A randomized controlled trial on the effect of incomplete milking during the first 5 days in milk on reproductive performance of dairy cows.

The main objective of the current study was to measure the effect of incomplete milking on luteal activity and on pregnancy hazard. We also aimed to study the effect of early-lactation hyperketonemia (i.e., ß-hydroxybutyrate blood concentration ≥1.4 mmol/L during the first 3 wk in milk) on those reproductive outcomes. Multiparous Holstein cows (n = 853) from 13 commercial herds were enrolled in a randomized controlled trial. Cows were assigned to a control or a treatment group, incompletely milked (10-14 L of milk collected/d) from 1 to 5 DIM. Blood samples were collected once a week during weeks in milk 1 to 3 for ß-hydroxybutyrate blood concentration, and a threshold of 1.4 mmol/L was used to define hyperketonemia. During weeks in milk 5 and 7, cows were sampled for progesterone blood concentration, and a threshold of 1 ng/mL was used to define luteal activity. Reproductive information and culling dates were obtained through herd records. Logistic regression models and survival analyses were used to assess the effect of treatment on luteal activity and on pregnancy hazard, respectively. Analogous models were used to investigate the effect of early-lactation hyperketonemia on reproductive outcomes. The odds of luteal activity for incompletely milked cows were 1.1 (95% confidence interval: 0.72-1.7) times those of conventionally milked cows. The effect of treatment on pregnancy hazard varied as a function of time, parity, and start of the breeding period. In second-parity cows that started the breeding period <55 d in milk, the pregnancy hazard (95% confidence interval) in incompletely milked cows was 576.3 (240.0-1,383.7), 36.9 (18.9-72.1), 6.8 (3.3-13.8), 2.5 (1.0-5.9), and 0.13 (0.07-0.26) times that of conventionally milked cows at 1 to 21, 22 to 43, 44 to 65, 66 to 87, and >87 d after the voluntary waiting period, respectively. The treatment did not have an effect on pregnancy hazard in cows in third parity or greater or in those starting the breeding period ≥55 d in milk. Early-lactation hyperketonemia was not associated with any of the reproductive outcomes. In conclusion, the incomplete milking protocol had no effect on luteal activity and had a positive effect on pregnancy hazard in second-parity cows in herds with a short voluntary waiting period (<55 d). We did not observe an effect of early-lactation hyperketonemia on luteal activity or on pregnancy hazard.

Effect of incomplete milking during the first 5 days in milk on udder and reproductive tract health: Results from a randomized controlled trial.

The aim of this study was to investigate the effect of an incomplete milking on risk of mastitis and reproductive tract disease. Multiparous dairy cows (n = 878) from 13 commercial herds were enrolled in a randomized controlled trial. Cows were randomly assigned to either a control (milked conventionally) or a treatment group, which consisted of an incomplete milking (10-14 L of milk collected/d) from 1 to 5 d in milk (DIM). Quarter milk samples were collected at approximately 11 and 18 DIM to measure somatic cell count (SCC). Quarters were considered negative for intramammary infection if SCC was <100,000 cells/mL and positive if SCC was ≥200,000 cells/mL. To calculate intramammary infection incidence, negative quarters of the initial samples collected were tested again 1 wk later. This was done to deter incidence of positive quarters. To calculate elimination rate, positive quarters were tested again 1 wk later to detect mastitis elimination. Farmers recorded clinical mastitis events. Cows were also examined at approximately 35 DIM with a Metricheck device (Simcro, Hamilton, New Zealand) for detection of purulent vaginal discharge (PVD) and with an endometrial cytobrush for presence of leukocytes [endometrial cytology for smear (ENDO) and for leukocyte esterase test (LE)]. A threshold ≥3 was used to define a positive PVD or LE test, whereas a polymorphonuclear cell count ≥6% was used to define a positive ENDO. Five generalized mixed models with cow or herd as random intercepts were used to determine the effects of incomplete milking on odds of new intramammary infection, odds of intramammary infection elimination, and odds of a positive PVD, LE, or ENDO status. To investigate time until first clinical mastitis event, a Cox model with a herd frailty term was used. The odds of new intramammary infection and intramammary infection elimination for incompletely milked cows were 0.90 [95% confidence interval (CI): 0.49, 1.7] and 2.9 (95% CI: 1.4, 6.0) times those of conventionally milked cows, respectively. The hazard of clinical mastitis in incompletely milked cows was 0.96 (95% CI: 0.59, 1.6) times that of conventionally milked cows. The odds of PVD, LE, and ENDO for incompletely milked cows were 1.4 (95% CI: 0.89, 2.1), 1.3 (95% CI: 0.88, 1.8), and 1.2 (95% CI: 0.81, 1.7) times those of conventionally milked cows. These results suggest that incomplete milking during the first 5 DIM increases the odds of a decrease in SCC from 11 to 18 DIM but does not affect odds of increase in SCC in the same period. The incomplete milking had no effect on clinical mastitis incidence in the first 90 DIM or on reproductive tract health at 35 DIM.

