The Buffalo Genome and the Application of Genomics in Animal Management and Improvement

The publication of the human genome sequence in 2001 was a major step forward in knowledge necessary to understand the variations between individuals. For farmed species, genomic sequence information will facilitate the selection of animals optimised to live, and be productive, in particular environments. The availability of cattle genome sequence has allowed the breeding industry to take the first steps towards predicting phenotypes from genotypes by estimating a genomic breeding value (gEBV) for bulls using genome-wide DNA markers. The sequencing of the buffalo genome and creation of a panel of DNA markers has created the opportunity to apply molecular selection approaches for this species.The genomes of several buffalo of different breeds were sequenced and aligned with the bovine genome, which facilitated the identification of millions of sequence variants in the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome compared with the bovine genome, 90,000 putative single nucleotide polymorphisms (SNP) were selected to create an Axiom (R) Buffalo Genotyping Array 90K. This SNP Chip was tested in buffalo populations from Italy and Brazil and found to have at least 75% high quality and polymorphic markers in these populations. The 90K SNP chip was then used to investigate the structure of buffalo populations, and to localise the variations having a major effect on milk production.

Molecular Evaluation of Developmental Competence of Oocytes Collected In Vivo from Buffalo and Bovine Heifers during Winter and Summer

Buffaloes and bovines are polyestrous and seasonal or annual livestock, respectively, that show reduced fertility during heat stress. To investigate whether reduced fertility is related to oocyte competence in both species, immature oocytes from buffalo and bovine heifers were collected during winter and summer and subjected to molecular analyses. In each season, heifers of both species had their follicular wave emergence synchronized with a standard protocol (Ferreira et al., 2011). Before being subjected to ovum pick up (OPU), cutaneous (CT; degrees C) and rectal (RT; degrees C) temperatures and respiratory rate (RR; breaths/min) were measured. Oocytes' RNA was extracted to evaluate the expression of target genes related to mtDNA replication/transcription (PPARGC1A, TFAM and MT-CO1), apoptosis (BAX and BCL2) and HS (HSP90AA1 and HSPA1AB). ACTB, HIST1H2AG and GAPDH were initially chosen as housekeeping genes. In buffaloes, CT (35.0 +/- 0.4 vs 23.8 +/- 0.5), RT (38.7 +/- 0.1 vs 38.0 +/- 0) and RR (21.3 +/- 1.2 vs 15.4 +/- 1.1) were higher during summer than winter. However, in bovine heifers, RT (38.7 +/- 0.1 vs 38.6 +/- 0.1) and RR (44.8 +/- 1.5 vs 40.6 +/- 1.5) were similar in both seasons, while CT (31.6 +/- 0.3 vs 30.2 +/- 0.3) was increased during summer. Reduced expression of ACTB, HIST1H2AG and GAPDH was evidenced during summer, disqualifying them as housekeeping genes. Similarly, the expression of all target genes was reduced during summer in oocytes of both species. In summary, physiological responses to heat stress seem to be more intense in buffalo than bovine heifers. However, in both species, negative effects of heat stress upon oocyte quality occur at the molecular level and affects genes related to several biological functions.

Genetic Parameter Estimates for Milk Yield and Lactation Length in Buffalo

The objective of this study was to estimate genetic parameters for milk yield at 244 days and lactation length in graded buffalo cows at the El Cangre Cattle Genetic Enterprise. Data were gathered from 2575 lactations, 1377 buffalo cows, 37 milking units and between 2002-2009 calving years. It was employed the Restricted Maximum Likelihood method (REML) for estimating (co) variance components with multi trait model. Average of milk yield at 244 days and lactation length were 864 kg and 240 days, respectively. Heritability was 0.15 for milk yield and 0.13 for lactation length. Genetic correlation between these traits was 0.63. It was concluded that it is necessary to intensify selection and to increase control of the information of the genetic herds to obtain high precision in the estimates and therefore, obtain bigger genetic progress in of this species in our country.

