A clone-free,single molecule map of the domestic cow (Bos taurus) genome

Background

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.

Results

The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).

Conclusion

Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI’s current designation of UMD3.1 sequence assembly as the “reference assembly” and the Btau4.6 as the “alternate assembly.” The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1823-7) contains supplementary material, which is available to authorized users.     

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.     

The characteristics of the reproductive capacity of hybrids of banteng (Bos (Bibos) javanicus d'Alton) with the domestic cow (Bos (Bos) primigenius taurus)]

The hybrid progeny of F1 produced by crossing of banteng and domestic cow is characterized by absolute sterility of the male line and fertility of the female line. The crossbred males become fertile in further progenies while crossing cross-females with males of initial forms. Successful use of inter-subgenetic hybrids of banteng and domestic cow in selection work is hindered by pathological deviations in their genitals structure as well as frequent deaths of the embryos and foetus in hybrid cows at the different stages of embryogenesis. It is suggested that those deviations (both in cow and in bulls) are caused mainly by genetic and immunological factors and are determined to a greater extent by combination of parental couples.     

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.     

Rumen ciliates of domestic cattle (Bos taurus taurus) in Kastamonu,Turkey, with the description of a new species

Species composition and distribution of ciliates were investigated in the rumen contents of 25 domestic cattle (Bos taurus taurus L.) living in Kastamonu, Turkey. Forty-seven species and 37 morphotypes representing 15 genera were identified. Of them, a new species of Ostracodinium was recognized and described as Ostracodinium anatolicum n. sp. This new species has two caudal lobes. The dorsal lobe is small and rounded and the ventral lobe is triangular shaped and bent toward the dorsal side like a thick hook. Furthermore, the anterior end of the macronucleus (1/5 of the length) is bent toward the left like a hook. The density of rumen ciliates in cattle was 96.8 ± 43.3 × 10⁴ cells mL⁻¹ and the mean number of ciliate species per host was 14.2 ± 4.4. Entodinium longinucleatum, E. nanellum, E. simulans and Isotricha prostoma were the most abundant species, each with a prevalence of 88%. Entodinium chatterjeei, E. bifidum m. monospinosum, Hsiungia triciliata, Oligoisotricha bubali, Ostracodinium dogieli, O. mammosum and O. munham are new host records for cattle from Turkey.     

Cerebral ventricles of the Friesian cow (Bos taurus L.). Conformation, relations and stereotaxic topography

Six heifers, aged 8-10 months, and 4 cows, aged 4-12 years, were used for studying the conformation of the cerebral ventricles on mouldings, and the topography on scanographs and frozen cuts. The morphologic changes with age concern the height of the 3rd ventricle, the extension of the pellucid septum and the stereotaxic topography. The stress is put on the variability of the volume of the lateral ventricles and the permanence of a vast and patent recessus olfactorius, with easy external landmarks.     

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.     

Interactions between red-billed oxpeckers, Buphagus erythrorhynchus, and domestic cattle, Bos taurus, in Zimbabwe

Many apparent interspecific mutualisms are poorly understood. Although theory has focused on the various evolutionary problems peculiar to mutualism, especially the need to identify mechanisms that protect a mutualism from cheating or exploitation, there are relatively few quantified examples of how organisms actually interact. Oxpeckers are believed to benefit their mammalian hosts by reducing tick loads, an assumption based on the fact that the birds include ticks in their diet. I watched red-billed oxpeckers foraging on domestic cattle in the Limpopo Valley between August 1996 and September 1997. From focal watches of 41 individually colour-ringed oxpeckers, I found that birds fed mainly on wounds, in ears and by 'scissoring' with the bill (a distinctive feeding technique). Observable tick feeding represented a very small percentage of their foraging time. Based on oxpecker behaviour at feeding sites, blood from open wounds appeared to be the favoured food: oxpeckers displaced each other significantly more, and were significantly less likely to be deterred by the cows' attempts to remove them, when feeding on a wound than at other feeding sites. The preference for blood, the inability of cows to prevent oxpeckers feeding on blood and the relatively small amount of visible tick feeding suggest that, certainly for cattle, oxpeckers may not be beneficial. However, as cows have not coevolved with oxpeckers, these results may not be representative of oxpecker relations with native African mammalian hosts. Copyright 1999 The Association for the Study of Animal Behaviour.     

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.     

Ciliated protozoa in the rumen of Turkish domestic cattle (Bos taurus L.)

