Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).

A primary challenge in the analysis of free-ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome-wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third-degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity-by-descent-based methods for pedigree reconstruction and shared segment-based inference of more distant relatedness. We compared the genotype-based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth-degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low-coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

Production of Transgenic Mice by Pronuclear Microinjection.

Pronuclear microinjection remains the most widely used method for the germline modification of mice and other species. The method is conceptually quite simple and at least in rodents can produce transgenic offspring with relatively high efficiency. Here, we describe the various components of the production of transgenic mice including a detailed list of materials and equipment. We outline in detail the preparation of animals, the retrieval, culture and transfer of embryos, the preparation of DNA, and the microinjection process. We have added a substantial collection of notes with helpful suggestions that reflect the many years of experience we have using this technology and our continuing efforts to improve animal welfare and the efficiency of producing transgenics.

SNP-based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen-free rhesus macaque (Macaca mulatta) populations.

BACKGROUND: The rhesus macaque is an important biomedical model organism, and the Tulane National Primate Research Center (TNPRC) has one of the largest rhesus macaque breeding colonies in the United States. METHODS: SNP profiles from 3266 rhesus macaques were used to examine the TNPRC colony genetic composition over time and across conventional or SPF animals of Chinese and Indian ancestry. RESULTS: Chinese origin animals were the least genetically diverse and the most inbred; however, since their derivation from their conventional forebearers, neither the Chinese nor the Indian SPF animals exhibit any significant loss of genetic diversity or differentiation. CONCLUSIONS: The TNPRC colony managers have successfully minimized loss in genetic variation across generations. Although founder effects and bottlenecks among the Indian animals have been successfully curtailed, the Chinese subpopulation still show some influences from these events.

The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences.

Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate in biomedical research, have the largest natural geographic distribution of any nonhuman primate, and have been the focus of much evolutionary and behavioral investigation. Consequently, rhesus macaques are one of the most thoroughly studied nonhuman primate species. However, little is known about genome-wide genetic variation in this species. A detailed understanding of extant genomic variation among rhesus macaques has implications for the use of this species as a model for studies of human health and disease, as well as for evolutionary population genomics. Whole-genome sequencing analysis of 133 rhesus macaques revealed more than 43.7 million single-nucleotide variants, including thousands predicted to alter protein sequences, transcript splicing, and transcription factor binding sites. Rhesus macaques exhibit 2.5-fold higher overall nucleotide diversity and slightly elevated putative functional variation compared with humans. This functional variation in macaques provides opportunities for analyses of coding and noncoding variation, and its cellular consequences. Despite modestly higher levels of nonsynonymous variation in the macaques, the estimated distribution of fitness effects and the ratio of nonsynonymous to synonymous variants suggest that purifying selection has had stronger effects in rhesus macaques than in humans. Demographic reconstructions indicate this species has experienced a consistently large but fluctuating population size. Overall, the results presented here provide new insights into the population genomics of nonhuman primates and expand genomic information directly relevant to primate models of human disease.

Development and validation of a SNP-based assay for inferring the genetic ancestry of rhesus macaques (Macaca mulatta).

Rhesus macaques (Macaca mulatta) are an important primate model species in several areas of biomedical research. The wide geographic distribution of this species has led to significant genetic differentiation among local and regional populations. These regional differences can be important factors in the selection of the most appropriate subjects for particular research studies, as animals from different populations can respond differently to the same experimental treatment. Consequently, it is valuable to confirm the ancestry of individual rhesus monkeys from geographically distinct populations. Using DNA samples obtained from rhesus macaques from six National Primate Research Centers, we tested a set of 384 potential ancestry informative single nucleotide polymorphisms (SNPs) and identified a final panel of 91 SNPs that can reliably distinguish Indian-origin from Chinese-origin rhesus monkeys. This genetic test can be used to determine the ancestral origin of animals and to detect individuals that are hybrids between these two regional populations. To demonstrate use of the SNP panel, we investigated the ancestry of 480 animals from the Yerkes NPRC (YNPRC) for which the colony records were insufficient to clearly establish ancestry. Three of the YNPRC animals tested were determined to be hybrids. This SNP ancestry tool will be useful to researchers, colony managers, and others who wish to evaluate the ancestral origin of individual rhesus macaques, and therefore will facilitate more effective and efficient use of these animals in biomedical research.

An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta).

We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller & Goodnight [1989] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management.

Reproductive efficiency of captive Chinese- and Indian-origin rhesus macaque (Macaca mulatta) females.

