Use of molecular markers for the identification of River Buffalo chromosomes: chromosome one

A standard karyotype for the River Buffalo has recently been established. The largest five chromosomes are biarmed and, based on the banding homology between cattle and buffalo chromosomes, were suggested to originate from the fusion of cattle acrocentric chromosomes. The origin of buffalo chromosome 1 is controversial due to the difficulty in differentiating between the small acrocentric cattle chromosomes. Using molecular markers assigned to cattle chromosomes, synteny between CD18, a marker for BTA1, and markers for small acrocentric cattle chromosomes BTA 24 to BTA 29 was investigated in buffalo/hamster somatic cell hybrids. The investigation revealed that CD18 is syntenic with ANT1, a marker for cattle chromosome 27. The present results confirm that buffalo BBU1 results from fusion of cattle BTA 1 and BTA 27. They also underline the importance of biarmed buffalo chromosomes for the identification of small cattle acrocentrics.     

Gene mapping in the river buffalo (Bubalus bubalis L.): five syntenic groups

SUMMARY: Forty-five somatic buffalo-hamster hybrid clones were analysed for the presence or absence of PCR products of 10 primers. Five syntenic groups were identified: CGA-D9S1; CD18-D1S4; OXT-PRNP; LDLR-D7S3; BSPN-D14S2. These same syntenic groups were reported to be syntenic in cattle and were assigned to U2 (BTA 9), U10 (BTA 1), U11 (BTA 13), U22 (BTA 7), and U24 (BTA 14), respectively. Based on chromosomal homology between cattle and river buffalo chromosomes, these syntenic groups are expected to be assigned to buffalo chromosomes BBU 10, BBU 1q, BBU 14, BBU 9, and BBU 15, respectively. ZUSAMMENFASSUNG: Genkartierung beim Flu?büffel (Bubalis bubalis L.): Fünf Synt?niegruppen Fünfundvierzig somatische Büffel-Hamster Hygrid Klone wurden bezüglich An-oder Abwesenheit von PCR Produkten von 10 primern analysiert. Es wurden 5 Synt?niegruppen identifiziert: CGA-D9S1; CD18-D1S4; OXT-PRNP; LDLR-D7S3; BSPN-D14S2. Dieselben Synt?niegruppen wurden in Rindern gfunden und zugeordnet zu U2(BTA 9), U10(BTA 1), U11(BTA 13), U22(BTA 7) und U24(BTA 14). Auf grund chromosomaler Homolgie zwischen beiden Arten sollten die Synt?niegruppen auf den Büffelchromosomen BBU 10, BBU 1q, BBU 14, BBU 9, und BBU 15 liegen.     

The banding patterns of normal canine chromosomes

The chromosomal banding patterns of canine normal chromosome were analyzed by G-, Q-, C- and N-banding techniques. The chromosomes of canine normal lymphocytes consisted of 38 acrocentric autosome pairs and X-, Y-metacentric sex chromosomes. Their G- and Q-banding patterns corresponded to the those reported by Manolache et al. in 1976. C-bands of chromosomes were found on the centromeric regions of the 7th, 26th, 34th, 35th, 37th and 38th pairs of chromosomes. In addition, N-bands whose location had not been confirmed until now were recognized on the telomitic regions of the 7th, 9th and 22nd pairs of chromosomes.     

The mitotic and meiotic chromosomes of the muskrat (Ondatra zibethica L.)

The chromosome number of the muskrat (Ondatra zibethica L.) was determined to be 54 in an investigation of the mitotic and meiotic chromosomes. All chromosomes are one-armed with the exception of one small pair which is biarmed. Further, the X chromosome, one of the largest of the complement, seems to have a small secondary arm making possible an identification of the pair. A systematic investigation of the chromosomes, and especially the sex chromosomes at different stages of the spcrmatocytogenesis, has been performed.     