A randomized controlled trial on the effect of incomplete milking during early lactation on ketonemia and body condition loss in Holstein dairy cows.

Limiting milk production for a short period of time in early lactation could be a relevant strategy to prevent hyperketonemia (HYK). From December 2013 to March 2015, 838 multiparous Holstein cows from 13 herds were enrolled in a randomized controlled trial evaluating the effect of incomplete milking in early lactation on ketonemia and its effect on body condition score (BCS) loss. Cows were randomly assigned 4 wk before expected calving date to 1 of 2 treatment groups, (1) a conventional milking protocol (CON) for which cows were completely milked or (2) an incomplete milking protocol (INC) for which a maximum of 10 to 14 kg of milk/d were withdrawn during the first 5 d in milk (DIM). ß-Hydroxybutyrate (BHB) concentrations were measured from blood samples collected on each cow 3 times at weekly intervals. Hyperketonemia was defined as BHB ≥1.4 mmol/L. Body condition score variation in the postcalving period was calculated by subtracting BCS assessed at wk 7 from BCS assessed at first week after calving. Effect of treatment on ketonemia and prevalence of HYK were evaluated for 4 specific time periods: 1 to 3, 4 to 7, 8 to 17, and 18 to 26 DIM. Effect of treatment on ketonemia was investigated using linear mixed models with natural logarithm of BHB measurements as outcome and treatment groups as fixed effect. Generalized linear mixed models with HYK as outcome, using logit link, and treatment groups as fixed effect were used to investigate effect of treatment on odds of HYK. A logistic regression model with BCS loss (<0.75 or ≥0.75) as outcome and treatment groups and herd as fixed effects was used to study effect of INC on odds of having BCS loss ≥0.75. A total of 813 lactations had complete data and were used for statistical analysis of ketonemia and HYK. A total of 709 lactations had complete data and were used for analysis of BCS loss. Geometric means of blood BHB concentrations during the 1 to 3, 4 to 7, 8 to 17, and 18 to 26 DIM periods were, respectively, 0.72 (95% confidence interval = 0.66, 0.80), 0.66 (0.60, 0.73), 0.90 (0.80, 1.01), and 0.93 (0.83, 1.05) mmol/L for INC, and 0.65 (0.59, 0.72), 0.79 (0.72, 0.87), 0.94 (0.84, 1.06), and 0.92 (0.82, 1.04) mmol/L for CON. Cows in INC group had lower ketonemia during the 4 to 7 DIM period. Predicted prevalence of HYK during the 1 to 3, 4 to 7, 8 to 17, and 18 to 26 DIM periods were, respectively, 2.8 (3.2, 15.1), 4.6 (2.0, 10.0), 13.4 (8.4, 20.0), and 23.0% (17.4, 29.7) for INC and 2.6 (2.5, 13.8), 10.7 (5.6, 19.3), 19.4 (13.0, 27.9), and 21.3% (16.0, 27.8) for CON. The INC treatment reduced the prevalence of HYK during the 4 to 7 and 8 to 17 DIM periods. No association was observed between INC and BCS loss in the postcalving period. Overall, the incomplete milking protocol was effective for reducing ketonemia and prevalence of HYK during the early postpartum period.

A randomized controlled trial on the effect of incomplete milking during the first 5 days in milk on culling hazard and on milk production and composition of dairy cows.

