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.

Cattle-Derived Microsatellite Markers to Study the Water Buffalo Genome

Microsatellites are well-known DNA markers used in a variety of studies such as genome mapping, genetic diversity analysis, genetic conservation and phylogenetic studies. Although microsatellites are important markers, their development and characterization demands extensive time and high cost. Thus, before new markers are developed for a particular species, it is worthwhile to test the available markers from related species. In the present study, we evaluate cattle-derived microsatellite markers for genetic studies of water buffalo. Eighty-five percents of a total of 120 microsatellite markers were optimized using buffalo DNA (Bubalus bubalis). The results showed in this paper were also deposited in the National Center for Biological Information database (NCBI) (ProbeDB and UniSTS) for use in population genetic studies of buffalo by the scientific community. The use of heterologous primers significantly reduces the cost of developing specific markers for buffalo, providing a useful short cut for the genetic population analysis and gene mapping studies.

Inbreeding, Average Relatedness Coefficient and Effective Population Size In Jaffarabadi Buffaloes Raised In Brazil

The major aim of this study was to evaluate the inbreeding (F), average relatedness coefficient (AR) and effective population size (Ne) in the Jaffarabadi buffalo breed from Brazil. Pedigree information of 1,272 animals born from 1966 was used. The effective population size was calculated in two ways: first, computed via individual increase in inbreeding and second estimated by individual increase in coancestry. The known generation numbers were 1.24, 1.76 and 2.64 for complete, equivalent and maximum generation, respectively. The effective size computed via individual increase in coancestry was small with a value of 10.82 +/- 1.29. The effective size computed by individual increase in inbreeding (10.40 +/- 3.69) was very similar but a little smaller than the previous reported value. The average values of F and AR for the population reference (1,059) were 4.22 and 12.5 percent. The mean of F for inbred animals (319) was 14.0%. The F and AR means were 5.7 and 13.3% for animals with at least 1.5 known equivalent generation and 9.3 and 15.97% for individuals having at least 2.5 equivalent generations known. It was found 78 matings between half sibs (6.14%) and 67 matings (5.27%) between parent-offspring. The estimated inbreeding increase per generation by considering maximum generation, complete generation and equivalent generation were 1.21%, 5.18% and 3.57%, respectively. Considering the uncompleted pedigree, the estimated inbreeding for the reference population could be underestimated.

Control of Buffalo Follicular Dynamics for Artificial Insemination, Superovulation and In Vitro Embryo Production

Currently, timed ovulation induction and timed artificial insemination (TAI) can be performed in buffalo using GnRH or estradiol plus progesterone/progestin (P4)-releasing devices and prostaglandin F-2 alpha (PGF(2 alpha)). The control of the emergence of follicular waves and of ovulation at predetermined times, without the need for estrus detection, has facilitated the management and improved the efficiency of AI programs in buffalo during the breeding and nonbreeding season. Multiple ovulations, embryo transfer, ovum collection and in vitro embryo production have been shown to be feasible in buffalo, although low efficiency and limited commercial application of these techniques have been documented as well. These results could be associated with low ovarian follicular pools, high levels of follicular atresia and failures of the oocyte to enter the oviduct after superstimulation of follicular growth. This review discusses a number of key points related to the manipulation of ovarian follicular growth to improve pregnancy rates following TAI and embryo transfer of in vivo- and in vitro-derived embryos in buffalo.

Progestin-Based Protocol for Synchronization of Follicular Wave Emergence in Buffaloes During Summer and Winter

The aim of the present study was to evaluate the effects of type of norgestomet auricular implant (new - N or previously used during 5 days - U), season of the year (summer - S and winter - W), and parity (12 heifers - H and 23 cows - C) on synchronization of follicular wave emergence in buffaloes. For this purpose, 35 buffaloes were examined daily by ultrasonography until follicular wave emergence was detected. Data were analysed by ANOVA, using PROC GLIMMIX. No interactions were observed in none variables. Time of follicular wave emergence and number of follicles at emergence were not affected by type of implant or season of the year. Parity also did not influence the number of follicles at emergence. However, follicular wave emergence occurred later in heifers than in cows. In conclusion, the previous use of a norgestomet auricular implant independent of the season of the year does not affect the time or the number of follicles at follicular wave emergence in buffaloes. Nevertheless, although heifers and cows had a similar number of follicles at emergence, the time of follicular wave emergence occurs earlier in cows than in heifers.

