Chromosomal evolution in bovids: a comparison of cattle, sheep and goat G- and R-banded chromosomes and cytogenetic divergences among cattle, goat and river buffalo sex chromosomes

A G- and R-banding comparison of cattle (Bos taurus, 2n = 60), goat (Capra hircus, 2n = 60) and sheep (Ovis aries, 2n = 54) chromosomes at the 450 band level was made. The study revealed a large number of banding homologies among the autosomes of the three species and resolved some ambiguities in arranging some of their small disputed acrocentrics by direct and indirect comparisons with some bovid marker chromosomes. A loss of the subcentromeric G-positive band in sheep chromosome 2g was observed when the G-banding patterns of sheep 2q and homologous cattle and goat chromosome 2 were compared. The chromosomal divergences among cattle, goat and river buffalo (Bubalus bubalis, 2n = 50) sex chromosomes are shown to have occurred by pericentric and paracentric inversions with a loss (or acquisition of constitutive heterochromatin.

Nucleotide diversity of mitochondrial DNAs between the swamp and the river types of domestic water buffaloes, Bubalus bubalis, based on restriction endonuclease cleavage patterns

Cleavage patterns of mitochondrial DNAs (mtDNAs) by 15 restriction endonucleases were analyzed for 10 swamp and 13 river types of domestic water buffaloes. Digestions with nine enzymes exhibited polymorphisms giving two or three kinds of cleavage patterns. Five mtDNA types were identified, three types in the swamp buffaloes of the Philippines, Vietnam, and Indonesia (S-types) and two types in the river buffaloes of Bangladesh and Pakistan (R-types). Nucleotide diversities ranged from 0.2 to 0.6% within the S- and R-types and from 1.9 to 2.4% between the R-types and the S-types. These values indicated that R-type and S-type mtDNAs differentiated at the subspecific level of other mammalian species reported. The possibility of polyphyletic domestication in different places is discussed for the origin of two distinct types of domestic water buffaloes.

Assessment of amplicons in the DNA from boiled tissue by PCR and AP-PCR amplification

Polymerase chain reaction (PCR) is a technique sensitive enough to amplify small DNA fragments a billion-fold. The generation of amplicons either by PCR with a set of oligo primers or by arbitrarily primed AP-PCR with a single oligonucleotide primer is based on the availability of intact template and priming sites. With these approaches, it is possible to generate specific and random amplicons to assess the extent of damage to DNA caused by any of the physical, chemical, or environmental factors. We report the amplification of sex chromosome and autosome specific loci in the buffalo (Bubalus bubalis) genome by symmetrical and AP-PCR performed on DNA samples isolated from the muscle tissues that were boiled (treated) for different lengths of time. No difference was noticed in the amplification profile of DNA cooked for various lengths of time. However, after HinfI treatment, AP-PCR amplification of these DNAs revealed more bands on agarose gel than unrestricted samples. The successful amplification of the DNA samples isolated from the boiled tissues is attributed to the intactness of the amplicons. This suggests that despite storage for more than a year and subsequent heat treatment to the muscle tissues, the DNA remains a good substrate for PCR and AP-PCR amplification. Relevance of this work in the context of DNA probe technology is discussed.

Hereditary suprabasilar acantholytic mechanobullous dermatosis in buffaloes (Bubalus bubalis)

A skin disease characterized by trauma-induced sloughing of haired skin, hooves, and horns is described in four calves from a herd of Murrah buffaloes (Bubalus bubalis) in Brazil. Affected calves were detected shortly after birth by the presence of lesions affecting the distal extremities, the scapular and gluteal regions, and the tip of the tail. On histologic evaluation of affected skin, the lesions were characterized by suprabasilar vesicles and acantholysis affecting the epidermis and outer root sheath of the hair follicle infundibulum. The basal cell layer was intact and appeared as a single layer of cuboidal cells attached to the dermis. Ultrastructurally, the region between the stratum basale and the lower stratum spinosum had widened intercellular spaces with loss of desmosomal attachments, which led to the suprabasilar separation. The disease appears to be inherited as an autosomal recessive trait.

Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes

To clarify the genetic relationship between Swamp and River buffaloes, the restriction fragment length polymorphisms (RFLPs) of nuclear genomic ribosomal DNA (rDNA) and cytoplasmic mitochondrial DNA (mtDNA) were analysed. Blood or liver samples from 73 Swamp and three River buffaloes were collected in East and South-east Asian countries. DNA samples from cattle, goats and sheep were used for comparisons. The analysis of rDNA allowed water buffaloes, cattle, goats and sheep to be characterized by four distinct repeat-types. However, swamp and river buffaloes showed the same repeat-type. Divergence of water buffalo and cattle is considered to have occurred approximately four to six million years ago. The RFLPs for mtDNA divided water buffaloes into three haplotypes, swamp-1, swamp-2 and river types. Swamp-1 accounted for 91% of all swamp buffaloes while swamp-2 was observed only in water buffaloes from Thailand (9%). All river buffaloes were of the same haplotype. No differences were observed between swamp and river buffaloes at the rDNA level. In contrast, a few distinct differences between them were found at the mtDNA level. Therefore, mtDNA polymorphisms provide an adequate means for classifying water buffaloes into either swamp or river buffaloes.

Localization of uridine monophosphate synthase (UMPS) gene to river buffalo chromosomes by FISH

Uridine monophosphate synthase plays an important role in pyrimidine synthesis, converting orotic acid to uridine 5' monophosphate. In cattle, UMPS deficiency is inherited as a monogenic autosomal recessive trait. While heterozygous carriers are phenotypically normal, homozygotes are lethal in utero (Shanks et al. 1992). UMPS has been mapped to human chromosome 3q13 (Qumsiyeh et al. 1989), sheep chromosome 1q (Burkin et al. 1993) and cattle chromosome 1q31 (Ryan et al. 1994). In the present study we used a cattle genomic probe to localize UMPS to river buffalo chromosomes by fluorescence in situ hybridization.

Standard karyotype of the river buffalo (Bubalus bubalis L., 2n = 50). Report of the committee for the standardization of banded karyotypes of the river buffalo

During the 10th European Colloquium on Cytogenetics of Domestic Animals held in Utrech, The Netherlands, in 1992, an international committee on river buffalo chromosomes was established. At the recent 8th North American Colloquium on Domestic Animal Cytogenetics and Gene Mapping in Guelph, Canada (1993), Q-, G- and R-banded river buffalo karyotypes were presented and discussed. This material was used to establish the first standard karyotype of the river buffalo.

Animal breeding and conservation genetics

Conservation genetics in an animal breeding context relates both to questions of preservation of rare and endangered breeds or populations, and to utilization with planned genetic change to improve viability, productivity, and efficiency of production. In the developed world, preservation is the primary issue, and various organizations exist which are committed to the preservation of rare and endangered breeds. In the developing world, breeds as such often are not defined or recognized, but many local populations exist that are adapted to and integrated into existing production systems. The genotypes of at least some of these populations could well also be crucial for future production systems, but many are threatened, primarily by crossbreeding with breeds introduced from the developed world. However, not all can be conserved, and priorities will have to be set for preservation, for development (breeding programs) and for evaluation for future programs. Some priorities will be set for pragmatic reasons, but the primary rational reason must be that a breed is in some way genetically unique, and makes a substantial contribution to the genetic diversity of the species. Thus, measures of genetic distance are essential to quantify the degree of genetic differentiation among populations, but such measures must be based on a large sample of loci. Although this has been emphasized many times, it still seems not to be adequately appreciated, and the effect of using a limited sample of loci is illustrated with an example from swamp buffalo populations. Comparative estimates of distances based on electrophoretic variation and direct DNA variation (both mitochondrial and genomic) are needed as a basis for future work on conservation of the global domestic animal diversity. Finally, studies of feral populations and wild relatives of domestic animals will provide a link between natural populations and domestic animal populations, and bring together these two areas, which to now have been largely separate.

Chromosomal localization of the lysozyme gene cluster in river buffalo (Bubalus bubalis L.)