An incomplete milking in early lactation could help limit negative energy balance in dairy cattle, but its potential effects on culling hazard and on milk production and composition throughout the entire lactation are unknown. The objective of this study was to evaluate the effect of an incomplete milking during the first 5 d in milk on culling hazard, milk weight, milk fat and protein concentrations, and energy-corrected milk (ECM) yield during the whole lactation. A randomized controlled trial was conducted in 13 dairy farms near St-Hyacinthe, Quebec, Canada. Approximately 1 mo before expected calving, Holstein multiparous cows calving between December 2013 and March 2015 (n = 846 cow lactations) were randomly assigned to a control or a treatment group. Cows in the control group were milked conventionally, whereas cows in the treatment group were submitted to an incomplete milking protocol (maximum of 10, 12, and 14 L/d of milk was collected on days in milk 1-3, 4, and 5, respectively). All farms were registered on Dairy Herd Improvement Association, which was used to obtain records on culling, monthly milk yield, and milk fat and protein concentrations. In addition, daily milk yield records were available for 6 farms. A Cox proportional hazards model with a herd frailty term was fitted to the data to compare culling hazard among treatment groups. Regarding milk production and composition, 4 linear mixed models with herd as a fixed effect, cow as a random effect, and using an autoregressive covariance structure were used to study the effect of the incomplete milking on (1) milk weight, (2) milk fat concentration, (3) milk protein concentration, and (4) ECM yield. Culling hazard did not differ among treatment groups (hazard ratio = 1.0; 95% CI = 0.82, 1.3). We observed no differences in milk weight, milk fat, or protein concentration among treatment groups between weeks in milk (WIM) 2 and 44 (the studied period). We noted a difference in ECM between treatment groups for WIM 38, with incompletely milked cows producing less milk than conventionally milked cows (-2.7 kg/d; 95% CI = -0.02, -5.2 kg/d), but no differences were found for any of the other WIM. These results suggest that this strategy for controlling the negative energy balance has negligible effect on cow productivity.

Short communication: An observational study investigating inter-observer agreement for variation over time of body condition score in dairy cows.

Body condition score (BCS) is strongly correlated with energy reserves. The ease, rapidity of scoring, and high intra- and inter-observer repeatability make it a widely used herd management tool in bovine practice and in scientific studies. Loss or gain of BCS, rather than a single BCS measurement, is frequently used to monitor energy balance in dairy cows. It is unknown if the difference between 2 BCS measures taken at different moments (ΔBCS) would demonstrate inter-observer agreement similar to that of a single BCS measurement. The objective of this study was to compare inter-observer agreement of BCS and ΔBCS in dairy cows when multiple observers perform data collection. An observational study was conducted between April and September 2015; 3 observers independently assessed BCS of 73 Holstein cows from 1 commercial dairy herd. Body condition score assessments of the animals were performed between 1 and 20 d in milk (early lactation; exam 1) and again between 41 and 60 d in milk (peak of milk production; exam 2). Quadratic weighted kappa (κw) was computed to quantify agreement between observers for single BCS measurements and ΔBCS. For single BCS measurements, κw of 0.79 (95% CI: 0.69, 0.85) and 0.84 (95% CI: 0.77, 0.89) were obtained for exam 1 and exam 2, respectively. Such values would be interpreted as strong agreement and are consistent with the available literature on BCS repeatability. When computing agreement for ΔBCS, a κw value of 0.49 (95% CI: 0.32, 0.63) was obtained, suggesting moderate agreement between observers. These findings suggest that studies investigating single BCS measures could use many observers with a high degree of accuracy in the results. When ΔBCS is the parameter of interest, more reliable results would be obtained if one observer conducts all assessments.

Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes.

Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from >1000 nuclear single-nucleotide polymorphisms (SNPs) and find evidence of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topology. To disentangle whether uncertainty in the phylogenetic inference of the relationships among ecotypes could also result from ancestral admixture events we reconstructed the relationship among the ecotypes as an admixture graph and estimated f4-statistics using TreeMix. The results were consistent with episodes of admixture between two of the North Pacific ecotypes and the two outgroups (populations from the Southern Ocean and the North Atlantic). Gene flow may have occurred via unsampled 'ghost' populations rather than directly between the populations sampled here. Our results indicate that because of ancestral admixture events and incomplete lineage sorting, a single bifurcating tree does not fully describe the relationship among these populations. The data are therefore most consistent with the genomic variation among North Pacific killer whale ecotypes resulting from multiple colonisation events, and secondary contact may have facilitated evolutionary divergence. Thus, the present-day populations of North Pacific killer whale ecotypes have a complex ancestry, confounding the tree-based inference of ancestral geography.

Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus).

The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India.

A quantitative trait locus for normal variation in forearm bone mineral density in pedigreed baboons maps to the ortholog of human chromosome 11q.