Efficiency of OPU-IVEP-ET of Fresh and Vitrified Embryos in Buffaloes

The present study aims to report ovum pickup (OPU), in vitro embryo production (IVEP) and embryo transfer (ET) outcomes of fresh and vitrified buffalo embryos. For this purpose, 36 buffalo donors were submitted to 11 OPU sessions (n = 201). A total of 998 oocytes (5.0 +/- 0.5/donor/session) and 584 viable oocytes (2.9 +/- 0.3/donor/session) were recovered. Viable oocytes (grades 1, 2 and 3) were subjected to IVM, IVF (D0) and IVC. On D2, 54.5% of cleavage rate was obtained. Embryo yield on D7 was 44.9% (grade 1: 229 embryos, grade 2: 5 embryos and grade 3: 28 embryos). From this total, 115 fresh (grades 1 to 3) and 70 vitrified embryos (only grade 1) were transferred into recipients previously synchronized with fixed time embryo transfer (FTET) protocol. Vitrification was performed using the cryotop method. Pregnancy diagnosis in fresh and in vitrified groups were, respectively: 43.5% (50/115) and 37.1% (26/70) on 30 days after embryo transfer, and 41.7% (48/115) and 31.4% (22/70) on 60 days after embryo transfer. In conclusion, our results demonstrate the possibilities for commercial use of the techniques of OPU, IVEP and ET of fresh and vitrified embryos in buffaloes.

Pregnancy Monitoring of In Vitro Produced Embryos in Buffaloes

In the present study, pregnancies obtained from 115 in vitro produced embryos were monitored by ultrasonography on days 30 and 60 after embryo transfer (ET), and at calving. Additionally, the health of newborns and recipients were also evaluated. On day 30 after ET, positive pregnancy was diagnosed in 50 animals (43.5%). A total of 8 fetal mortalities (16.0%) were verified from 30 days until calving, in which 2 occurred from 30 to 60 days after ET (4.0%), and 6 occurred from 60 days until calving (12.0%). In this last period of pregnancy, 3 pregnancy losses were due to abortion, and the other 3 were stillbirth. One additional animal was eliminated from the study, remaining 41 pregnancies. From these 41 pregnancies, a total of 20 female calves (48.8%) and 21 male calves (51.2%) were born. Pregnancies from female and male calves had a mean length of 309.8 and 310.9 days, respectively (range 300 to 328 days, and 297 to 320 days, respectively). Weight at calving was a mean of 31.4 and 33.8 kg for female and male calves, respectively. All calving occurred without intervention and dystocia was not observed in any case. No large offspring syndrome, hydramnios, hydroallantois, or umbilical cord anomalies were observed in calves. Delivery was normal in all recipients, and no puerperal infections, or retained placenta occurred. Suckling assistance was not necessary in any newborn. All genetic pedigree was confirmed later by DNA tests.

Influence of Parity and Season of the Year on Oocyte Quality and Number in Buffaloes

The aim of the present study was to evaluate the effects of season of the year (summer and winter) and parity (heifers and cows) on oocyte quality and number in buffaloes. For this purpose, 71 buffaloes had follicular wave emergence synchronized before OPU. OPU of all follicles >= 2mm was done 5 days after the beginning of the hormonal protocol, in 4 replicates (two for each season). Data were analyzed by ANOVA using PROC GLIMMIX, in a 2 x 2 factorial arrangement of treatments. No interactions were observed in following variables: number of follicles, number of total and viable oocytes, recovery rate, percentage of viable oocytes, grade I oocytes, grade II oocytes, grade III oocytes, denuded oocytes, expanded cumulus oocytes, and atretic/degenerated oocytes. Number of follicles visualized at OPU and recovery rate were not affected by parity or season. Relative to parity, number of total and viable oocytes were greater in heifers than in cows, respectively. Concerning season of the year, number of viable oocytes and viable oocyte rate were increased in winter. In conclusion, better oocyte quality can be obtained from heifers and during winter in buffaloes. However, the number of total oocytes seems to be more influenced by parity than by season of the year in this species.

Multiple-trait genomic evaluation for milk yield and milk quality traits using genomic and phenotypic data in buffalo in Brazil

The use of markers distributed all long the genome may increase the accuracy of the predicted additive genetic value of young animals that are candidates to be selected as reproducers. In commercial herds, due to the cost of genotyping, only some animals are genotyped and procedures, divided in two or three steps, are done in order to include these genomic data in genetic evaluation. However, genomic evaluation may be calculated using one unified step that combines phenotypic data, pedigree and genomics. The aim of the study was to compare a multiple-trait model using only pedigree information with another using pedigree and genomic data. In this study, 9,318 lactations from 3061 buffaloes were used, 384 buffaloes were genotyped using a Illumina bovine chip (Illumina Infinium (R) bovineHD BeadChip). Seven traits were analyzed milk yield (MY), fat yield (FY), protein yield (PY), lactose yield (LY), fat percentage (F%), protein percentage (P%) and somatic cell score (SCSt). Two analyses were done: one using phenotypic and pedigree information (matrix A) and in the other using a matrix based in pedigree and genomic information (one step, matrix H). 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-calving season), number of milking (2 levels), and age of buffalo 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. The heritability estimates using matrix A were 0.25, 0.22, 0.26, 0.17, 0.37, 0.42 and 0.26 and using matrix H were 0.25, 0.24, 0.26, 0.18, 0.38, 0.46 and 0.26 for MY, FY, PY, LY, % F, % P and SCCt, respectively. The estimates of the additive genetic effect for the traits were similar in both analyses, but the accuracy were bigger using matrix H (superior to 15% for traits studied). The heritability estimates were moderated indicating genetic gain under selection. The use of genomic information in the analyses increases the accuracy. It permits a better estimation of the additive genetic value of the animals.