Cattle Chromosomes Research Articles

Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human

A comprehensive physical map was generated for Ovis aries chromosome X (OARX) based on a cytogenomics approach. DNA probes were prepared from bacterial artificial chromosome (BAC) clones from the CHORI-243 sheep library and were assigned to G-banded metaphase spreads via fluorescence in-situ hybridization (FISH). A total of 22 BACs gave a single hybridization signal to the X chromosome and were assigned out of 32 tested. The positioned BACs contained 16 genes and a microsatellite marker which represent new cytogenetically mapped loci in the sheep genome. The gene and microsatellite loci serve to anchor between the existing radiation hybrid (RH) and virtual sheep genome (VSG) maps to the cytogenetic OARX map, whilst the BACs themselves also serve as anchors between the VSG and the cytogenetic maps. An additional 17 links between the RH and cytogenetic maps are provided by BAC end sequence (BES) derived markers that have also been positioned on the RH map. Comparison of the map orders for the cytogenetic, RH, and virtual maps reveals that the orders for the cytogenetic and RH maps are most similar, with only one locus, represented by BAC CH243-330E18, mapping to relatively different positions. Several discrepancies, including an inverted segment are found when comparing both the cytogenetic and RH maps with the virtual map. These discrepancies highlight the value of using physical mapping methods to inform the process of future in silico map construction. A detailed comparative analysis of sheep, human, and cattle mapping data allowed the construction of a comparative map that confirms and expands the knowledge about evolutionary conservation and break points between the X chromosomes of the three mammalian species.

The karyotype of the domestic sheep (Ovis aries) identified by quinacrine mustard staining and fluorescence microscopy.

The modal chromosome number of the domestic sheep (Ovis aries) is 54. It is possible to identify 25 out of the 27 pairs of chromosomes by means of quinacrine mustard staining and fluorescence microscopy. There is often a considerable difference in length between the homologues of the same pair. The submetacentric autosomes may be derived from the basic karyotype of the family Bovidae by Robertsonian fusion. Consequently, the karyotype of the sheep chromosomes has been arranged in another way than in the goat and cattle. The Q-band pattern of the sheep autosomes is identical with that of the goat autosomes, except the Robertsonian fusions, and with cattle autosomes, except Pair No. 16. In the sheep, the X chromosome is one of the largest chromosomes of the karyotype. Its relative length is about 0.5 per cent smaller than in the other two species studied. Nevertheless, the number of Q-bands in the X chromosome of the sheep seems to be the same as in the goat and cattle, but the sequence of the bands is different. The Y chromosome of the sheep is the smallest chromosome, and its fluorescence is identical with the Y chromosome of goat and cattle.

Recognition of the cattle chromosomes by the Q- and G-banding techniques.

Utilization of the quinacrine mustard fluorescence technique supported by photoelectric recordings, and a modified Giemsa staining technique with trypsin pretreatment has made possible an accurate analysis of the cattle chromosomes. All individual chromosome pairs have been identified, and the most clear-cut distinguishing characteristics have been described.

Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20

BackgroundFluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method.ResultsAs proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis) chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46%) were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly.ConclusionDissociation curve analysis is reliable and efficient for radiation hybrid panel scoring, and is more sensitive and robust than conventional gel-based typing methods. Several markers could be scored only by the new method, and ambiguous scores were reduced. PCR-based dissociation curve analysis decreases both time and resources needed for construction of radiation hybrid panel marker maps and represents a significant improvement over gel-based methods in any species.