Baboons share many anatomical, physiological, and developmental characteristics with humans that make them excellent models for human bone maintenance and turnover. We conducted statistical genetic analyses, including a whole-genome linkage screen, of dual-energy x-ray absorptiometry-acquired measures of areal bone mineral density (aBMD), currently the most reliable single predictor of susceptibility to osteoporotic fracture in humans, from three forearm sites on the radius and ulna of 667 pedigreed baboons. We used a maximum likelihood-based variance decomposition approach to detect and quantify the effects of genes on normal variation in aBMD in the forearm of these baboons and to localize these effects to chromosomal regions. We estimated significant heritability for aBMD at all three sites and found evidence for a quantitative trait locus (QTL) contributing significantly to the genetic effects on this trait in a region of the baboon genome homologous to human chromosome 11q12-13. This first reported genome-wide linkage screen in a nonhuman primate for QTLs affecting forearm aBMD provides important cross-species replication of a QTL found in humans. The concordance of our results in a nonhuman primate with those reported for humans provides strong evidence that a gene (or genes) in this region affects normal variation in BMD.

Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method.

Abstract Genetic analysis using noninvasively collected samples such as faeces continues to pose a formidable challenge because of unpredictable variation in the extent to which usable DNA is obtained. We investigated the influence of multiple variables on the quantity of DNA extracted from faecal samples from wild mountain gorillas and chimpanzees. There was a small negative correlation between temperature at time of collection and the amount of DNA obtained. Storage of samples either in RNAlater solution or dried using silica gel beads produced similar results, but significantly higher amounts of DNA were obtained using a novel protocol that combines a short period of storage in ethanol with subsequent desiccation using silica.

Patterns of nuclear DNA degeneration over time--a case study in historic teeth samples.

The amount of nuclear DNA extracted from teeth of 279 individual red fox Vulpes vulpes collected over a period spanning the last three decades was determined by quantitative polymerase chain reaction (PCR). Although teeth were autoclaved during initial collection, 73.8% of extracts contained sufficient DNA concentration (> 5 pg/ micro L) suitable for reliable microsatellite genotyping but the quantity of nuclear DNA decayed significantly over time in a nonlinear pattern. The success of PCR amplification across four examined canine microsatellites over time was dependent on fragment size. By including data from two different tests for human contamination and from frequencies of allelic dropout and false alleles, the methodological constraints of population genetic studies using microsatellite loci amplified from historic DNA are discussed.

Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus).

Noninvasive samples are useful for molecular genetic analyses of wild animal populations. However, the low DNA content of such samples makes DNA amplification difficult, and there is the potential for erroneous results when one of two alleles at heterozygous microsatellite loci fails to be amplified. In this study we describe an assay designed to measure the amount of amplifiable nuclear DNA in low DNA concentration extracts from noninvasive samples. We describe the range of DNA amounts obtained from chimpanzee faeces and shed hair samples and formulate a new efficient approach for accurate microsatellite genotyping. Prescreening of extracts for DNA quantity is recommended for sorting of samples for likely success and reliability. Repetition of results remains extensive for analysis of microsatellite amplifications beginning from low starting amounts of DNA, but is reduced for those with higher DNA content.

Osteoporosis and apolipoprotein E genotype in older adults: the Rancho Bernardo study.

Recent studies reported an association between apolipoprotein E (ApoE) 4 and osteoporosis. We examined the association of ApoE 4 genotype with bone mineral density (BMD), bone loss and fracture risk in 596 men and 332 community-dwelling women aged 45-95 years. Women were postmenopausal and not using estrogen. At the baseline visit, BMD was measured at the ultradistal and midshaft radius using single photon densitometry, and at the hip and lumbar spine using dual-energy X-ray absorptiometry. Hip and lumbar spine BMD levels were remeasured 4 years later. Self-reported fractures were confirmed by radiology reports in 95% of cases. ApoE allele distribution did not vary by age; 25% of men and 20% of women had one ApoE 4 allele. There were no differences in BMD at the lumbar spine, total hip, ultradistal or midshaft radius in men or women with the ApoE 4 allele compared with men or women without the ApoE 4 allele. After an average 4 year interval, there were also no differences in the annualized percent change in BMD at the hip or lumbar spine in men or women with or without an ApoE 4 allele. One or more clinical fractures were reported by 55 men and 109 women. Fewer, not more, clinical fractures were reported in men and women with an ApoE 4 allele; these differences were not statistically significant (p = 0.21 and p = 0.62, respectively). These data do not support the hypotheses that there is an association between ApoE genotype and BMD, bone loss or osteoporotic fractures in older community-dwelling men or women.

Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time.

The isolation of phylogenetically distinct primate immunodeficiency viruses from at least seven wild-born, captive chimpanzees indicates that viruses closely related to HIV-1 may be endemic in some wild chimpanzee populations. The search for the chimpanzee population or populations harbouring these viruses is therefore on. This paper attempts to answer the question of whether or not such populations of chimpanzees are likely to exist at all, and, if so, where they are likely to be found. We summarize what is known about gene flow in wild populations of chimpanzees, both between major phylogeographical subdivisions of the species, and within these subdivisions. Our analysis indicates that hitherto undocumented reproductively isolated chimpanzee populations may in fact exist. This conclusion is based on the observation that, despite limited geographical sampling and limited numbers of genetic loci, conventional notions of the nature and extent of chimpanzee gene flow have recently been substantially revised. Molecular genetic studies using mitochondrial DNA sequences and hypervariable nuclear microsatellite markers have indicated the existence of heretofore undocumented barriers to chimpanzee gene flow. These studies have identified at least one population of chimpanzees genetically distinct enough to be classified into a new subspecies (Pan troglodytes vellerosus). At the same time, they have called into question the long-accepted genetic distinction between eastern chimpanzees (Pan troglodytes schweinfurthii) and western equatorial chimpanzees (Pan troglodytes troglodytes). The same studies have further indicated that gene flow between local populations is more extensive than was previously thought, and follows patterns sometimes inconsistent with those documented through direct behavioural observation. Given the apparently incomplete nature of the current understanding of chimpanzee gene flow in equatorial Africa, it seems reasonable to speculate that a chimpanzee population or populations may exist which both harbour the putative HIV-1 ancestor, and which have remained reproductively isolated from other chimpanzee populations over the time-scale relevant to the evolution of the SIVcpz-HIV-1 complex of viruses. Continued extensive sampling of wild chimpanzee populations, both for their genes and their viruses, should be performed quickly considering the high probability of extinction that many wild chimpanzee populations face today. The history of human-chimpanzee contacts is discussed.

Genome screen for quantitative trait loci underlying normal variation in femoral structure.

Femoral structure contributes to bone strength at the proximal femur and predicts hip fracture risk independently of bone mass. Quantitative components of femoral structure are highly heritable traits. To identify genetic loci underlying variation in these structural phenotypes, we conducted an autosomal genome screen in 309 white sister pairs. Seven structural variables were measured from femoral radiographs and used in multipoint sib-pair linkage analyses. Three chromosomal regions were identified with significant evidence of linkage (log10 of the odds ratio [LOD] > 3.6) to at least one femoral structure phenotype. The maximum LOD score of 4.3 was obtained for femur neck axis length on chromosome 5q. Evidence of linkage to chromosome 4q was found with both femur neck axis length (LOD = 3.9) and midfemur width (LOD = 3.5). Significant evidence of linkage also was found to chromosome 17q, with a LOD score of 3.6 for femur head width. Two additional chromosomal regions 3q and 19p gave suggestive (LOD > 2.2) evidence of linkage with at least two of the structure phenotypes. Chromosome 3 showed evidence of linkage with pelvic axis length (LOD = 3.1), midfemur width (LOD = 2.8), and femur head width (LOD = 2.3), spanning a broad (60 cm) region of chromosome 3q. Linkage to chromosome 19 was supported by two phenotypes, femur neck axis length (LOD = 2.8) and femur head width (LOD = 2.8). This study is the first genome screen for loci underlying variation in femoral structure and represents an important step toward identifying genes contributing to the risk of osteoporotic hip fracture in the general population.

Association between the T29-->C polymorphism in the transforming growth factor beta1 gene and breast cancer among elderly white women: The Study of Osteoporotic Fractures.

