When and how did Bos indicus introgress into Mongolian cattle?

The Mongolian cattle are one of the most widespread breeds with strictly Bos taurus morphological features in northern China. In our current study, we presented a diversity of mitochondrial DNA (mtDNA) D-loop region and Y chromosome SNP markers in 25 male and 8 female samples of Mongolian cattle from the Xinjiang Uygur autonomous region in Western China, and detected 21 B. taurus and four Bos indicus (zebu) mtDNA haplotypes. Among four B. indicus mtDNA haplotypes, two haplotypes belonged to I1 haplogroup and the remaining two haplotypes belonged to I2 haplogroup. In contrast, all 25 male Mongolian cattle samples revealed B. taurus Y chromosome haplotype and no B. indicus haplotypes were found. Historical and archeological records indicate that B. taurus was introduced to Xinjiang during the second millennium BC and B. indicus appeared in this region by the second century AD. The two types of cattle coexisted for many centuries in Xinjiang, as depicted in clay and wooden figurines unearthed in the Astana cemetery in Turfan (3rd–8th century AD). Multiple lines of evidence suggest that the earliest B. indicus introgression in the Mongolian cattle may have occurred during the 2nd–7th centuries AD through the Silk Road around the Xinjiang region. This conclusion differs from the previous hypothesis that zebu introgression to Mongolian cattle happened during the Mongol Empire era in the 13th century.     

Resynchronization with unknown pregnancy status using progestin-based timed artificial insemination protocol in beef cattle

Two experiments were designed to evaluate the use of resynchronization (RESYNCH) protocols using a progestin-based timed artificial insemination (TAI) protocol in beef cattle. In experiment 1, 475 cyclic Nelore heifers were resynchronized 22 days after the first TAI using two different inducers of new follicular wave emergence (estradiol benzoate [EB; n = 241] or GnRH [n = 234]) with the insertion of a norgestomet ear implant. At ear implant removal (7 days later), a pregnancy test was performed, and nonpregnant heifers received a dose of prostaglandin plus 0.5 mg of estradiol cypionate, with a timed insemination 48 hours later. The pregnancy rate after the first TAI was similar (P = 0.97) between treatments (EB [41.9%] vs. GnRH [41.5%]). However, EB-treated heifers (49.3%) had a greater (P = 0.04) pregnancy per AI (P/AI) after the resynchronization than the GnRH-treated heifers (37.2%). In experiment 2, the pregnancy loss in 664 zebu females (344 nonlactating cows and 320 cyclic heifers) between 30 and 60 days after resynchronization was evaluated. Females were randomly assigned to one of two groups (RESYNCH 22 days after the first TAI [n = 317] or submitted only to natural mating [NM; n = 347]). Females from the NM group were maintained with bulls from 15 to 30 days after the first TAI. The RESYNC-treated females were resynchronized 22 days after the first TAI using 1 mg of EB on the first day of the resynchronization, similar to experiment 1. No difference was found in P/AI (NM [57.1%] vs. RESYNC [61.5%]; P = 0.32) or pregnancy loss (NM [2.0%] vs. RESYNC [4.1%]; P = 0.21) after the first TAI. Moreover, the overall P/AI after the RESYNCH protocol was 47.5%. Thus, the administration of 1 mg of EB on day 22 after the first TAI, when the pregnancy status was undetermined, promotes a higher P/AI in the resynchronized TAI than the use of GnRH. Also, the administration of 1 mg of EB 22 days after the TAI did not affect the preestablished pregnancy.     

Reproductive performance of prepubertal Bos indicus heifers after progesterone-based treatments