Chromosome evolution in the subtribe Bovina (Mammalia, Bovidae): The karyotype of the Cambodian banteng (Bos javanicus birmanicus) suggests that Robertsonian translocations are related to interspecific hybridization

Three subspecies of banteng (Bos javanicus) have been described: B. j. javanicus in Java, B. j. lowi in Borneo, and B. j. birmanicus in Cambodia, Lao PDR, Myanmar, Thailand and Vietnam. In this paper we provide the first description of the karyotype of the Cambodian banteng. The chromosomal complement of B. j. birmanicus differs from that of B. j. javanicus, which was previously found to be similar to that of cattle, Bos taurus (2n = 60). The Cambodian banteng karyotype has a diploid number of 2n = 56 (FN = 62) and the karyotype consists of 26 pairs of acrocentric chromosomes and two pairs of submetacentric chromosomes. Comparisons with other species of the subtribe Bovina show that the two pairs of bi-armed chromosomes resulted from two centric fusions involving the equivalent of cattle chromosomes 1 and 29, and 2 and 28, respectively. Cross-species fluorescence in-situ hybridization (FISH) with B. taurus whole chromosome paints and satellite DNA I probes was used to identify the chromosomes involved in the translocations, and their orientation. We suggest that Robertsonian translocations (1;29) and (2;28) have been fixed in the common ancestor of Cambodian banteng as a consequence of hybridization with the kouprey (Bos sauveli) during the Pleistocene epoch.

TIGER: A software system for fine-mapping quantitative trait loci

Abstract. The localisation of quantitative trait loci which contribute significantly to phenotype variation of economically important traits in domestic species has become an important goal in animal genomics. Several such loci have been roughly identified using linkage analyses; however the focus has now shifted towards fine mapping and pinpointing causal mutations. In the context of a cooperative national research project, the software system TIGER was developed. TIGER is a UNIX script linking several individual Fortran programmes and is used for comprehensive variance component analysis of fine mapping data. Starting with raw genotype data, pedigree and marker map information and ending with a residual maximum likelihood-based test for each putative quantitative trait locus position, the software provides the user with an "all in one" package capable of linkage analysis, linkage disequilibrium analysis and combined linkage/linkage disequilibrium analysis. The software system has been employed in 4 fine mapping projects on 4 distinct cattle chromosomes.

An extended river buffalo (Bubalus bubalis, 2n = 50) cytogenetic map: assignment of 68 autosomal loci by FISH-mapping and R-banding and comparison with human chromosomes

We report an extended river buffalo (Bubalus bubalis, 2n = 50; BBU) cytogenetic map including 388 loci, of which 68 have been FISH-mapped on autosomes in the present study. Ovine and caprine BAC clones containing both type I loci (known genes) and type II loci (simple sequence repeats (SRs), microsatellite marker, sequence-tagged sites (STSs)), previously assigned to sheep chromosomes, have been localized on R-banded river buffalo chromosomes (BBU), which expands the cytogenetic map of this important domestic species and increases our knowledge of the physical organization of its genome. The loci mapped in the present study correspond to loci already localized on homoeologous cattle (and sheep) chromosomes and chromosome bands, further confirming the high degree of chromosome homoeologies among bovids. The comparison of the integrated cytogenetic maps of BBU2p/BBU10 and BBU5p/BBU16 with those of human chromosomes (HSA) 6 and 11, respectively, identified, at least, nine conserved chromosome segments in each case and complex rearrangements differentiating river buffalo (and cattle) and human chromosomes.

Limousin myostatin F94L variant affects semitendinosus tenderness

Texture parameters (peak force and compression), muscle myofibre diameter, and hydroxyproline were measured in semitendinosus samples from a cattle gene-mapping herd. The data were analysed to determine the relationships between these traits. The traits were also mapped by genetic linkage analysis to identify quantitative trait loci, and hence, candidate genes for these traits. Neither texture parameters were affected by the muscle structural traits of myofibre diameter or collagen content (as measured by hydroxyproline), despite significant variation in these traits between animals. QTL for the texture parameters of peak force and compression, as well as collagen content, were found on cattle chromosome 2 (BTA2) and attributed to the myostatin gene. Within the cattle population used for the QTL mapping, a gene variant of myostatin, F94L, has been previously shown to increase muscle mass, predominantly in the semitendinosus. It was determined herein that the F94L myostatin homozygous animals had more tender meat as measured by both peak force and compression. The variant was also responsible for a reduction in the collagen/elastin content of muscle. The myostatin F94L variant had no effect on muscle myofibre diameter of the semitendinosus, even though the variant causes substantial increases in muscle mass. Consequently, the increase in muscle mass of the variant must be due to myofibre hyperplasia and not hypertrophy. In addition, myostatin effects on tenderness are caused by changes in the extracellular matrix rather than muscle myofibre diameter.