Lysozyme (LYZ) is an antibacterial enzyme which allows the digestion of bacteria present in tears and saliva. In the true stomach of ruminants LYZ breaks open the bacteria of the foregut, which are subsequently digested by typical mammalian digestive enzymes, allowing the incorporation of nutrients from the bacteria. Southern analysis with a single exon from a cow lysozyme gene revealed that there are about 10 genes in ruminants (Irwin & Wilson 1989), while pig and primates have a single lysozyme gene (Swanson et al. 1991) and camels have two (Irwin et al. 1992). The higher number of LYZ genes in ruminants is believed to be the result of gene duplication associated with the evolution of foregut fermentation (Irwin et al. 1992). Recently, the genomic organization of the lysozyme gene family has been determined in domestic cattle, and, using a cocktail of genomic clones, the lysozyme gene cluster (LYZ/) was assigned to chromosome (Chr) 5, band 23 by fluorescence in situ hybridization (FISH) (Gallagher et al. 1993). In our continued effort to test the genetic homology of conserved chromosome banding regions between cattle and river buffalo, and to extend the river buffalo physical gene map, we have mapped the LYZ/ by FISH and R-banding.

Detection of genome specific monomorphic loci in Bos taurus and Bubalus bubalis with oligodeoxyribonucleotide probe

A synthetic oligodeoxyribonucleotide probe (OAT36) comprising nine repeats of 5'GACA 3' and several enzymes were used to analyse cow, (Bos taurus) and buffalo (Bubalus bubalis) genomes and a number of monomorphic loci were detected in both the species. Different animals from the same species showed an almost 'similar' monomorphic hybridization pattern but animals from two separate species showed a different 'genome specific' pattern. The overall hybridization with any enzyme and probe combination was found to be unique to one species. This forms the basis of genome specific hybridization which is substantiated by our zoo-blot hybridization studies. The evolutionary aspect of these loci in the context of sequence polymorphisms is discussed.

Genetic studies of water buffalo blood markers. I. Red cell acid phosphatase, albumin, catalase, red cell alpha-esterase-3, group-specific component, and protease inhibitor

We have developed the methodologies for typing and family studies to establish the modes of inheritance of water buffalo red cell acid phosphatase (Acp), protease inhibitor (Pi), and group-specific component (Gc) on isoelectric focusing and albumin (Alb), red cell alpha-esterase-3 (Est-3), and catalase (Cat) on polyacrylamide gel electrophoresis. Family studies showed that Pi, Gc, Alb, and Cat are coded by autosomal genes with two codominant alleles, while Est-3 is autosomal with two codominant alleles and a recessive null allele and Acp exhibits three codominant alleles.

Chromosomal localization of omega and trophoblast interferon genes in cattle and river buffalo by sequential R-banding and fluorescent in situ hybridization

Fluorescent in situ hybridization (FISH) of the cattle cDNA probe bTP-509 to RBA-banded cattle (Bos taurus L.) chromosomes confirmed the assignment of the omega (IFNW) and trophoblast (IFNT) interferon genes to chromosome 8q15. Using the same probe, these genes were also localized to river buffalo (Bubalus bubalis L.) chromosome 3q15 following sequential RBA-banding and FISH. The extensive G- and R-banding homology observed between cattle chromosome 8 and river buffalo chromosome arm 3q supports the conserved chromosomal location of the IFNW and IFNT genes in these two species.

Electrophoretic and chromatographic evidence for allelic polymorphisms in the river buffalo alpha-globin gene complex

Isoelectric focusing in the ultranarrow immobilized (7.1-7.5) pH gradient (IPG) of hemoglobin and high-performances liquid chromatography (HPLC) of globin chains were used to investigate Hb polymorphism in Italian river buffalo. Six different phenotypes, each characterized by two or four different Hbs, were detected by IPG, whereas two different II alpha-globin chains were separated from two different I alpha-chains by HPLC. Two alpha-chains (I alpha 1 and II alpha 3), and Hbs with similar mobilities (Hb1 and Hb3), were associated with the AA Hb phenotype: two alpha-chains (I alpha 2 and II alpha 4), and Hbs with different mobilities (Hb2 and Hb4), were associated with the BB phenotype: two sets of doublet Hbs were associated with the AB phenotype, thus suggesting allelic polymorphisms at the two alpha loci. An allele at the beta locus is responsible for increasing to as many as eight the number of different Hbs, thus further complicating the notable Hb polymorphism of the river buffalo.