Genetic Parameters for Productive and Reproductive Traits for Milk Buffalo in Brazil

Knowing the genetic parameters of productive and reproductive traits in milking buffaloes is essential for planning and implementing of a program genetic selection. In Brazil, this information is still scarce. The objective of this study was to verify the existence of genetic variability in milk yield of buffaloes and their constituents, and reproductive traits for the possibility of application of the selection. A total of 9,318 lactations records from 3,061 cows were used to estimate heritabilities for milk yield (MY), fat percentage (%F), protein percentage (%P), length of lactation (LL), age of first calving (AFC) and calving interval (CI) and the genetic correlations among traits MY, %F and %P. The (co) variance components were estimated using multiple-trait analysis by Bayesian inference method, applying an animal model, through Gibbs sampling. The model included the fixed effects of contemporary groups (herd-year and calving season), number of milking (2 levels), and age of cow at calving as (co) variable (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. Estimated heritability values for MY, % F, % P, LL, AFC and CI were 0.24, 0.34, 0.40, 0.09, 0.16 and 0.05, respectively. The genetic correlation estimates among MY and % F, MY and % P and % F and % P were -0.29, -0.18 and 0.25, respectively. The production of milk and its constituents showed enough genetic variation to respond to a selection program. Negative estimates of genetic correlations between milk production and its components suggest that selection entails a reduction in the other.

Interference of Vaccinal Antibodies on Serological Diagnostic of Leptospirosis in Vaccinated Buffalo using Two Types of Commercial Vaccines

The vaccinal antibodies interference represents one of the problems in the leptospirosis diagnostic on serum. The present study aimed to determine the pattern of serum agglutinins anti-Leptospirae spp in vaccinated female buffaloes against leptospirosis using two types of commercial vaccines: bacterin and extern membrane. The temporal interference of vaccinal titers on serum diagnostic was evaluated. Three groups of 11 adult female buffaloes were established as follows: G1 control, non-vaccinated; G2: vaccinated with bacterin containing six serovars and G3 with extern membrane vaccine containing five serovars. A booster was administered at 30 days from the first vaccination (dfv) and two re- vaccinations were performed in each semester (days 210 and 390). Serum samples were collected on days 0, 15, 30, 45 and 60 and every 30 days until 540 dfv, being submitted to Serum Agglutination Microscopy (SAM) against the serovars present in the vaccine. G1 remained always negative. Both vaccines induced serologic responses when assessed by SAM at 150 days post first vaccination against all serovars and they revealed maximum titers around days 45 and 60 after first vaccination. At the re-vaccination there was an increase on agglutinin levels, but of less intensity than the levels previously observed. After six months from the second revaccination (540 dfv), they were almost zero, which demonstrates the short duration of diagnostic interference. The serologic monitoring of the vaccinated herds can be an efficient method to evaluate the status of protection provided by the vaccine.

Effect of testicular thermoregulation on the quality of buffalo sperm

The process of spermatic division and differentiation (spermatogenesis) occurs with intratesticular temperature lower that the corporal temperature and for that is essential that the testicular thermoregulation mechanism occurs properly. For evaluation of the scrotal surface temperature can be used the infrared thermography or testicular sensors, besides that, can be evaluated the blood flux in the spermatic cord through the Doppler ultrasonography. Thus, the aim of this study is to analyze the testicular thermoregulation in adult buffaloes through scrotal thermography and Doppler ultrasound of testicular artery and verify its effect on sperm quality. For that were used seven healthy buffaloes, with age of 3 and 4 years, of the Murrah breed. The animals were subjected to 3 semen collections using artificial vagina, with one day of interval. In addiction, the retal temperature measurement (RT) with dry bulb thermometer, the measurement of scrotal surface temperature (SST) and body surface temperature (BST) through infrared thermography and the pulsatility (PI) and resistivity (RI) index of testicular artery by Doppler ultrasonography, were performed using 2 distinct moments: animals previously placed to shade (M1) and animals subjected to 4 hours of sun (M2). All parameters were compared by T test and the correlations were performed by Pearson test using the In Stat Graph Pad 3 (R) program. The significant level considered was 5%. There was an increase (p<0,05) of RT, SST, SNT and RI in M2. increasing trend was observed (0,05>p>0,01) PI and RI between M1 and M2. There was a low correlation between SST and semen quality. The results of this study allow us to conclude that adult buffaloes have low ability to perform body and testicular thermoregulation in situations of enviromental heat stress. However, this low capacity of testicular temperature maintenance demonstrated no correlation with the sperm kinetic parameters and sperm morphological defects in buffalo spermatozoa.