Microdissected Bovine X Chromosome Segment Delineates Homologous Chromosomal Regions in Sheep and Goat

In this study we microdissected the proximal part band Xq24 of the bovine X chromosome long arm, in which the Xist gene is located in cattle. The obtained DNA fragment was PCR amplified, labelled and used as a probe for cattle, sheep and goat chromosomes. In cattle, as expected, distinct hybridization signals were observed on Xq24. The painting signals were also observed on Xq24 in sheep and goat. The chromosome painting probes can be used for comparative mapping and searching for internal X chromosome rearrangements in Bovidea and may contribute to the understanding of mammalian sex chromosome evolution.

Analysis of chromosomal localization of loci controlling milk production traits in cattle

Analysis of the pattern of the chromosomal localization of quantitative trait loci (QTLs) is necessary for comprehensively understanding their functions. The chromosomal localization of QTLs controlling milk production traits has been studied in cattle chromosomes. The distribution of QTLs between chromosomes has proved to be binomial. Their distribution along each chromosome was, in general, uniform, except for the QTLs controlling the somatic cell score (SCS), which tended towards telomeric location. However, there are chromosomes either enriched with or particularly poor in QTLs. The QTL distribution patters are the most similar for the milk yield (M) and milk protein yield (P) and for milk fat yield (F) and milk fat content (%F). The pattern of the SCS QTLs stands out among those of other QTLs. The distance between the QTLs of contrasting traits is the shortest for M and P QTLs, longer for M and milk protein content (%P) QTLs, and still longer for M and %F QTLs, which may be explained by QTL pleiotropy, a common phenomenon in cattle.

A comparative radiation hybrid map of sheep chromosome 10

Comparative radiation hybrid (RH) maps of individual ovine chromosomes are essential to identify genes governing traits of economic importance in sheep, a livestock species for which whole genome sequence data are not yet available. The USUoRH5000 radiation hybrid panel was used to generate a RH map of sheep chromosome 10 (OAR10) with 59 markers that span 1,422 cR over an estimated 92 Mb of the chromosome, thus providing markers every2 Mb (equivalent to every 24 cR). The markers were derived from 46 BAC end sequences (BESs), a single EST, and 12 microsatellites. Comparative analysis showed that OAR10 shares remarkable conservation of gene order along the entire length of cattle chromosome 12 and that OAR10 contains four major homologous synteny blocks, each related to segments of the homologous human chromosome 13. Extending the comparison to the horse, dog, mouse, and chicken genome showed that these blocks share conserved synteny across species.

Fluorescent in-situ hybridization of cattle and sheep chromosomes with cloned human fragile-X DNA

An extensive study on spontaneous and 5-Fluorodeoxyuridine induced fragile sites identified Xq31 in cattle (Bos taurus) and (Xq24, Xq26) in sheep (Ovis aries) in addition to several autosomal fragile sites (under publication). A ZOO-FISH study using three cloned human fragile-X probes with CCG/CGG(n) trinucleotide repeat sequence was carried out to determine homology between human and bovine fragile-X. The hybridisation results showed only a weak signal on a human chromosome that was not an X with all three fragile site probes. No signals were detected in sheep chromosomes. The signal of all three human fragile-X probes on cattle chromosomes was however, medium-prominent sub-centromeric signal on two homologues. BrdU administration in 12 h before harvesting identified these homologues to be chromosome number 5. In addition retrospective slides of cattle and sheep chromosomes used for fragile site studies showed no signals whatsoever. It was therefore concluded that no homology existed between human and bovine fragile-X.