The objective was to evaluate the effects of exogenous progesterone (P4) on reproductive performance of prepubertal Bos indicus heifers. Prepubertal Nelore heifers (n = 589; 24.0 ± 1.13 mo; 298.0 ± 1.89 kg; body condition score of 3.2 ± 0.26; mean ± SEM) were randomly assigned to receive, between experimental Days −12 and 0: no treatments (CIDR0; n = 113); a new intravaginal insert (CIDR) containing 1.9 g of P4 (CIDR1; n = 237); or a similar insert previously used three times, with each use occurring for 9 d (CIDR4; n = 239). An additional treatment group was pubertal heifers given 12.5 mg dinoprost tromethamine im on Day 0 (PGF; n = 346), and used as controls for evaluation of conception rates. On Day 0, transrectal palpation was done for uterine score evaluation (UtS; 1-3 scale), blood samples were taken for serum P4 concentrations, and follicle diameter (FD) was measured. The breeding season started on Day 1 and consisted of AI after detection of estrus between Days 1 and 45, and exposure to bulls between Days 46 and 90. There were effects of treatment (P < 0.05) on serum concentrations of P4 on Day 0 (0.37 ± 0.16, 2.31 ± 0.11, and 1.20 ± 0.11 ng/mL for CIDR0, CIDR1, and CIDR4, respectively; mean ± SEM), FD on Day 0 (9.45 ± 0.24, 9.72 ± 0.17, and 11.42 ± 0.16 mm), UtS on Day 0 (1.49 ± 0.06, 1.88 ± 0.04, and 2.24 ± 0.04), estrus detection rates at 7 d (19.5, 42.6, and 38.3%) and 45 d (52.2, 72.1, and 75.3%) of the breeding season, and on pregnancy rates at 7 d (5.3, 14.3, and 18.4%), 45 d (27.4, 39.2, and 47.7%) and 90 d (72.6, 83.5, and 83.7%) of the breeding season. Conception rate 7 d after the start of the breeding season was greater (P < 0.05) in heifers from the CIDR4 (46.8%) and PGF (43.8%) groups than in the CIDR0 (27.3%) and CIDR1 (33.7%) groups. In conclusion, exogenous P4 hastened puberty and improved pregnancy rates at the beginning of the breeding season in prepubertal Bos indicus heifers. Furthermore, previously used CIDR inserts were better than new inserts.     

Inferences of body energy reserves on conception rate of suckled Zebu beef cows subjected to timed artificial insemination followed by natural mating

The influence of body condition score (BCS), rump fat thickness (RFAT), and live weight (LW), and the changes in these parameters during the interval from 165 of prepartum (i.e., 125 days of prior gestation) to 112 postpartum on first service conception and pregnancy rates were investigated in suckled Zebu (Bos indicus) beef cows (n = 266) subjected to timed artificial insemination (TAI) followed by natural mating. The aforementioned parameters were recorded at 165 ± 14 days (mean ± standard error) prepartum (concurrent with the weaning of previous calf), at parturition, and at 42 ± 7 days (at the onset of the synchronization of ovulation protocol), 82 ± 7 days (30 days after TAI), and 112 ± 7 days (60 days after TAI) postpartum. At the start of the breeding season (BS), cows were subjected to a synchronization of ovulation program for TAI. Bulls were placed with cows 10 days after TAI and remained until the end of the study (112 days postpartum). Cows with the highest BCS at parturition had an increased probability of first service conception rate at 60 days after TAI (P = 0.02) and a reduced probability of occurrence of pregnancy loss (P = 0.05). Also, cows had a greater likelihood of conceiving postpartum if they had greater RFAT and BCS at 165 ± 14 days prepartum (P = 0.01 and P = 0.03, respectively) and at parturition (P = 0.0007 and P = 0.003, respectively). Cows that had an increase in RFAT and BCS during the dry period (i.e., interval from weaning of the previous calf to parturition) also had a greater likelihood of conceiving (P = 0.03 and P = 0.06, respectively) during the BS. Among the different time points, RFAT and BCS at parturition had the largest impact on risk of conception during the BS. The LW was a poor predictor of conception during the BS (P = 0.11–0.68) except for LW at 165 ± 14 days prepartum (P = 0.01). Collectively, the findings indicated that the likelihood of conception during the BS was highest in cows that had an improvement in RFAT and BCS during the dry period. Therefore, assuring a good nutritional status in the dry period (BCS ≥ 3.0 at 165 ± 14 days prepartum and ≥3.25 at parturition) is an important aim to optimize the postpartum conception rate of suckled Zebu beef cows subjected to TAI followed by natural mating.     

How do SNP ascertainment schemes and population demographics affect inferences about population history?

Background

The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F_ST and principal components analysis (PCA).

Results

Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of F_ST between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong.

Conclusions

Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of F_ST, time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1469-5) contains supplementary material, which is available to authorized users.     

Cattle demographic history modelled from autosomal sequence variation

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.     