我国牦牛染色体研究现状

综述了近10年来我国牦牛染色体研究的情况,认为牦牛与普通牛在部分常染色体和Y染色体结构上的差异是导致犏牛雄性不育的原因之一,并指出我国牦牛染色体的研究,今后应以染色体带型标准化,染色体带型与经济性状的相关性,牦牛与其它牛种染色体的比较研究等为主攻方向。     

发酵刺梨渣对贵州水牛×摩拉水牛杂交育肥牛生产性能、肉品质、胃肠道及血液生化指标的影响

试验旨在研究发酵刺梨渣对贵州水牛×摩拉水牛杂交育肥牛生产性能、肉品质、胃肠道发育、血液生化指标的影响.试验选取30头健康贵州水牛×摩拉水牛杂交育肥牛,随机分为3组,每组10头.对照组、试验组1和试验组2饲粮中分别添加0、13％、18％的发酵刺梨渣进行饲喂试验.试验周期90 d.结果显示:3组杂交育肥牛平均日增重差异不显...     

Quantitative trait loci analysis for growth and carcass traits in a half-sib family of purebred Japanese Black (Wagyu) cattle

We used a half-sib family of purebred Japanese Black (Wagyu) cattle to locate economically important quantitative trait loci. The family was composed of 348 fattened steers, 236 of which were genotyped for 342 microsatellite markers spanning 2,664 cM of 29 bovine autosomes. The genome scan revealed evidence of 15 significant QTL (<5% chromosome-wise level) affecting growth and carcass traits. Of the 15 QTL, six QTL were significant at the 5% experiment-wise level and were located in bovine chromosomes (BTA) 4, 5, and 14. We analyzed these three chromosomes in more detail in the 348 steers, with an average marker interval of 1.2 cM. The second scan revealed that the same haplotype of the BTA 4 region (52 to 67 cM) positively affected LM area and marbling. We confirmed the QTL for carcass yield estimate on BTA 5 in the region of 45 to 54 cM. Five growth-related QTL located on BTA 14, including slaughter and carcass weights, were positively affected by the same region of the haplotype of BTA 14 (29-51 cM). These data should provide a useful reference for further marker-assisted selection in the family and positional cloning research. The research indicates that progeny design with moderate genotyping efforts is a powerful method for detecting QTL in a purebred half-sib family.     

The first detection of anti-West Nile virus antibody in domestic ruminants in Egypt

West Nile virus (WNV) is a mosquito-borne disease, usually present as a symptomatic disease but can cause various clinical signs ranged from mild fever to severe encephalitis and death in various animals and humans. In Egypt, the epidemiological data about WNV infection in different animal species particularly in domestic ruminants are scarce. The present study aimed to investigate the seroprevalence of WNV in cattle, buffalo, camel, sheep, and goats at some Governorates northern Egypt. In total, 360 serum samples (100 cattle, 50 buffalo, 50 camels, 85 sheep, and 75 goats) were examined using ELISA. The results revealed that the seroprevalence of WNV among ruminants was highly significant (P = 0.03) at Kafr El Sheikh Governorate (17.6%) in comparison with other the Governorates. Besides, the seroprevalence of WNV antibodies significantly differed between the examined species (P = 0.0001); it was 22%, 0%, 40%, 3.5%, and 5.3% in cattle, buffalo, camel, sheep, and goats, respectively. This is the first study to confirm that domestic ruminants act as a reservoir in the epidemiology of WNV infection and represent a risk for human and equine infections in Egypt.

     

Detection of quantitative trait loci affecting non-return rate in French dairy cattle

The purpose of this study was to map quantitative trait loci (QTL) influencing female fertility estimated by non-return rate (NRR) in the French dairy cattle breeds Prim'Holstein, Normande and Montbeliarde. The first step was a QTL detection study on NRR at 281 days after artificial insemination on 78 half-sib families including 4993 progeny tested bulls. In Prim'Holstein, three QTL were identified on Bos taurus chromosomes BTA01, BTA02 and BTA03 (p < 0.01), whereas one QTL was identified in Normande on BTA01 (p < 0.05). The second step aimed at confirming these three QTL and refining their location by selecting and genotyping additional microsatellite markers on a sub-sample of 41 families from the three breeds using NRR within 56, 90 and 281 days after AI. Only the three QTL initially detected in Prim'Holstein were confirmed. Moreover, the analysis of NRR within 56, 90 and 281 days after AI allowed us to distinguish two FF QTL on BTA02 in Prim'Holstein, one for NRR56 and one for NRR90. Estimated QTL variance was 18%, 14%, 11.5% and 14% of the total genetic variance, respectively, for QTL mapping to BTA01, BTA02 (NRR90 and NRR56) and BTA03.     