Values of 13,14-Dihydro-15-Keto-PGF(2 alpha), Progesterone and Oestradiol After Injection of Prostaglandin at Different Periods of Buffalo Puerperium

Knowledge of the effectiveness of prostaglandins in uterine involution process led to the development of protocols with its analogues in postpartum period. However, this hormone mechanism of action is not yet fully elucidated. Thus, the objective of this study was to verify if chloprostenol administration, at early or intermediary puerperium, can induce changes on progesterone, PGFM and oestradiol plasma concentrations. 30 Murrah postpartum buffaloes were randomly divided into three groups: CONT (saline, n = 10); CLO2 (chloprostenol at days 2 and 5 postpartum, n = 10) and; CLO15 (chloprostenol at days 15 and 20 postpartum, n = 10). Blood samples were collected from jugular vein to measure progesterone, PGFM and oestradiol plasma concentrations at days 2, 7, 14, 21 and 28 postpartum. CLO2 group presented lower progesterone and PGFM plasma concentrations in relation to CONT and CLO15 groups (0.23 +/- 0.00 and 0.32 +/- 0.11, 0.19 +/- 0.00 and 0.23 +/- 0.11, 0.23 +/- 0.00 and 0.30 +/- 0.19, for groups CONT, CLO2 and CLO15, respectively; P < 0.05). There was no significant difference in oestradiol plasma concentration between experimental groups (P > 0.05). Prostaglandin synthetic analogue administration induced hormonal changes in postpartum buffaloes, which can partially explain its positive effect under reproductive function of this specie.

Comparison of Botu-bov and Tris as Freezing Extenders of Buffalo Sperm Recovered from Epididymal Cauda

Valuable genetic material can be preserved by the cryopreservation of epididymal sperm. This study evaluated the viability of pre-freezing and post-thawed sperm samples recovered from the epididymal cauda of buffaloes. Epididymides from eight Murrah buffaloes with 18 months of age were used. Semen samples were diluted in two different freezing extenders: Botu-bov (BB) and Tris (TRIS). Immediately after slaughter, both testicles from each animal were collected and transported at 4 degrees C for six hours interval. In laboratory, the removed epididymides were flushed to obtain sperm and the fractions were diluted in both freezing extenders (BB and TRIS). Semen doses were analyzed before and after frozen at -196 degrees C. BB and TRIS pre-freezing results were 38.54 +/- 22.33%(b) and 14.17 +/- 12.78%(a) for total motility (TM), 25.00 +/- 16.12(a) and 9.44 +/- 9.11(a) for progressive motility (PM), 7.21 +/- 0.98(a) and 5.09 +/- 2.65(a) for percentage of rapid cells (RAP), 91.08 +/- 12.53(b) and 63.33 +/- 31.47(a) for velocity of trajectory (VAP), 73.54 +/- 20.17(b) and 49.50 +/- 9.11(a) for linear progressive velocity (VSL), 172.21 +/- 24.55(a) and 116.94 +/- 59.48(a) for curvilinear velocity (VCL), respectively (P < 0.05). BB and TRIS post-thawing results were 42.25 +/- 21.50(b) and 17.62 +/- 19.46(a) for TM, 27.25 +/- 24.86(a) and 18.00 +/- 13.68(a) for PM, 7.35 +/- 0.98(a) and 6.26 +/- 1.13(a) for RAP, 91.42 +/- 16.86(a) and 75.96 +/- 13.17(a) for VAP, 67.96 +/- 12.13(a) and 60.04 +/- 10.42(a) for VSL, 177.54 +/- 23.53(b) and 141.29 +/- 24.97a for VCL, respectively (P < 0.05). The sperm recovered from the epididymal cauda, after 6 h storage of epididymides at 5 degrees C ensures sperm preservation demonstrating that the diluent Botu-bov had higher total motility both pre-and post-freezing when compared with TRIS. Additionally, the sperm frozen with the diluent Botu-bov showed higher values of VSL at post-thawing. These findings may reflect in improvement of conception rates.

