Genome-Wide Characterization of Endogenous Retroviruses in the Bat Myotis lucifugus Reveals Recent and Diverse Infections

Bats are increasingly recognized as reservoir species for a variety of zoonotic viruses that pose severe threats to human health. While many RNA viruses have been identified in bats, little is known about bat retroviruses. Endogenous retroviruses (ERVs) represent genomic fossils of past retroviral infections and, thus, can inform us on the diversity and history of retroviruses that have infected a species lineage. Here, we took advantage of the availability of a high-quality genome assembly for the little brown bat, Myotis lucifugus, to systematically identify and analyze ERVs in this species. We mined an initial set of 362 potentially complete proviruses from the three main classes of ERVs, which were further resolved into 13 major families and 86 subfamilies by phylogenetic analysis. Consensus or representative sequences for each of the 86 subfamilies were then merged to the Repbase collection of known ERV/long terminal repeat (LTR) elements to annotate the retroviral complement of the bat genome. The results show that nearly 5% of the genome assembly is occupied by ERV-derived sequences, a quantity comparable to findings for other eutherian mammals. About one-fourth of these sequences belong to subfamilies newly identified in this study. Using two independent methods, intraelement LTR divergence and analysis of orthologous loci in two other bat species, we found that the vast majority of the potentially complete proviruses identified in M. lucifugus were integrated in the last ∼25 million years. All three major ERV classes include recently integrated proviruses, suggesting that a wide diversity of retroviruses is still circulating in Myotis bats.     

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

Background

The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a Bos taurus or Bos indicus ancestor.

Methods

Phenotype data on one or more traits and SNP genotype data for 10 181 cattle from Bos taurus, Bos indicus and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. indicus or B. taurus on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin.

Results

Fitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies.

Conclusions

The results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. indicus and B. taurus cattle. Thus, the QTL that segregate in current populations likely resulted from mutations that occurred in one of the subspecies and can have both positive and negative effects on the traits. There was no evidence that selection has increased the frequency of alleles that increase body weight.     

Estimate of the population of preantral follicles in the ovaries of Bos taurus indicus and Bos taurus taurus cattle

The number of oocytes recovered from Bos taurus indicus females subjected to ovum pick-up averaged two to four times greater compared to Bos taurus taurus females. The objective of the present study was to test the hypothesis that this difference in oocyte yield was due to more preantral follicles in the ovaries of Bos indicus females. Ovaries (n = 64) from Nelore (Bos indicus) fetuses (n = 10), heifers (n = 12), and cows (n = 10), and Aberdeen Angus (Bos taurus) fetuses (n = 10), heifers (n = 12), and cows (n = 10) were cut longitudinally into halves, fixed, and processed for histological evaluation. The number of preantral follicles was estimated by counting them in each histological section, using the oocyte nucleus as a marker and employing a correction factor. The average number of preantral follicles in the ovaries of Bos indicus vs Bos taurus was (mean ± SD) 143,929 ± 64,028 vs 285,155 ± 325,195 for fetuses, 76,851 ± 78,605 vs 109,673 ± 86,078 for heifers, and 39,438 ± 31,017 vs 89,577 ± 86,315 for cows (P > 0.05). The number of preantral follicles varied greatly among individual animals within the same category, as well as between breeds. In conclusion, we inferred that the higher oocyte yield from Bos indicus females was not due to a greater ovarian reserve of preantral follicles. Therefore, mechanisms controlling follicle development after the preantral stage likely accounted for differences between Bos indicus and Bos taurus females in number of oocytes retrieved at ovum pick-up.     

Influence of the breed of bull (Bos taurus indicus vs. Bos taurus taurus) and the breed of cow (Bos taurus indicus, Bos taurus taurus and crossbred) on the resistance of bovine embryos to heat