Reproductive and survival records (n=2,913) from 313 Chinese-origin and 365 Indian-derived rhesus macaques at the Tulane National Primate Research Center (TNPRC) spanning three generations were studied. Least-squares analysis of variance procedures were used to compare reproductive and infant survival traits while proportional hazards regression procedures were used to study female age at death, number of infants born per female, and time from last birth to death. Chinese females were older at first parturition than Indian females because they were older when placed with males, but the two subspecies had similar first postpartum birth interval (1st PPBI) and lifetime postpartum birth interval (LPPBI). Females that gave birth to stillborn infants had shorter first postpartum birth intervals (1st PPBI) than females giving birth to live infants. Postpartum birth intervals decreased in females from age 3 to 12 but then increased again with advancing age. Chinese infants had a greater survival rate than Indian infants at 30 days, 6 months, and 1 year of age. Five hundred and forty-three females (80.01%) had uncensored, or true records for age at death, number of infants born per female, and time from the birth until death whereas 135 females (19.91%) had censored records for these traits. Low- and high-uncensored observations for age at death were 3 and 26 years for Chinese, and 3 and 23 years for Indian females. Uncensored number of infants born per female ranged from 1 to 15 for Chinese females and 1 to 18 for Indian females. Each of these traits was significantly influenced by the origin×generation interaction in the proportional hazards regression analyses, indicating that probabilities associated with age at death, number of infants born per female, and time from last birth to death for Chinese and Indian females did not rank the same across generations.

Estimates of heritability for reproductive traits in captive rhesus macaque females.

Records from a colony of captive Indian rhesus macaques (Macaca mulatta) were used to estimate heritability for a number of reproductive traits. Records were based on a total of 7,816 births by 1,901 females from 1979 to 2007. Heritability was estimated with a linear animal model using a multiple trait derivative free REML set of programs. Because no male parents were identified, the numerator relationship matrix contained female kinships established over six generations. Reproductive traits included female age at the birth of the first, second and last infant, age at death, inter-birth intervals, number of infants born per female and infant survival. Heritability for each trait was estimated as the ratio of the additive genetic variance to phenotypic variance adjusted for significant fixed effects. Estimates of heritability for early reproduction ranged from 0.000+/-0.072 for birth interval after the first reproduction to 0.171+/-0.062 for age of female at the first infant. Higher estimates of heritability were found for female longevity [0.325+/-0.143] and for productivity of deceased females born before 1991 [0.221+/-0.138]. Heritability for infant survival ranged from 0.061+/-0.018 for survival from 30 days to 1 year to 0.290+/-0.050 for survival from birth to 30 days when adjusted to an underlying normal distribution. Eight of the 13 estimates of heritability for reproductive traits in this study were different from zero [P<0.05]. Generally, heritability estimates reported in this study for reproductive traits of captive rhesus macaque females are similar to those reported in the literature for free-ranging rhesus macaque females and for similar reproductive traits of other species. These estimates of heritability for reproductive traits appear to be among the first for a relatively large colony of captive rhesus macaque females.

Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs).

The National Primate Research Centers (NPRCs) established Working Groups (WGs) for developing resources and mechanisms to facilitate collaborations among non-human primate (NHP) researchers. Here we report the progress of the Genome Banking and the Genetics and Genomics WGs in developing resources to advance the exchange, analysis and comparison of NHP genetic and genomic data across the NPRCs. The Genome Banking WG has established a National NHP DNA bank comprising 1250 DNA samples from unrelated animals and family trios from the 10 NHP species housed within the NPRC system. The Genetics and Genomics WG is developing SNP arrays that will provide a uniform, highly informative, efficient and low-cost method for rhesus and long-tailed macaque genotyping across the eight NPRCs. This WG is also establishing a Biomedical Informatics Research Network-based portal for shared bioinformatics resources including vital statistics, genotype and population data and information on the National NHP DNA bank.

Resource brief: the National Non-Human Primate DNA Bank.

A National Non-Human Primate (NHP) DNA bank has been established by the National Primate Research Centers and the National Center for Research Resources, NIH, providing a new resource for comparative genomic studies. The collection includes genomic DNA samples from macaques, chimpanzees, baboons, vervets, marmosets, sooty mangabeys and titi monkeys. The repository includes DNAs from 697 unrelated animals, suitable for comparing allele representation within and between species. Another 474 DNAs are derived from family-trios (dam, sire, off spring), and are useful for verifying the segregation of genetic variants. The National NHP DNA Bank includes specified holdings within each of the eight National Primate Research Centers, though detailed information on the entire collection is available through a common website.

Postthaw survival of rhesus macaque sperm: variation in the response of individual males to different freezing protocols.