CONTEXT: Transgenic animal experiments suggest that increased expression of transforming growth factor beta1 (TGF-beta1) is protective against early tumor development, particularly in breast cancer. A T-->C (thymine to cytosine) transition in the 29th nucleotide in the coding sequence results in a leucine to proline substitution at the 10th amino acid and is associated with increased serum levels of TGF-beta1. OBJECTIVE: To determine whether an association exists between this TGF-beta1 polymorphism and breast cancer risk. DESIGN, SETTING, AND PARTICIPANTS: The Study of Osteoporotic Fractures, a prospective cohort study of white, community-dwelling women aged 65 years or older who were recruited at 4 US centers between 1986 and 1988. Three thousand seventy-five women who provided sufficient clinical information, buffy coat samples, and adequate consent for genotyping are included in this analysis. MAIN OUTCOME MEASURE: Breast cancer cases during a mean (SD) follow-up of 9.3 (1.9) years, verified by medical chart review and compared by genotype. RESULTS: Risk of breast cancer was similar in the 1124 women with the T/T genotype (56 cases; 5.4 per 1000 person-years) and the 1493 women with the T/C genotype (80 cases; 5.8 per 1000 person-years) but was significantly lower (P =.01) in the 458 women with the C/C genotype (10 cases; 2.3 per 1000 person-years). In analyses that adjusted for age, age at menarche, age at menopause, estrogen use, parity, body mass index, and bone mineral density, women with the C/C genotype had a significantly lower risk of developing breast cancer compared with women with the T/T or T/C genotype (hazard ratio [HR], 0.36; 95% confidence interval [CI], 0.17-0.75). There was no significant difference between the risk for women with the T/C genotype compared with women with the T/T genotype (adjusted HR, 1.04; 95% CI, 0.73-1.48). CONCLUSIONS: Our findings suggest that TGF-beta1 genotype is associated with risk of breast cancer in white women aged 65 years or older. Because the T allele is the common variant and confers an increased risk, it may be associated with a large proportion of breast cancer cases.

A quantitative trait locus influencing estrogen levels maps to a region homologous to human chromosome 20.

Estrogen, a steroid hormone, regulates reproduction and has been implicated in several diseases. We performed a genome-wide scan using multipoint linkage analysis implemented in a general pedigree-based variance component approach to identify genes with measurable effects on variation in estrogen levels in baboons. A microsatellite polymorphism, D20S171, located on human chromosome 20q13.11, showed strong evidence of linkage with a LOD score of 3.06 (P = 0.00009). This region contains several potential candidate genes including melanocortin 3 receptor (MC3R), cytochrome P-450 subfamily XXIV (CYP24), and breast carcinoma amplified sequence (BCAS1). This is the first evidence of a quantitative trait locus with a significant effect on estrogen.

Genome screen for QTLs contributing to normal variation in bone mineral density and osteoporosis.

A major determinant of the risk for osteoporosis is peak bone mineral density (BMD), which is largely determined by genetic factors. We recently reported linkage of peak BMD in a large sample of healthy sister pairs to chromosome 11q12-13. To identify additional loci underlying normal variations in peak BMD, we conducted an autosomal genome screen in 429 Caucasian sister pairs. Multipoint LOD scores were computed for BMD at four skeletal sites. Chromosomal regions with LOD scores above 1.85 were further pursued in an expanded sample of 595 sister pairs (464 Caucasians and 131 African-Americans). The highest LOD score attained in the expanded sample was 3.86 at chromosome 1q21-23 with lumbar spine BMD. Chromosome 5q33-35 gave a LOD score of 2.23 with femoral neck BMD. At chromosome 6p11-12, the 464 Caucasian pairs achieved a LOD score of 2.13 with lumbar spine BMD. Markers within the 11q12-13 region continued to support linkage to femoral neck BMD, although the peak LOD score was decreased to 2.16 in the sample of 595 sibling pairs. Our study is the largest genome screen to date for genes underlying variations in peak BMD and represents an important step toward identifying genes contributing to osteoporosis in the general population.

A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms.

A first-generation genetic linkage map of the baboon (Papio hamadryas) genome was developed for use in biomedical and evolutionary genetics. Pedigreed baboons (n = 694) were selected from the breeding colony maintained by the Southwest Foundation for Biomedical Research. To facilitate comparison with the human genome, the baboon linkage map consists primarily of human microsatellite loci amplified using published human PCR primers. Genotypes for 325 human microsatellites and 6 novel baboon microsatellites were used in linkage analyses performed with the MultiMap expert system. The resulting sex-averaged meiotic recombination map covers all 20 baboon autosomes, with average spacing among loci of 7.2 cM. Direct comparison among homologous (orthologous) loci reveals that, for 7 human autosomes, locus order is conserved between humans and baboons. For the other 15 autosomes, one or more rearrangements distinguish the two genomes. The total centimorgan distances among homologous markers are 28.0% longer in the human genome than in the baboon, suggesting that rates of recombination may be higher in humans. This baboon linkage map is the first reported for any nonhuman primate species and creates opportunities for mapping quantitative trait loci in baboons, as well as for comparative evolutionary analyses of genome structure.