Fixed-time artificial insemination with estradiol and progesterone for Bos indicus cows I: Basis for development of protocols

Five experiments were conducted on commercial farms in Brazil aiming to develop a fixed-time artificial insemination (TAI) protocol that achieved pregnancy rates between 40% and 55% in Bos indicus cows. These studies resulted in the development of the following protocol: insertion of an intravaginal device containing 1.9 g of progesterone (CIDR) plus 2.0 mg im estradiol benzoate on Day 0; 12.5 mg im dinoprost tromethamine on Day 7 in cycling cows or on Day 9 in anestrous cows; CIDR withdrawal plus 0.5 mg im estradiol cypionate plus temporary calf removal on Day 9; TAI (48 h after CIDR withdrawal) plus reuniting of calves with their dams on Day 11. Reduced dose of prostaglandin F_2α (PGF_2α; 12.5 mg im dinoprost tromethamine) effectively caused luteolysis. In cycling cows, fertility was greater when the treatment with PGF_2α was administered on Day 7 than on Day 9, but in anestrous cows, no effects of time of the PGF_2α treatment were found. Estradiol cypionate effectively replaced estradiol benzoate or gonadotropin-releasing hormone as the ovulatory stimulus, reducing labor and cost. In this protocol, CIDR inserts were successfully used four times (9 d each use) with no detrimental effects on fertility.     

Fixed-time artificial insemination with estradiol and progesterone for Bos indicus cows II: Strategies and factors affecting fertility

In Experiments 1, 2, and 3, we evaluated the effects of temporary weaning (TW), equine chorionic gonadotropin (eCG), and follicle-stimulating hormone (FSH) treatments on results of a fixed-time artificial insemination (TAI) protocol in postpartum Bos indicus cows. In Experiment 1, treatment with 400 IU eCG or with TW for 48 h consistently improved pregnancy rates (PRs) at TAI, but, in Experiment 2, FSH treatment was less effective than eCG or TW. In Experiment 3, the inclusion of eCG treatment in cows subjected to TW did not improve PRs. We concluded that TW or 400 IU eCG should be included in the TAI protocol in postpartum Bos indicus cows to enhance fertility. In Experiment 4, we used records from heifers and cows treated with the proposed protocol during the 2006-2007 (n = 27,195) and 2007-2008 (n = 36,838) breeding seasons from multiple locations in Brazil to evaluate factors potentially affecting PRs. Overall PR at TAI was 49.6% (31,786 of 64,033). Pregnancy rate differed (P < 0.01) among farm within location (results ranging between 26.8% and 68.0%; P < 0.01), cow group within farm, by breed (Bos indicus, 48.3% [26,123 of 54,145]; Bos taurus, 61.7% [3652 of 5922]; and crossbred Bos indicus × Bos taurus, 50.7% [2011 of 3966]), category (nulliparous, 39.6% [2095 of 5290]; suckled primiparous, 45.2% [3924 of 8677]; suckled multiparous, 51.8% [24,245 of 46,767]; and nonsuckled multiparous, 46.1% [1522 of 3299]), body condition score at TAI (≤2.5, 43.0% [3409 of 7923]; 3.0, 49.6% [18,958 of 38,229]; and ≥3.5, 52.7% [9419 of 17,881]). Days postpartum at beginning of protocol did not affect PR (30 to 60 d, 47.6% [4228 of 8881]; 61 to 90 d, 51.7% [16,325 to 31,572]; and 91 to 150 d, 50.8% [7616 to 14,991]; P > 0.1). Pregnancy rate was also consistently affected (P < 0.01) by sire (results ranging from 7.2% to 77.3%) and artificial insemination technician (results ranging from 15.1% to 81.8%).     

Local immune response against larvae of Rhipicephalus (Boophilus) microplus in Bos taurus indicus and Bos taurus taurus cattle

Bos taurus indicus cattle are less susceptible to infestation with Rhipicephalus (Boophilus) microplus than Bos taurus taurus cattle but the immunological basis of this difference is not understood. We compared the dynamics of leukocyte infiltrations (T cell subsets, B cells, major histocompatibility complex (MHC) class II-expressing cells, granulocytes) in the skin near the mouthparts of larvae of R. microplus in B. t. indicus and B. t. taurus cattle. Previously naïve cattle were infested with 50,000 larvae (B. t. indicus) or 10,000 larvae (B. t. taurus) weekly for 6 weeks. One week after the last infestation all of the animals were infested with 20,000 larvae of R. microplus. Skin punch biopsies were taken from all animals on the day before the primary infestation and from sites of larval attachment on the day after the first, second, fourth and final infestations. Infiltrations with CD3⁺, CD4⁺, CD8⁺ and γδ T cells followed the same pattern in both breeds, showing relatively little change during the first four weekly infestations, followed by substantial increases at 7 weeks post-primary infestation. There was a tendency for more of all cell types except granulocytes to be observed in the skin of B. t. indicus cattle but the differences between the two breeds were consistently significant only for γδ T cells. Granulocyte infiltrations increased more rapidly from the day after infestation and were higher in B. t. taurus cattle than in B. t. indicus. Granulocytes and MHC class II-expressing cells infiltrated the areas closest to the mouthparts of larvae. A large volume of granulocyte antigens was seen in the gut of attached, feeding larvae.     