This study was designed to assess the effects of various cryopreservation protocols on the postthaw survival of rhesus macaque sperm. Multiple ejaculates of five mature males were collected and frozen by each of four different methods. Cryopreservation significantly reduced motility in all samples, regardless of the method, and the response of different ejaculates of the same male to each method proved to be consistent. The freezing method was a significant factor in determining the immediate postthaw motility, although this effect disappeared after 4 hr. Moreover, there was a significant interaction between individual males and freezing method suggesting that developing a single freezing protocol that is universally suitable may be difficult.

Age as a determinant of reproductive success among captive female rhesus macaques (Macaca mulatta).

A retrospective analysis was performed on fertility outcomes among a colony of captive Indian rhesus monkeys. The analysis covered over 30 years and was based on 1443 females with a total of 11,453 pregnancies. Various determinants of fertility were assessed including birth rates, pregnancy loss, infant survival, interbirth intervals, and interval from last birth to death. Binary variables were analyzed with generalized linear models with random intercepts, while linear mixed models were used for analysis of continuous variables. Age of the dam was a significant factor in determining whether a pregnancy resulted in a birth and whether an infant survived the first 30 days with primiparous or older mothers being less likely to produce an infant surviving to that age. In contrast, sex proved to be the only significant factor in determining whether an infant lived to 1 year, with females being more likely to survive. The interval between births proved to be affected primarily by dam age, while the late death of an infant depressed the likelihood of an extended time interval between her last birth and her death. Overall, these results demonstrate that maternal age contributes significantly to a decline in fertility and older females can live relatively long periods following birth of their last infant.

Male-to-male differences in post-thaw motility of rhesus spermatozoa after cryopreservation of replicate ejaculates.

BACKGROUND: The efficiency of controlled propagation to produce rhesus monkeys of particular genotypes can be maximized by use of cryopreserved spermatozoa collected from specific males to inseminate appropriate females. But this assumes that semen from males with different genotypes can be cryopreserved with equal effectiveness. METHODS: To investigate whether spermatozoa from different Macaca mulatta males can be effectively cryopreserved when frozen under identical conditions, we collected and froze semen specimens from 13 adult, fertile males maintained at three primate research centers. RESULTS: Survival, based on post-thaw motility normalized to the pre-freeze value, was assayed within 30 minutes after thawing; it varied from 50% to 70% but declined thereafter. To examine the response of semen from individual males, we collected and froze three to six ejaculates per male from each of seven males. CONCLUSIONS: In general, semen from a given male responded reproducibly to freezing, but there were significant differences among males. The cause of these differences among M. mulatta males in post-thaw sperm survival remains unidentified.

Nuclear and cytoplasmic localization of interferon-tau in in vitro-produced bovine blastocysts.

Experiments were conducted to detect interferon-tau in bovine in vitro-derived blastocysts by transmission electron (TEM) and confocal microscopy. TEM showed the presence of IFN-tau in the cytoplasm and the nuclei of expanded blastocysts. Confocal microscopy similarly confirmed the presence of IFN-tau in the trophectoderm of blastocysts. The distribution of IFN-tau appeared variable with some cells showing strong labeling while others appeared to be devoid of the protein.

Birth of rhesus macaque (Macaca mulatta) infants after in vitro fertilization and gestation in female rhesus or pigtailed (Macaca nemestrina) macaques.

A study was conducted to assess the possibility of using pigtailed macaques (Macaca nemestrina) as recipients for rhesus macaque (Macaca mulatta) embryos. A total of 250 oocytes were collected from 11 rhesus monkeys during 12 follicular aspirations. We performed 15 embryo transfers with two embryos each into rhesus recipients, which resulted in eight pregnancies, of which two were lost during the second trimester. Among the remaining six pregnant rhesus macaques, two were carrying twins, resulting in the birth of eight infants. Twelve transfers of rhesus embryos into pigtailed macaques resulted in one pregnancy and the birth of one infant. Fetal growth and development were monitored by monthly ultrasound examinations, during which biparietal measurements were taken and compared with those derived from 22 pregnant control monkeys. In vitro fertilization-derived singletons tended to develop faster than did twins and naturally conceived control singletons during the initial months of pregnancy and weighed more at birth than did twins. There were pronounced morphologic changes in the placenta of the rhesus that developed in the female pigtailed macaque. These included an irregular shape, elevated placenta-to-birth-weight ratio, and an abnormal length and diameter of the umbilical cord. Histologic analyses of the rhesus-pigtailed placenta showed evidence of maternal-placental floor infarction and thrombosis of the spiral artery with resulting infarction of the villi. These results demonstrate that pigtailed macaques can carry rhesus fetuses to term, but further studies are necessary to determine the cause of the decreased pregnancy rates and observed placental abnormalities.

Identification of bovine and novel interferon-tau alleles in the American plains bison (Bison bison) by analysis of hybrid cattle x bison blastocysts.