ABSTRACT. Rumen Contents obtained from 28 domesticated cattle ( Bos taurus L.) slaughtered at abatoirs near Izmir, Turkey were surveyed for ciliate protozoa. Protozoa are known to make an appreciable contribution to ruminal fiber digestion in many different geographical areas; however, little if any Information is available on their occurrence in Turkish cattle. As a result of our survey, 13 genera including 52 species were identified. Nine of the species were further divided into 36 forma. The average ciliate density in our cattle (52.44 X 10⁴/ml) was higher than that of Turkish domestic sheep and other domestic cattle reported previously from different geographical areas. Entodinium basoglui, Entodinium williamsi f. williamsi, E. williamsi f. turcicum, E. dalli f. rudidorsospinatum, Entodinium imai, Entodinium oektemae, Eudiplodinium dehorityi, Epidinium graini, Ophryoscolex purkynjei f. bifidobicinctus , and Ophryoscolex purkynjei f. bifidoquadricinctus have previously been reported from Turkey and appear to be endemic. All of the remaining species represent a new host record for domestic Turkish cattle. This study also reports for the second time the presence of Entodinium constrictum in herbivorous mammals, and is the first record of its occurrence in domesticated cattle.     

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.     

Synaptonemal complex analysis of the Holstein-Friesian, Piemontese and Simmental breeds of Bos taurus taurus

The synaptonemal complex (SC) of specimens of Bos taurus taurus from the Holstein-Friesian, Piemontese, and Simmental breeds, was analysed. The analysis included quantification of the frequency of various types of abnormalities in the SC, and the frequency of cells with SC abnormalities. All animals had 29 autosomal bivalents and one sexual bivalent and the most frequently recorded abnormality was pairing failure. The number of cells with abnormalities in the Holstein-Friesian breed was 29.41%, in the Piemontese breed was 30.00% and in the Simmental breed it was 29.54%. The subspecies Bos taurus taurus had 29.63% of cells showing abnormalities with 57.33% of these abnormalities occurring in zygotene and 42.67% occurring in pachytene. Statistical analyses showed that there were no significant differences in the number of cells with SC abnormalities among the breeds studied. The frequency of cells with abnormalities, and the efect on the fertility of the Holstein-Friesian, Piemontese and Simmental breeds are discussed.     

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%).     

A polymorphism in randomly amplified DNA that differentiates the Y chromosomes of Bos indicus and Bos taurus

A small number of west African Bos taurus cattle breeds, including the N'Dama, constitute a valuable genetic resource by virtue of their ability to remain productive under trypanosomiasis challenge. However, introgression of Bos indicus genes into the trypanotolerant breeds, particularly by introduction of zebu bulls, is a threat to this resource. This work describes the characterization and cloning of a bovine randomly amplified polymorphic DNA (RAPD) that is generated in polymerase chain reaction (PCR) with the 10 base primer ILO1065 from Bos indicus male templates, but not from B. taurus male templates or female templates of either type. Male-specific sequences with homology to the RAPD also occur in B. taurus breeds. This suggests that the polymorphism may be due to base substitution(s) in an ILO1065 priming site, or insertion/deletion events either affecting priming sites or occurring between sites on the cattle Y chromosome. We have shown that cattle, whether of B. indicus or B. taurus phenotype, which possess a typically B. indicus metaphase Y chromosome on the basis of QFQ banding, have a B. indicus ILO1065-generated genotype. The ILO1065-primed RAPD can be used in a simple dot blot assay as a probe of RAPD-PCR products, to provide a convenient, reliable and effective means of detecting introgression of zebu genes in B. taurus cattle populations.     

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.     

Isolation and characterization of the Bos taurus beta-casein gene

The expression of casein genes in the mammary cells is regulated by peptide and steroid hormones. To investigate the controlling mechanisms we have isolated and characterized the bovine beta-casein gene. The gene has the size of 8.6 kb, which is 7.8 times longer than the corresponding mRNA composed of nine exons. The genomic clones include additional 8.5-kb and 4.5-kb sequences of the 5'- and 3'-flanking regions. We have determined the sequences of the 5' and 3' ends of the gene and compared them with the respective sequences of the rat beta-casein gene. Conserved sequences are identical or homologous to the potential binding sites for nuclear factors and for glucocorticoid and progesterone receptors. The regulatory region contains two different TATA signals and a repeat sequence between them.