Neither plasma progesterone concentrations nor exogenous eCG affects rates of ovulation or pregnancy in fixed-time artificial insemination (FTAI) protocols for puberal Nellore heifers

The objective was to evaluate the effects of plasma progesterone (P4) concentrations and exogenous eCG on ovulation and pregnancy rates of pubertal Nellore heifers in fixed-time artificial insemination (FTAI) protocols. In Experiment 1 (Exp. 1), on Day 0 (7 d after ovulation), heifers (n = 15) were given 2 mg of estradiol benzoate (EB) im and randomly allocated to receive: an intravaginal progesterone-releasing device containing 0.558 g of P4 (group 0.5G, n = 4); an intravaginal device containing 1 g of P4 (group 1G, n = 4); 0.558 g of P4 and PGF_2α (PGF; 150 μg d-cloprostenol, group 0.5G/PGF, n = 4); or 1 g of P4 and PGF (group 1G/PGF, n = 3). On Day 8, PGF was given to all heifers and intravaginal devices removed; 24 h later (Day 9), all heifers were given 1 mg EB im. In Exp. 2, pubertal Nellore heifers (n = 292) were treated as in Exp. 1, with FTAI on Day 10 (30 to 36 h after EB). In Exp. 3, pubertal heifers (n = 459) received the treatments described for groups 0.5G/PGF and 1G/PGF and were also given 300 IU of eCG im (groups 0.5G/PGF/eCG and 1G/PGF/eCG) at device removal (Day 8). In Exp. 1, plasma P4 concentrations were significantly higher in heifers that received 1.0 vs 0.588 g P4, and were significantly lower in heifers that received PGF on Day 0. In Exp. 2 and 3, there were no significant differences among groups in rates of ovulation (65-77%) or pregnancy (Exp. 2: 26-33%; Exp. 3: 39-43%). In Exp. 3, diameter of the dominant ovarian follicle on Day 9 was larger in heifers given 0.558 g vs 1.0 g P4 (10.3 ± 0.2 vs 9.3 ± 0.2 mm; P < 0.01). In conclusion, lesser amounts of P4 in the intravaginal device or PGF on Day 0 decreased plasma P4 from Days 1 to 8 and increased diameter of the dominant follicle on Day 9. However, neither of these nor 300 IU of eCG on Day 8 significantly increased rates of ovulation or pregnancy.     

Strategies to improve fertility in Bos indicus postpubertal heifers and nonlactating cows submitted to fixed-time artificial insemination

