimize production of affected foals.

Prevalence of inherited disorders among mixed-breed and purebred dogs: 27,254 cases (1995–2010)

OBJECTIVE To determine the proportion of mixed-breed and purebred dogs with common genetic disorders. DESIGN Case-control study. ANIMALS 27,254 dogs with an inherited disorder. PROCEDURES Electronic medical records were reviewed for 24 genetic disorders: hemangiosarcoma, lymphoma, mast cell tumor, osteosarcoma, aortic stenosis, dilated cardiomyopathy, hypertrophic cardiomyopathy, mitral valve dysplasia, patent ductus arteriosus, ventricular septal defect, hyperadrenocorticism, hypoadrenocorticism, hypothyroidism, elbow dysplasia, hip dysplasia, intervertebral disk disease, patellar luxation, ruptured cranial cruciate ligament, atopy or allergic dermatitis, bloat, cataracts, epilepsy, lens luxation, and portosystemic shunt. For each disorder, healthy controls matched for age, body weight, and sex to each affected dog were identified. RESULTS Genetic disorders differed in expression. No differences in expression of 13 genetic disorders were detected between purebred dogs and mixed-breed dogs (ie, hip dysplasia, hypo- and hyperadrenocorticism, cancers, lens luxation, and patellar luxation). Purebred dogs were more likely to have 10 genetic disorders, including dilated cardiomyopathy, elbow dysplasia, cataracts, and hypothyroidism. Mixed-breed dogs had a greater probability of ruptured cranial cruciate ligament. CONCLUSIONS AND CLINICAL RELEVANCE Prevalence of genetic disorders in both populations was related to the specific disorder. Recently derived breeds or those from similar lineages appeared to be more susceptible to certain disorders that affect all closely related purebred dogs, whereas disorders with equal prevalence in the 2 populations suggested that those disorders represented more ancient mutations that are widely spread through the dog population. Results provided insight on how breeding practices may reduce prevalence of a disorder.

Y chromosome haplotype analysis in purebred dogs

In order to evaluate the genetic structure of purebred dogs, six Y chromosome microsatellite markers were used to analyze DNA samples from 824 unrelated dogs from 50 recognized breeds. A relatively small number of haplotypes (67) were identified in this large sample set due to extensive sharing of haplotypes between breeds and low haplotype diversity within breeds. Fifteen breeds were characterized by a single Y chromosome haplotype. Breed-specific haplotypes were identified for 26 of the 50 breeds, and haplotype sharing between some breeds indicated a common history. A molecular variance analysis (AMOVA) demonstrated significant genetic variation across breeds (63.7%) and with geographic origin of the breeds (11.5%). A network analysis of the haplotypes revealed further relationships between the breeds as well as deep rooting of many of the breed-specific haplotypes, particularly among breeds of African origin.

Long-term observations on the dynamics of bovine digital dermatitis lesions on a California dairy after topical treatment with lincomycin HCl.

The objective of this study was to observe the dynamics of clinical cure and recurrence of the lesions of bovine digital dermatitis for 11 months after treatment with topical lincomycin HCl. The study was a clinical follow-up of 39 active bovine digital dermatitis lesions (from 29 cows). Cows with active, painful bovine digital dermatitis (BDD) lesions on the interdigital commissure of the rear feet were identified on day 0. On day 1, lesions in all cows were photographed and full-skin thickness 6mm punch biopsies were obtained for histological evaluation. All lesions on all cows were treated with topical lincomycin paste under a light bandage. On days 12 and 23, a subsample of 10 lesions was randomly selected, photographed, and biopsied. On day 37, all lesions on all cows were photographed and biopsied. After day 37, lesions were evaluated on a monthly basis. All lesions were photographed at each observation until day 341 (end of study) but only cows that had macroscopically active lesions were biopsied. Of the 39 lesions treated on day 1, 21 (54%) required re-treatment on at least one occasion before day 341. Macroscopic classification agreed well with histological classification when lesions were small, focal and active (M1 lesions) or large, ulcerative and active (M2), but agreement was variable for lesions that had healed macroscopically (M5) or that were chronic (M4). A transition model showed that M1 and M2 lesions were 27 times more likely to be an M2 lesion on the next observation than to be a healed (M5) lesion.