Signatures of selection in Charolais beef cattle identified by genome‐wide analysis

Charolais cattle are one of the most important breeds for meat production worldwide; in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8–59.3 Mb on BTA 4; 67.5–69.3 on BTA 5; 39.5–41.0 Mb on BTA 6; and 26.4–29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits.     

Identification of genomic regions related to age at first calving and first calving interval in water buffalo using single-step GBLUP

In Brazil, water buffaloes have been used to produce milk for mozzarella cheese production. Consequently, the main selection criterion applied for the buffalo genetic improvement is the estimated mozzarella yield as a function of milk, fat and protein production. However, given the importance of reproductive traits in production systems, this study aimed to use techniques for identifying genomic regions that affect the age at first calving (AFC) and first calving interval (FCI) in buffalo cows and to select candidate genes for the identification of QTL and gene expression studies. The single-step GBLUP method was used for the identification of genomic regions. Windows of 1 Mb containing single-nucleotide polymorphisms were constructed and the 10 windows that explained the greatest proportion of genetic variance were considered candidate regions for each trait. Genes present into the selected windows were identified using the UOA_WB_1 assembly as the reference, and their ontology was defined with the Panther tool. Candidate regions for both traits were identified on BBU 3, 12, 21 and 22; for AFC, candidates were detected on BBU 6, 7, 8, 9 and 15 and for first calving interval on BBU 4, 14 and 19. This study identified regions with great contribution to the additive genetic variance of age at first calving and first calving interval in the population of buffalo cows studied. The ROCK2, PMVK, ADCY2, MAP2K6, BMP10 and GFPT1 genes are main candidates for reproductive traits in water dairy buffaloes, and these results may have future applications in animal breeding programs or in gene expression studies of the species.     

Detection of Water Buffalo Sex Chromosomes in Spermatozoa by Fluorescence in situ Hybridization

In order to identify X‐ and Y‐bearing spermatozoa in water buffalo by fluorescence in situ hybridization (FISH), some available probes of closely related species were examined. An X‐ and Y‐specific probe set, made from flow sorted yak chromosomes, labelled in somatic metaphases of water buffalo the whole X and Y, respectively, except their centromere regions. A cattle Y‐chromosome repeat sequence (BC1.2) showed strong signal on the telomere region of the buffalo Y‐chromosome, demonstrating the evolutionary conservation of this locus in water buffalo. In hybridization experiments with spermatozoa from five buffaloes, the yak X‐Y paint set demonstrated clear signals in more than 92% (46.8% X and 45.8% Y) of the cells. Using the cattle Y‐chromosome specific BC1.2 probe, clear hybridization signal was detected in more than 48% of the cells. Statistical analysis showed that there was no significant difference between bulls or from the expected 50 : 50 ratio of X‐ and Y‐bearing cells. The probes presented here are reliable to assess separation of X‐ and Y‐bearing spermatozoa.     

Isolation of a herpesvirus serologically related to bovine herpesvirus 1 from a reindeer (Rangifer tarandus)

Serological evidence of exposure of reindeer (Rangifer tarandus) to a virus related to bovine herpesvirus 1 (BHV1) (Synonym: Infectious bovine rhinotracheitis (IBR) virus) has been reported in Canada (El Azhary 1979) and the USA (Dieterich 1981). A serological survey conducted in Finnish Lapland also detected neutralising antibodies to BHV1 in reindeer sera; 23 % of 300 reindeer had detectable antibodies, whereas none of 300 cattle sera from the same region contained antibodies to BHV1 (Ek-Kommonen et al. 1982). There is currently no evidence of BHV1 infection of cattle in Finland, so the isolation and characterisation of the reindeer herpesvirus was of considerable interest. This short communication describes the isolation and preliminary characterisation of a herpesvirus from a reindeer following the administration of dexamethasone.     