Sister chromatid exchange in chromosomes of cattle from three different breeds reared under similar conditions

A homogeneous group (same sex, age and environmental conditions) of 35 Italian cattle of the Podolian, Friesian, and Romagna breeds was investigated concerning the spontaneous incidence of sister chromatid exchange (SCE). The mean values of SCEs/cell were 7.9 +/- 3.4, 7.1 +/- 3.3, and 7.3 +/- 3.2 in the Podolian, the Friesian, and the Romagna breeds, respectively, with significant differences between the Podolian and the Friesian breeds. Simultaneous disclosure of SCEs and fluorescent G-bands in the lighter chromatid made possible the identification of chromosome 1, in addition to the biarmed X and Y chromosomes. The inter-chromosomal SCE-distribution revealed a nonrandom pattern due to significantly increased values of SCEs in chromosomes 1 and X, particularly in the Romagna breed.

Chromosomal localization of the glucose phosphate isomerase (GPI) gene in cattle, sheep and goat by in situ hybridization - chromosomal banding homology versus molecular conservation in Bovidae

A porcine genomic glucose phosphate isomerase (GPI) DNA probe was used for in situ hybridization with metaphase chromosomes in cattle, sheep and goat. The probe gave distinct signals on the q22----proximal part of the q24 segment of chromosome 18, 14 and 18 in cattle, sheep and goat, respectively, indicating the location of GPI gene. The three species belong to the family Bovidae and have high resemblance in chromosome banding patterns. The localization of the GPI locus to the same site on chromosomes with almost similar banding patterns suggests high degree of homology at these sites in the three species. Correlation between banding homologies and possible similarities at the molecular level is discussed.

High-resolution studies on late-replicating segments (G + C bands) in mammalian chromosomes.

High resolution of late-replicating segments (G + C bands) in chromosomes of human, cattle and water buffalo was obtained by using 5-bromodeoxyuridine incorporation early in the cell cycle, simultaneous with methotrexate treatment combined with reduced colcemid treatment and addition of ethidium bromide, which increased the proportion of prometaphase cells. Giemsa counterstaining, following fluorescence microscopy observation and treatment with 2 x SSC, improved the resolution of the banding patterns, particularly in the pericentromeric regions. Acrocentric bovine and water buffalo chromosomes, which were seen to be C-positive by fluorescence microscopy observation and C-negative after counterstaining, showed the presence of subcentromeric G-positive bands within the heterochromatic blocks of several chromosomes.

Centromeric loss in translocation of centric fusion type in cattle and water buffalo.

Iannuzzi, L., Di Berardino, D., Gustavsson, I., Ferrara, L. and Di Meo, G. P. 1987. Centromeric loss in translocations of centric fusion type in cattle and water buffalo. - Hereditas 106: 73–81. Lund, Sweden. ISSN 0018–0661. Received March 15, 1986 Robertsonian translocations in Podolian and Romagna cattle (Bos taurus L.) and Asiatic river buffaloes (Bubulus bubalis L.) were studied with C, G + C, and R-banding techniques. The investigation demonstrated: (a) presence of one block of constitutive heterochromatin in the q-arm of the cattle translocation chromosome; (b) chromosomes identified as 1 and 25 according to the system used - but presumptively 1 and 29 as earlier described - being involved in the cattle centric fusions, with the centromere region of chromosome 25(29) being lost and that of chromosome 1 being retained; (c) no constitutive heterochromatin in the q-chromosome arm of the bi-armed chromosomes 1 and 5 in the water huffaloes (with retention of the constitutive heterochromatin in their p-arms) and partial losses of centromeric heterochromatin in both arms of chromosomes 2, 3 and 4; (d) presence of a C-positive segment in the telomere region of the p-arm of chromosome 4 in the water buffalo; (e) no bi-armed chromosome common for the two species. Karyotype evolution is discussed and the urgency of an appropriate nomenclature system for cattle and buffalo chromosomes is briefly stressed.