In vitro studies have shown that Bos taurus indicus (B. t. indicus) embryos submitted to heat shock at early stages of development are better able to survive as compared to Bos taurus taurus embryos. Embryo genotype influences resistance to heat shock thus leading to the question as to whether embryos sired by thermo-tolerant breeds exhibit the same resistance to heat shock. In the present study the influence of both oocyte and semen, on the resistance to heat shock (HS) at early stages of in vitro development, was assessed in B. t. indicus [Nelore (N) breed], B. t. taurus [Holstein (H) and Angus (A) breeds] and crossbreds. In Experiment 1, Nelore and crossbred oocytes were collected from slaughterhouse ovaries and fertilized with spermatozoa from Nelore and Angus bulls. Presumptive embryos were collected and randomly assigned to control (39 degrees C) or HS at 12, 48 or 96 h post insemination (hpi; 41 degrees C for 12h) treatments. The cleavage rates and proportion of embryos developing to the blastocyst and hatched blastocyst stages were recorded on Days 2, 8 and 10, respectively. Heat shock treatment decreased development of both Nelore and crossbred embryos. There was a significant interaction between time (12, 48 or 96 hpi) and temperature for blastocyst rates, i.e., the embryos became more thermotolerant as development proceeded. In Experiment 2, oocytes from Nelore and Holstein cows were fertilized with semen from bulls of either Nelore or Angus breeds, and subjected to 12 h HS at 96 hpi. Heat shock at 96 hpi, decreased embryo development. Additionally, cowxtreatment and bullxtreatment interactions were significant for blastocyst rates, i.e., both breed of cow and breed of bull affected the decline in blastocyst rate caused by heat shock treatment. In conclusion, the present results indicate that Nelore embryos (indicus) are more resistant to heat shock than Holstein (taurus) at early stages of in vitro development, and that embryos become more thermo-tolerant as development proceeds. Additionally, the resistance to heat shock was a result of the genetic contribution from both oocyte and spermatozoa.     

Effect of early luteolysis in progesterone-based timed AI protocols in Bos indicus, Bos indicus x Bos taurus, and Bos taurus heifers

The objective of this study was to evaluate the effects of treatment with an intravaginal progesterone-releasing device (CIDR) and estradiol benzoate (EB) on follicular dynamics in Bos indicus (n=23), Bos taurus (n=25), and cross-bred (n=23) heifers. To assess the influence of reduced serum progesterone concentrations during 8 days of treatment with a progesterone-releasing device on follicular dynamics, half of the heifers received PGF at CIDR insertion (Day 0; 3 x 2 factorial design). Mean (+/-S.E.M.) serum progesterone concentrations during CIDR treatment varied (P<0.05) among genetic groups: B. indicus (5.4+/-0.1 ng/mL), B. taurus (3.3+/-0.0 ng/mL), and cross-bred (4.3+/-0.1 ng/mL). Maximum diameter of the dominant follicle (DF) was smaller (P<0.01) in B. indicus heifers (9.5+/-0.5 mm) than in cross-bred (12.3+/-0.4 mm) or B. taurus heifers (11.6+/-0.5 mm). B. indicus experienced lower (P<0.01) ovulation rate (39.1%) than did B. taurus (72.7%) and cross-bred (84.0%). Heifers treated with PGF on Day 0 had lower (P<0.05) serum progesterone concentrations during progesterone treatment. The PGF treatment on Day 0 increased (P<0.01) the diameter of the DF (11.9+/-0.4 mm vs. 10.5+/-0.4 mm). Moreover, greater (P=0.02) ovulation rates (78.8 vs. 54.0%) occurred in heifers treated with PGF on Day 0. In summary, B. indicus heifers had greater serum progesterone concentrations, smaller DF diameter, and a lower ovulation rate compared to B. taurus heifers. Prostaglandin treatment on the day of CIDR insertion reduced serum progesterone during treatment, and resulted in increased maximum DF diameter and ovulation rate.     

Plasma progesterone concentration in Bos taurus and Bos indicus heifers

Progesterone concentrations were determined by radioimmunoassay in the plasma of heifers of German Brown Swiss, Holstein-Friesian and White Fulani cattle during two consecutive estrous cycles in the dry and wet seasons in a tropical climate. Seasonal differences in the levels were not significant but peak levels were significantly higher in the $\text{Bos}$$\text{taurus}$ than in the $\text{Bos}$$\text{indicus}$ heifers. The low levels at estrus and the gradual rise five days after estrus were similar among the heifers. The levels on the 1st and 2nd days preceding estrus were significantly higher in the $\text{Bos}$$\text{taurus}$ than in the $\text{Bos}$$\text{indicus}$ heifers, and suggest a possible tendency for the former to be more susceptible to infertility arising from high progesterone levels 1 and 2 days preceding estrus and insemination. The genital tract and ovaries at the mature luteal phase were generally smaller in the $\text{Bos}$$\text{indicus}$ than in the $\text{Bos}$$\text{taurus}$ heifers.     