Comparison of fattening performance in Brahman grade cattle (Bos indicus) and crossbred water buffalo (Bubalus bubalis) fed on high roughage diet

The objective of this study was to compare the fattening performance in Brahman grade cattle (crossbred cattle) and crossbred water buffalo at the same young age and fed with high roughage based fattening rations in the Philippines. Ten crossbred cattle and 10 crossbred water buffalo, aged between 18 and 24 months old were used in this experiment. The animals were fed diets consisting of 85% Napier or Para grass and 15% concentrate mixture (CM) on a dry matter (DM) basis. The grass, total DM intake and bodyweight gain were significantly (P < 0.01) higher for the crossbred water buffalo than for the cattle. There was no species significant difference in the digestion coefficient and feed conversion rate between the crossbred cattle and water buffalo. The return over feed cost for fattening was significantly (P < 0.05) higher in the crossbred water buffalo than in the cattle. These results clearly indicate that under high roughage‐based fattening rations, young crossbred water buffalo are better able to utilize the roughage and they perform better in terms of feed intake and live weight gains than the crossbred cattle in the Philippines.     

Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle

Feed intake and feed efficiency are economically important traits in beef cattle because feed is the greatest variable cost in production. Feed efficiency can be measured as feed conversion ratio (FCR, intake per unit gain) or residual feed intake (RFI, measured as DMI corrected for BW and growth rate, and sometimes a measure of body composition, usually carcass fatness, RFI(bf)). The goal of this study was to fine map QTL for these traits in beef cattle using 2,194 markers on 24 autosomes. The animals used were from 20 half-sib families originating from Angus, Charolais, and University of Alberta Hybrid bulls. A mixed model with random sire and fixed QTL effect nested within sire was used to test each location (cM) along the chromosomes. Threshold levels were determined at the chromosome and genome levels using 20,000 permutations. In total, 4 QTL exceeded the genome-wise threshold of P < 0.001, 3 exceeded at P < 0.01, 17 at P < 0.05, and 30 achieved significance at the chromosome-wise threshold level (at least P < 0.05). No QTL were detected on BTA 8, 16, and 27 above the 5% chromosome-wise significance threshold for any of the traits. Nineteen chromosomes contained RFI QTL significant at the chromosome-wise level. The RFI(bf) QTL results were generally similar to those of RFI, the positions being similar, but occasionally differing in the level of significance. Compared with RFI, fewer QTL were detected for both FCR and DMI, 12 and 4 QTL, respectively, at the genome-wise thresholds. Some chromosomes contained FCR QTL, but not RFI QTL, but all DMI QTL were on chromosomes where RFI QTL were detected. The most significant QTL for RFI was located on BTA 3 at 82 cM (P = 7.60 x 10(-5)), for FCR on BTA 24 at 59 cM (P = 0.0002), and for DMI on BTA 7 at 54 cM (P = 1.38 x 10(-5)). The RFI QTL that showed the most consistent results with previous RFI QTL mapping studies were on BTA 1, 7, 18, and 19. The identification of these QTL provides a starting point to identify genes affecting feed intake and efficiency for use in marker-assisted selection and management.     

Comparison of serologic tests for detection of Brucella infections in cattle and water buffalo (Bubalus bubalis)

OBJECTIVE: To estimate sensitivity and specificity of 4 commonly used brucellosis screening tests in cattle and domestic water buffalo of Trinidad, and to compare test parameter estimates between cattle and water buffalo. ANIMALS: 391 cattle and 381 water buffalo. PROCEDURE: 4 Brucella-infected herds (2 cattle and 2 water buffalo) and 4 herds (2 of each species) considered to be brucellosis-free were selected. A minimum of 100 animals, or all animals > 1 year of age, were tested from each herd. Serum samples were evaluated for Brucella-specific antibodies by use of standard plate agglutination test (SPAT), card test (CT), buffered plate agglutination test (BPAT), and standard tube agglutination test (STAT). A Bayesian approach was used to estimate sensitivity and specificity of diagnostic tests without the use of a gold standard, assuming conditional independence of tests. RESULTS: Sensitivity and specificity estimates in cattle, respectively, were SPAT, 66.7 and 98.9; CT, 72.7 and 99.6; BPAT, 88.1 and 98.1; and STAT, 80.2 and 99.3. Corresponding test estimates in water buffalo, respectively, were SPAT, 51.4 and 99.3; CT, 90.4 and 99.4; BPAT, 96.3 and 90.7; and STAT, 75.0 and 98.8. Sensitivity of the CT and specificity of the BPAT were different between cattle and water buffalo with at least 95% probability. CONCLUSIONS AND CLINICAL RELEVANCE: Brucellosis serologic test performance varied by species tested, but BPAT had the highest sensitivity for screening cattle and water buffalo. Sensitivity and specificity of more than 2 screening tests can be estimated simultaneously without a gold standard by use of Bayesian techniques.     