Fluorescent G- and C-bands in mammalian chromosomes by using early BrdU incorporation simultaneous to methotrexate treatment.

Fluorescent G- and C-bands were obtained in human and cattle chromosomes of lymphocytes grown at 37.5D for 72–76 hours. 24 hours before the completion of the culture, 5-bromodeoxyuridine (BrdU) in a final concentration of 20 μg/ml and increasing doses of methotrexate (MTX) were added. After 17 hours the cells were washed and allowed to recover for 6 hours in a medium containing thymidine. Colcemid treatment lasted 1.5 hours. The air dried slides were stained with acridine orange and observed under fluorescence microscopy. Compared to the control (without MTX), it was possible by increasing the MTX doses to increase the number of cells in the first cycle of replication in the presence of BrdU (G-bands in both chromatids) with a concomitant reduction of the number of cells in the second cycle of replication (G-bands in one chromatid), which also allows demonstration of SCEs. The advantages of this technique and the different cellular responses between the two species are discussed.

The origin of selection signatures on bovine chromosome 6

The extent and pattern of linkage disequilibrium (LD) between closely spaced markers contain information about population history, including past population size and selection history. Selection signatures can be identified by comparing the LD surrounding a putative selected allele at a locus to the putative non-selected allele. In livestock populations, locations of selection signatures identified in this way should be correlated with QTL affecting production traits, as the populations have been under strong artificial selection for these traits. We used a dense SNP map of bovine chromosome 6 to characterize the pattern of LD on this chromosome in Norwegian Red cattle, a breed which has been strongly selected for milk production. The pattern of LD was generally consistent with strong selection in regions containing QTL affecting milk production traits, including a strong selection signature in a region containing a mutation known to affect milk production. The results demonstrate that in livestock populations, the origin of selection signatures will often be QTL for livestock production traits, and illustrate the value of selection signatures in uncovering new mutations with potential effects on quantitative traits.

Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam

BackgroundThe wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci.ResultsOne hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively.ConclusionExtensive conservation of cattle microsatellite loci in the wild gaur genome, as shown by our results, indicated a high applicability of bovine microsatellites for genetic characterization and population genetic studies of this species. Moreover, the low genetic diversity observed in Vietnamese wild gaur further underlines the necessity of specific strategies and appropriate management plans to preserve this endangered species from extinction.

Effect of myostatin F94L on carcass yield in cattle

In this study, a highly significant quantitative trait locus (QTL) for meat percentage, eye muscle area (EMA) and silverside percentage was found on cattle chromosome 2 at 0-15 cM, a region containing the positional candidate gene growth differentiation factor 8 (GDF8), which has the common alias myostatin (MSTN). Loss-of-function mutations in the MSTN gene are known to cause an extreme 'double muscling' phenotype in cattle. In this study, highly significant associations of MSTN with cattle carcass traits were found using maternally inherited MSTN haplotypes from outbred Limousin and Jersey cattle in a linkage disequilibrium analysis. A previously reported transversion in MSTN (AF320998.1:g.433C>A), resulting in the amino acid substitution of phenylalanine by leucine at position 94 of the protein sequence (F94L), was the only polymorphism consistently related to increased muscling. Overall, the size of the g.433C>A additive effect on carcass traits was moderately large, with the g.433A allele found to be associated with a 5.5% increase in silverside percentage and EMA and a 2.3% increase in total meat percentage relative to the g.433C allele. The phenotypic effects of the g.433A allele were partially recessive. This study provides strong evidence that a MSTN genotype can produce an intermediate, non-double muscling phenotype, which should be of significant value for beef cattle producers.