Response of prepubertal Bos taurus and Bos indicus x Bos taurus heifers to melengestrol acetate with or without gonadotropin-releasing hormone

The effectiveness of treatments to induce estrus in prepubertal beef heifers was evaluated. Angus x Hereford (n = 148) and Brahman x Hereford (n = 148) heifers were sorted after weaning by body weight into light and heavy weight blocks. Heifers were assigned to diets, calculated to reach a target weight of 55% or 65% of their projected mature weight by the start of breeding. Cyclicity was determined after a 160-d observation period and from concentrations of progesterone in serum determined 10 d before and on the day that treatments began to induce puberty. The remaining nonpubertal heifers, with concentrations of progesterone in serum of less than 1 ng/ml (0 or 10 d before treatment), were assigned randomly within breed and nutrition group to either a melengestrol acetate + saline (MGA+S) or MGA + gonadotropin-releasing hormone (MGA+GnRH) treatment. Prepubertal Angus x Hereford heifers (n = 11) and Brahman x Hereford heifers (n = 49) were fed 0.5 mg MGA for 7 d. Forty-eight hours after MGA, heifers were injected with 500 ug s.c. GnRH or 5 ml of saline. Blood samples were collected from all prepubertal heifers every 3 d after GnRH or saline for 30 d. There was no difference between treatments in the proportion of heifers that exhibited estrus by Day 7 after treatment. However, a larger (P<0.05) proportion of MGA+S-treated heifers exhibited estrus within 14 d after treatment than MGA+GnRH-treated heifers (87 vs 63%). Among heifers that exhibited estrus during that time period, the proportion with increased progesterone was higher (P<0.10) for the MGA+GnRH group than for the MGA+S group (71 vs 41%, Day 7; 79 vs 54%, Day 14). There was no difference in conception rate at first service between treatment groups. Thirty-seven and 53%, respectively, of the MGA+S and MGA+GnRH-treated heifers had short estrous cycles after treatment, and 44 and 50%, respectively, of those short cycles were repeated. Pregnancy rates at the end of 45 d were numerically higher for MGA+S heifers than for MGA+GnRH treated counterparts (63 vs 53%).     

Endogenous Retroviruses in Domestic Animals

Endogenous retroviruses (ERVs) are genomic elements that are present in a wide range of vertebrates. Although the study of ERVs has been carried out mainly in humans and model organisms, recently, domestic animals have become important, and some species have begun to be analyzed to gain further insight into ERVs. Due to the availability of complete genomes and the development of new computer tools, ERVs can now be analyzed from a genome-wide viewpoint. In addition, more experimental work is being carried out to analyze the distribution, expression and interplay of ERVs within a host genome. Cats, cattle, chicken, dogs, horses, pigs and sheep have been scrutinized in this manner, all of which are interesting species in health and economic terms. Furthermore, several studies have noted differences in the number of endogenous retroviruses and in the variability of these elements among different breeds, as well as their expression in different tissues and the effects of their locations, which, in some cases, are near genes. These findings suggest a complex, intriguing relationship between ERVs and host genomes. In this review, we summarize the most important in silico and experimental findings, discuss their implications and attempt to predict future directions for the study of these genomic elements.     

A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle

A number of cattle breeds have become highly specialized for milk or beef production, following strong artificial selection for these traits. In this paper, we compare allele frequencies from 9323 single nucleotide polymorphism (SNP) markers genotyped in dairy and beef cattle breeds averaged in sliding windows across the genome, with the aim of identifying divergently selected regions of the genome between the production types. The value of the method for identifying selection signatures was validated by four sources of evidence. First, differences in allele frequencies between dairy and beef cattle at individual SNPs were correlated with the effects of those SNPs on production traits. Secondly, large differences in allele frequencies generally occurred in the same location for two independent data sets (correlation 0.45) between sliding window averages. Thirdly, the largest differences in sliding window average difference in allele frequencies were found on chromosome 20 in the region of the growth hormone receptor gene, which carries a mutation known to have an effect on milk production traits in a number of dairy populations. Finally, for the chromosome tested, the location of selection signatures between dairy and beef cattle was correlated with the location of selection signatures within dairy cattle.     

Assessing sex-drive in young Bos taurus bulls

Objectives in this study were to determine the accuracy of different methods of evaluating libido score (L), service rate (SR) and reaction time to service (RTS) in yearling Bos taurus bulls. Using restrained, non-estrus females, 26 yearling Bos taurus bulls were evaluated a total of eight times (four sessions, two tests per session) over 2 consecutive months for L, SR, and RTS. Individual bull variation influenced both L (P<0.0001) and SR (P<0.003). Repeatability was moderate for L (R=0.64) and low for both SR (R=0.12) and RTS (R=0.04). Under the conditions of this study and characteristics of these tests, variance was reduced to 69-73% for L and 26-23% for SR with four to eight repetitions, respectively. Bulls that scored highly in the first session, however, tended to score highly throughout. Although, three bulls did not serve in any test, RTS was independent of effects. However, the tendency of RTS to decrease, and for L and SR to both increase with consecutive tests, suggests influences other than genetic, such as learning and/or environmental factors. These tendencies were most evident in bulls which obtained low L scores at the first session. It was concluded that, despite the important degree of individual variability observed in L and SR, accurate quantitative evaluation of the sex-drive in young Bos taurus beef bulls would benefit from use of test procedures of greater repeatability.     