A male bovine linkage map for the ADR granddaughter design

The aim of this paper is to present the construction of a male genetic linkage map as a result of the bovine genome mapping project, which is a common effort of the German cattle breeding federation (ADR), four animal breeding institutes, three blood group laboratories and two animal data and breeding value evaluation centres. In total 20 grandsires with 1074 sires were provided from the German cattle population as reference families, 16 of these paternal half‐sib groups are German Holstein families (DH), three are German Simmental (ST) families, and one is a Brown Swiss family (BS). Of 265 markers included in the linkage map, 248 were microsatellite markers, five were bovine blood group systems, eight SSCP markers and four proteins and enzymes. More than 239 000 genotypes resulted from typing the offspring for the respective markers and these were used for the construction of the map. On average 478 informative meioses were provided from each marker of the map. The summarized map length over all chromosomes was 3135.1 cM with an average interval size of 13.34 cM. About 17, 35.7 and 79.1% of the map intervals showed a maximum genetic distance between the adjacent markers of 5, 10 and 20 cM, respectively. The number of loci ranged from two (pseudoautosomal region of the sex chromosome, BTAY) to 15 (BTA23) with an average of 8.8 markers per chromosome. Comparing the length of the chromosomes shows variation from 49.6 cM for BTA26 to 190.5 cM for BTA1 with a mean of 107.7 cM for all autosomes of the genetic linkage map. It was possible to identify chromosomal discrepancies in locus order and map intervals by comparison with other published maps. The map provided sufficient marker density to serve as a useful tool for a scan of segregating quantitative trait loci.     

Sequence diversity and molecular evolutionary rates between buffalo and cattle

Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow. The cross‐species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study, gene diversity between buffalo and cattle was determined using 86 gene orthologues. There was approximately 3% difference in all genes in terms of nucleotide diversity and 0.267 ± 0.134 in amino acids, indicating the possibility for successfully using cross‐species strategies for genomic studies. There were significantly higher non‐synonymous substitutions both in cattle and buffalo; however, there was similar difference in terms of dN– dS (4.414 versus 4.745) in buffalo and cattle, respectively. Higher rate of non‐synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure. Results for relative rate test were assessed with the chi‐squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non‐synonymous sites, indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.     

Cloning,Bioinformatics and Expression Pattern Analysis of Buffalo MC1R Gene

The aim of this study was to clone and analyze the expression pattern of buffalo MC1R gene.A pair of specific primers was designed according bovine MC1R sequence (GenBank accession No.:JN123363.1),with genome DNA of swamp buffalo,White swamp buffalo,Murrah buffalo and Yellow cattle as template,MC1R was amplified by PCR.Then relative expression level of MC1R gene of swamp buffalo,White swamp buffalo,Murrah buffalo and Yellow cattle was analyzed using QRT-PCR,and protein expression was detected by Western blotting method.The results showed that the 954 bp coding region of buffalo MC1R gene was successfully cloned and sequenced,which code for 317 amino acids.The MC1R gene nucleotide sequences and amino acid sequences of swamp buffalo,White swamp buffalo,Murrah buffalo and Yellow cattle were highly conserved.Five polymorphic sites were found between White swamp buffalo and swamp buffalo of MC1R gene,including 476 T→C,618 G→C,881 G→A,930 G→A and 931 A→G,which caused three nonsynonymous mutation sites of Phe159Ser,Glu310Ala and Asp294Ala.The QRT-PCR result showed that relative expressions of MC1R gene of Murrah buffalo,swamp buffalo and Yellow cattle were significant higher than that of White swamp buffalo (P<0.05).The Western blotting results revealed that MC1R protein expression level in swamp buffalo was higher than that of White swamp buffalo.In conclusion,there were amino acids mutation in White swamp buffalo MC1R gene,and MC1R gene relative expression of White swamp buffalo was lower than that of other buffalo,which was the main reason of lacking of melanin production in White swamp buffalo.