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.

What is an “Adverse” Environment? Interactions of Rearing Experiences and MAOA Genotype in Rhesus Monkeys

BACKGROUND Studies have been inconsistent in demonstrating that early adversity and specific genotype can be joint risk factors for poor behavioral outcomes. Using a rhesus monkey model, we examined how social context and different forms of early adversity influence whether a specific genotype (polymorphism in the promoter region of monoamine oxidase A [MAOA]) affects display of aggressive, fearful, and anxious behaviors. METHODS Rhesus monkey infants (n = 473) were exposed to brief social challenge at age 3-4 months. Infants were reared 1) with mothers and up to 150 other animals in large cages; 2) with mothers in smaller social groups; 3) with mother and access to, at most, one other mother-infant pair; and 4) without mother but with access to a same-age peer in a nursery. RESULTS No effects of genotype were found for infants reared by mothers in large social cages, although several genotype by rearing environment interactions were evident. Animals reared in smaller social groups were more likely to display aggression, which was especially true of animals possessing the low-activity MAOA genotype. In addition, animals with low-activity genotypes that had experienced restricted mother rearing showed more anxious behavior (scratch, yawn). CONCLUSIONS Among mother-reared animals, broader contextual features, associated with the social environment and experience of the mother, can affect the extent to which genotype contributes to behavioral expression under conditions of challenge. Results also suggest that different forms of early adverse experience can affect the types of responses displayed by animals of different genotypes.

A threshold model analysis of deafness in Dalmatians

To elucidate the inheritance of deafness in Dalmatian dogs, 825 dogs in 111 litters were evaluated for abnormalities in hearing through the brainstem auditory evoked response (BAER). Recorded along with their quality of hearing (normal, unilaterally deaf, or bilaterally deaf) were the sex, coat color, eye color and the presence or absence of a color patch. The analysis considered deafness an ordered categorical trait in a threshold model. The underlying, unobservable continuous variate of the threshold model was assumed to be a linear function of sex of dog, coat color (black or liver and white), color patch (presence or absence), eye color, the deafness phenotype of the parents and a random family effect. Twenty-six percent of dogs were deaf in at least one ear. Eye color, color patch, sex and the hearing status of the parents were all significant contributions to deafness. The heritability of deafness, on the continuous unobservable scale, was 0.21. This value was computed after correction for eye color, color patch, parental hearing status and sex, implying that significant genetic variation exists beyond the contribution of several single loci.

Necrotizing meningoencephalitis of Pug Dogs associates with dog leukocyte antigen class II and resembles acute variant forms of multiple sclerosis

Necrotizing meningoencephalitis (NME) is a disorder of Pug Dogs that appears to have an immune etiology and high heritability based on population studies. The present study was undertaken to identify a genetic basis for the disease. A genome-wide association scan with single tandem repeat (STR) markers showed a single strong association near the dog leukocyte antigen (DLA) complex on CFA12. Fine resolution mapping with 27 STR markers on CFA12 further narrowed association to the region containing DLA-DRB1, -DQA1 and, -DQB1 genes. Sequencing confirmed that affected dogs were more likely to be homozygous for specific alleles at each locus and that these alleles were linked, forming a single high risk haplotype. The strong DLA class II association of NME in Pug Dogs resembles that of human multiple sclerosis (MS). Like MS, NME appears to have an autoimmune basis, involves genetic and nongenetic factors, has a relatively low incidence, is more frequent in females than males, and is associated with a vascularly orientated nonsuppurative inflammation. However, NME of Pug Dogs is more aggressive in disease course than classical human MS, appears to be relatively earlier in onset, and involves necrosis rather than demyelination as the central pathobiologic feature. Thus, Pug Dog encephalitis (PDE) shares clinical features with the less common acute variant forms of MS. Accordingly, NME of Pug Dogs may represent a naturally occurring canine model of certain idiopathic inflammatory disorders of the human central nervous system.