Adding Motility Stimulants to Improve Freezing of Buffalo Sperm Recovered from Epididymal Cauda

The cryopreservation of epididymal sperm is important to preserve genetic material from valuable buffalo bulls. This study evaluated the viability of post-thawed sperm samples recovered from the epididymal cauda adding motility inductors. For that, were used epididymides from eight Murrah buffaloes with 18 months of age. Semen samples were submitted to three different conditions: (CT - control) without adding medium, (SPERM) adding Sperm Talp medium, and (FERT) adding Fert Talp medium. Immediately after slaughter, both testicles from each animal were collected and transported at 4 degrees C at maximum six hours interval. In laboratory, the removed epididymides was flushed to obtain sperm and diluted in the freezing extender. Each buffalo sperm were divided and fractions were submitted to all conditions (CT, SPERM and FERT). Semen doses were frozen at -196 degrees C. CT, SPERM and FERT post-thawing results were 13.63 +/- 8.91, 38.77 +/- 8.91 and 42.83 +/- 8.91 for total motility, 7.30 +/- 8.74, 24.87 +/- 8.74 and 29.70 +/- 8.74 for progressive motility, 6.04 +/- 0.92, 6.74 +/- 0.92 and 6.93 +/- 0.92 for percentage of rapid cells (P < 0.05). In conclusion, diluted semen supplementation with Sperm or Fert talp increases the motility of cauda epididymal sperm of buffalo bulls.

Uterine Involution, Fluid Accumulation and Ovarian Activity after Injection of Prostaglandin at Different Periods of Buffalo Puerperium

This study aimed to evaluate the effect of chloprostenol administration, at early or intermediary puerperium, under uterine involution, intrauterine fluid accumulation and ovarian activity return. 30 Murrah postpartum buffaloes were randomly divided into three groups: CONT (saline, n = 10); CLO2 (chloprostenol at days 2 and 5 postpartum, n = 10) and; CLO15 (chloprostenol at days 15 and 20 postpartum, n = 10). Gynecological exams were performed at days 2, 7, 14, 21 and 28 postpartum, when uterine involution degree (1 to 3 scale, by transrectal palpation), intrauterine fluid accumulation (0 to 3 scale, by ultrasound exam) and ovarian activity (B-mode ultrasound exam) were evaluated. CLO2 group presented higher uterine involution (2.00 +/- 0.23, 1.66 +/- 0.23, 1.58 +/- 0.23 for groups CLO2, CONT and CLO15, respectively) and faster ovarian activity return in relation to groups CONT and CLO15 (P < 0.05). Groups CLO2 and CLO15 showed lower intrauterine fluid accumulation compared to CONT group (2.04 +/- 0.20, 1.58 +/- 0.20, 1.92 +/- 0.20 for groups CONT, CLO2 and CLO15, respectively; P < 0.05). Prostaglandin analogue administration in postpartum buffalo benefited uterine involution, lochia expulsion and ovarian activity return, improving reproductive efficiency in this specie.

Single Nucleotide Variations in the Buffalo Kappa-Casein Gene (CSN3)

Caseins are the major milk proteins associated with lactation performance, milk composition and cheese yield efficiency, representing around 80% of the total amount of proteins found in milk. Among the caseins, kappa-casein is the protein that stabilizes micelle structure during milk coagulation process and being used during the cheese production. The kappa-casein gene (CSN3) has been previously mapped to buffalo chromosome 7 using a radiation hybrid panel and a comparative map was established using the sequence from bovine chromosome 6. The molecular structure of this gene has also been established in river buffalo, with a total length of 13,191 bp (GenBank: AM900443.1) and containing five exons. In this study we searched for single nucleotide variations in specific regions of the CSN3 gene in three animals representing the Murrah breed. Sequencing reactions were performed using ABI3730xl sequencer. The primer walking method was used to span the 5'-UTR and intron 2 regions of the gene, for which ten primer pairs were designed using Oligo 6 software. BLAST tool was used to verify the primers specificity. DNA sequences assemblies from all three animals were performed with Sequencher (R) software 4.1, while multiple alignments were performed using Clustal W software to identify single nucleotide variations. The sequencing revealed a total of 19 single nucleotide variations with 13 located in the upstream regulatory region of the gene (5'-UTR) and six on intron 2. These variations can be validated using commercial populations segregating specific economic traits.