The objective of this study was to generate bison x cattle hybrid embryos by in vitro fertilization, to assess their developmental potential, to determine the pattern of secretion of the embryonic signaling molecule interferon-tau (IFN-tau), and to identify novel IFN-tau mRNA polymorphism in the American plains bison. A total of 600 bovine oocytes were inseminated with frozen-thawed bison semen. Of these, 40.7% cleaved and 14.8% proceeded to the blastocyst stage. Individual blastocysts were cultured on a basement membrane (Matrigel) and their ability to attach and form outgrowths was monitored. A total of 36 blastocysts were cultured of which 22 formed outgrowths. During individual culture, medium samples were collected and their IFN-tau concentration was measured. On day 6 after onset of individual culture, attached outgrowths produced significantly more IFN-tau than unattached viable or degenerate blastocysts. At this time, female conceptuses also produced significantly more IFN-tau than their male cohorts. However, by day 12 this difference had disappeared. Total mRNA was extracted from three individual outgrowths and analyzed by RT-PCR. Subsequent sequencing of 28 clones showed several known bovine IFN-tau sequences as well as two novel sequences termed bisIFN-tau1 and 2. To determine the origin of these, DNA was extracted from bison semen and analyzed by PCR. One bovine IFN-tau sequence (bovIFN-tau1d) as well as bisIFN-tau2 and a third novel sequence bisIFN-tau3 were detected. This study demonstrates the feasibility of using hybrid embryos for the analysis of developmentally regulated gene expression in species where embryos may not be available.

Role of the mitochondrial genome in assisted reproductive technologies and embryonic stem cell-based therapeutic cloning.

Mitochondria play a pivotal role in cellular metabolism and are important determinants of embryonic development. Mitochondrial function and biogenesis rely on an intricate coordination of regulation and expression of nuclear and mitochondrial genes. For example, several nucleus-derived transcription factors, such as mitochondrial transcription factor A, are required for mitochondrial DNA replication. Mitochondrial inheritance is strictly maternal while paternally-derived mitochondria are selectively eliminated during early embryonic cell divisions. However, there are reports from animals as well as human patients that paternal mitochondria can occasionally escape elimination, which in some cases has led to severe pathologies. The resulting existence of different mitochondrial genomes within the same cell has been termed mitochondrial heteroplasmy. The increasing use of invasive techniques in assisted reproduction in humans has raised concerns that one of the outcomes of such techniques is an increase in the incidence of mitochondrial heteroplasmy. Indeed, there is evidence that heteroplasmy is a direct consequence of ooplasm transfer, a technique that was used to 'rescue' oocytes from older women by injecting ooplasm from young oocytes. Mitochondria from donor and recipient were found in varying proportions in resulting children. Heteroplasmy is also a byproduct of nuclear transfer, as has been shown in studies on cloned sheep, cattle and monkeys. As therapeutic cloning will depend on nuclear transfer into oocytes and the subsequent generation of embryonic stem cells from resulting blastocysts, the prospect of mitochondrial heteroplasmy and its potential problems necessitate further studies in this area.

Interferon-tau in bovine blastocysts following parthenogenetic activation of oocytes: pattern of secretion and polymorphism in expressed mRNA sequences.

A series of experiments were conducted to examine the pattern of production and secretion of interferon-tau (IFN-tau) by blastocysts following parthenogenetic activation of bovine oocytes. In the first experiment, 36.8, 24.1, and 33.2% of IVF-derived and parthenogenetically activated oocytes cultured in the presence or absence of a monolayer of buffalo rat liver cells, respectively, reached the blastocyst stage. Following individual culture of blastocysts, IFN-tau concentration in medium droplets was similar among the three groups, although IVF-derived blastocysts contained significantly more cells. In the second experiment, 156 IVF-derived blastocysts were sexed by PCR with 75 and 81, respectively, being male and female. IFN-tau secretion of these was compared to that of 70 parthenogenetic blastocysts. Female and parthenogenetic blastocysts produced significantly more IFN-tau than their male counterparts. In the third experiment, the ability of hatched blastocysts to form outgrowths and the pattern of their IFN-tau secretion were examined. Of the 48 IVF-derived blastocysts, 44 formed outgrowths compared to 41 of the 42 hatched parthenotes. Parthenogenetic outgrowths were significantly larger after 7 days, but this difference had disappeared after 14 days. IFN-tau secretion did not differ between the two groups. Lastly, sequence analyses of expressed mRNA from individual parthenogenetic blastocyst outgrowths showed four different transcript types which, based on their predicted amino acid sequence, belong to two subgroups, IFN-tau1 and IFN-tau3. In addition, one new transcript sequence was identified, encoding a new protein isoform.