Two experiments were designed to evaluate strategies to increase fertility of Bos indicus postpubertal heifers and nonlactating cows submitted to a fixed-time artificial insemination (TAI) protocol consisting of an intravaginal device containing 1.9 g of progesterone (CIDR) insertion + estradiol benzoate on Day 0, CIDR withdrawal + estradiol cypionate on Day 9, and TAI on Day 11. In Experiment 1, heifers (n = 1153) received a new or an 18-d previously used CIDR and, on Day 9, prostaglandin F_2α (PGF_2α) + 0, 200, or 300 IU equine chorionic gonadotropin (eCG). Heifers treated with a new CIDR had greater (least squares means ± SEM) serum concentration of progesterone on Day 9 (3.06 ± 0.09 ng/mL vs. 2.53 ± 0.09 ng/mL; P < 0.05) and a smaller follicle at TAI (11.61 ± 0.11 mm vs. 12.05 ± 0.12 mm; P < 0.05). Heifers with smaller follicles at TAI had lesser serum progesterone concentrations on Day 18 and reduced rates of ovulation, conception, and pregnancy (P < 0.05). Treatment with eCG improved (P < 0.05) follicle diameter at TAI (11.50 ± 0.10 mm, 11.90 ± 0.11 mm, and 12.00 ± 0.10 mm for 0, 100, and 200 IU, respectively), serum progesterone concentration on Day 18 (2.77 ± 0.11 ng/mL, 3.81 ± 0.11 ng/mL, and 4.87 ± 0.11 ng/mL), and rates of ovulation (83.8%, 88.5%, and 94.3%) and pregnancy (41.3%, 47.0%, and 46.7%). In Experiment 2, nonlactating Nelore cows (n = 702) received PGF_2α treatment on Days 7 or 9 and, on Day 9, 0 or 300 IU eCG. Cows receiving PGF_2α on Day 7 had lesser serum progesterone concentrations on Day 9 (3.05 ± 0.21 ng/mL vs. 4.58 ± 0.21 ng/mL; P < 0.05), a larger follicle at TAI (11.54 ± 0.21 mm vs. 10.84 ± 0.21 mm; P < 0.05), and improved (P < 0.05) rates of ovulation (85.4% vs. 77.0%), conception (60.9% vs. 47.2%), and pregnancy (52.0% vs. 36.4%). Treatment with eCG improved (P < 0.05) serum progesterone concentration on Day 18 (3.24 ± 0.14 ng/mL vs. 4.55 ± 0.14 ng/mL) and the rates of ovulation (72.4% vs. 90.0%) and pregnancy (37.5% vs. 50.8%). In conclusion, giving PGF_2α earlier in the protocol in nonlactating cows and eCG treatment in postpubertal heifers and nonlactating cows improved fertility in response to a TAI (progesterone + estradiol) protocol.     

Ovum pick up, in vitro embryo production, and pregnancy rates from a large-scale commercial program using Nelore cattle (Bos indicus) donors

The objective was to clarify in vitro production of bovine embryos in Brazil. Data from 656 ovum pick-up/in vitro production (OPU/IVP) procedures, performed on 317 Nelore (Bos indicus) donors, without hormone stimulation or control of ovarian follicular waves, were analysed. Donors were subjected to OPU from one to nine times (no specific schedule), with < 15 d between consecutive procedures. There were 20,848 oocytes, of which 15,747 (75.53%) were considered viable, 5,446 embryos were obtained, 5,398 embryos were immediately transferred, resulting in 1,974 pregnancies (36.57%) at Day 30 and 1,788 (33.12%) pregnancies at Day 60. The average number of total and viable oocytes produced per OPU session was (mean ± SEM) 30.84 ± 0.88 and 23.35 ± 0.7 (average of 8.1 ± 0.3 embryos and 3.0 ± 0.1 pregnancies per OPU-IVP procedure). Since oocyte production varied widely among donor, they were designated as very high, high, intermediate, and low, with 58.94 ± 2.04, 32.61 ± 0.50, 22.13 ± 0.50, and 10.26 ± 0.57 oocytes, respectively, produced by 78, 80, 79, and 80 donors. The number of viable oocytes recovered ranged from 0 to 128; since donors with numerous viable oocytes produced many viable embryos and pregnancies, oocyte production was useful for donor selection. However, there was no significant effect of the number of OPU sessions per donor on mean numbers of oocytes produced. In conclusion, we confirmed field reports of high oocyte production by some Nelore donors and demonstrated individual variation in oocyte yield, which was associated with embryo production and pregnancy rates.     

A pilot study on lignocelluloses to ethanol and fish feed using NMMO pretreatment and cultivation with zygomycetes in an air-lift reactor

A complete process for the production of bioethanol and fungal biomass from spruce and birch was investigated. The process included milling, pretreatment with N-methylmorpholine-N-oxide (NMMO), washing of the pretreated wood, enzymatic hydrolysis, and cultivation of the zygomycetes fungi Mucor indicus. Investigated factors included wood chip size (0.5-16 mm), pretreatment time (1-5 h), and scale of the process from bench-scale to 2 m high air-lift reactor. Best hydrolysis yields were achieved from wood chips below 2 mm after 5 h of pretreatment. Ethanol yields (mg/g wood) of 195 and 128 for spruce, and 175 and 136 for birch were achieved from bench-scale and airlift, respectively. Fungal biomass yields (mg/g wood) of 103 and 70 for spruce, and 86 and 66 for birch from bench scale and airlift respectively were simultaneously achieved. NMMO pretreatment and cultivation with M. indicus appear to be a good alternative for ethanol production from birch and spruce.