Detection of genome specific monomorphic loci in Bos taurus and Bubalus bubalis with oligodeoxyribonucleotide probe

A synthetic oligodeoxyribonucleotide probe (OAT36) comprising nine repeats of 5'GACA 3′ and several enzymes were used to analyse cow, (Bos taurus) and buffalo (Bubalus bubalis) genomes and a number of monomorphic loci were detected in both the species. Different animals from the same species showed an almost ‘similar’ monomorphic hybridization pattern but animals from two separate species showed a different ‘genome specific’ pattern. The overall hybridization with any enzyme and probe combination was found to be unique to one species. This forms the basis of genome specific hybridization which is substantiated by our zoo-blot hybridization studies. The evolutionary aspect of these loci in the context of sequence polymorphisms is discussed.     

Fertility of Bos indicus and Bos indicus x Bos taurus crossbreed cattle after estrus synchronization

Ninety-five cows (79 Boran and 16 Boran-Brahman crossbreeds) and 107 heifers (55 Boran and 52 Boran x Friesian F1 crossbreeds) were used to determine estrus response, estrus response interval and pregnancy rate following synchronization with prostaglandin (PGF(2)alpha), a progesterone-releasing intravaginal device (PRID) and Synchro-mate B (SMB). The proportion of cattle responding to synchronization treatment was 62.5, 43.5 and 57.7% for cows and 85.7, 68.0 and 81.5% for heifers using PGF(2)alpha, PRID and SMB, respectively. The overall mean response was 59 and 81.8% for cows and heifers, respectively. The estrus response of the control animals over a 45-d breeding period was 72.7 and 90% for cows and heifers, respectively. The estrus response interval for cows was 31.8, 22.1 and 18.0 h and it was 51.1, 38.0 and 21.6 h for heifers with PGF(2)alpha, PRID and SMB treatment, respectively. Mean pregnancy rate for cows was 50.0, 34.8, 46.2 and 68.8% and for heifers it was 60.7, 40.0, 55.6 and 77.8% in the PGF(2)alpha, PRID, SMB and control groups, respectively. Based on these findings, it was concluded that both PGF(2)alpha and SMB produce a satisfactory estrus response and pregnancy rate in the cattle studied.     

Differences of skin morphology in Bos indicus,Bos taurus,and their crossbreds

Cutaneous evaporation is the main avenue by which cattle dissipate heat via the involvement of sweat glands and other skin components. The difference in skin morphology between B. indicus and B. taurus has been recognized, as well as differences in their ability to tolerate heat. The objective of this study was to compare skin morphology between B. indicus, B. taurus, and their crossbreds. Skin samples of Sahiwal (B. indicus) (n?=?10, reddish brown skin) and Holstein Friesian (HF) (B. taurus) (n?=?10, black and white skin) and crossbred of HF75% (n?=?10, black and white skin) and HF87.5 % (n?=?10, black and white skin) were biopsied for histological study, followed by measurement of skin components. The results indicated that breed significantly affected sweat gland morphology. The shape of the sweat gland, as indicated by the ratio of length/diameter, in Sahiwal was baggier in shape compared to HF (5.99 and 9.52) while values for crossbreds were intermediate (7.82, 8.45). The density and volume of sweat glands in Sahiwal (1,058 glands/cm²; 1.60 μ³?×?10^?6) were higher than in HF (920 glands/cm²; 0.51 μ³x10^?6) and crossbreds, both HF 75 % (709 glands/cm²; 0.68 μ³?×?10^?6) and HF 87.5 % (691 glands/cm²; 0.61 μ³?×?10^?6) respectively. However, capillary surface area was greater for HF (2.07 cm²) compared to Sahiwal (1.79 cm²); accordingly, the lower genetic fraction of HF in crossbred cattle showed less capillary surface area (1.83 and 1.9 cm² for HF75% and HF87.5 %) (P?<?0.01). Nerve density was not significantly different between Sahiwal and HF but was higher in the crossbred (P?<?0.01) cattle. Moreover, the effect of skin color (black and white) was evaluated and it was found that there was an interaction (P?<?0.01) between breed and skin color on the skin components. This study reveals that there are differences in skin morphology among B. indicus, B. taurus and their crossbreds, with these differences being more or less related to the genetic fraction of HF. This may imply that capability for cutaneous evaporative heat loss and tolerance to heat in crossbred cattle could be related to skin morphology.