Transferrin and albumin polymorphisms in buffaloes from Brazil

Starch gel electrophoresis disclosed six transferrin phenotypes, explainable by three alleles (TF A, TF D, TF E), and three albumin phenotypes, determined by two alleles (ALB A, ALB B). Their prevalences suggest that the Brazilian populations have admixed river and swamp buffalo ancestry, the frequency of ALB A being much higher than those found in other regions.

The HK/LK polymorphism of erythrocyte cation content in two wild species of east African bovids: demonstrated in wildebeest but not in African buffalo

Concentrations of K and Na were determined in erythrocytes from wildebeest and African buffalo resident in Tanzania. The object was to determine if these species possess the HK/LK polymorphism which is typical of other bovid species, but not of other mammals. The polymorphism is characterized by individuals that are either of the HK phenotype (high K and low Na concentrations in red cells) or LK phenotype (low K and high Na concentrations in red cells). Wildebeest were shown to be polymorphic, with the distribution of phenotypes resembling that in domestic cattle. By contrast the polymorphism was not found in the African buffalo; all 59 individuals examined exhibited the HK phenotype. This was unexpected, since the polymorphism has been observed in five divergent bovid species, including two species (water buffalo and domestic cow) that are closely related to the African buffalo, and classified in the same subfamily (Bovinae). The most parsimonious interpretation of this pattern is that the trait was lost from the African buffalo after species in the Bovinae diverged. The biological significance of the HK/LK polymorphism, and reasons for its presence or absence among species in the Bovidae, remain obscure.

Identification of crossbred buffalo genotypes and their chromosome segregation patterns

Chromosome analysis on different breed types of water buffaloes (Bubalus bubalis) was undertaken to identify their karyotypes and to determine the pattern of chromosome segregation in crossbred water buffaloes. Altogether, 75 purebred and 198 crossbred buffaloes including 118 from Malaysia and 80 from the Philippines, were analyzed in this study. The diploid chromosome number of the swamp buffalo from both countries was 48 and that of the river buffalo was 50, while all F1 hybrids exhibited 49 chromosomes. The F2 hybrids consisted of three different karyotype categories (2n = 48, 2n = 49, and 2n = 50), whereas the backcrosses included two different karyotype categories each, with 2n = 48 and 2n = 49 in the three quarters swamp types and 2n = 49 and 2n = 50 in the three quarters river types. Chi-square tests on pooled data from Malaysia and the Philippines indicated that the distribution of different karyotype categories of F2 animals did not deviate significantly from the 1:2:1 ratio expected if only balanced gametes with 24 and 25 chromosomes were produced by the F1 hybrids. In the three quarters swamp and three quarters river types, the respective karyotypic categories were in ratios approximating 1:1. The distribution of chromosome categories among the F2 hybrids and backcrosses suggests that only genetically balanced gametes of the F1 hybrids are capable of producing viable F2 and backcross generations.

Levels of conservation and variation of heterochromatin and nucleolus organizers in the Bovidae

Chromomycin A3 banding of the mitotic sets of 10 species of Bovidae (cattle, wisent, yak, banteng, gaur, red buffalo, swamp buffalo, sheep, mufflon, and goat) serves to demarcate both centromeric constitutive heterochromatin and R-banding patterns capable of identifying all the chromosomes within a given complement. In all species significant amounts of chromomycin-bright heterochromatin are present at the centromeres of all autosomes, though there was a high degree of intra- and inter-individual variation in the size of the heterochromatic blocks. Marked interspecies differences in the centromeric patterns were evident. The X chromosomes contained appreciable amounts of centromeric heterochromatin only in the two buffaloes. All the animals studied lacked distamycin A - diamidinophenylindole type heterochromatin. AgNO3 staining was applied sequentially to detect the location of active nucleolus organizer regions (NORs). The distribution of NORs was reasonably conservative in most of the species. An exceptional situation was found in the two buffaloes, where only one NOR pair matched with the standard karyotype of the Bovidae.

Testicular cells in hybrid water buffaloes (Bubalus bubalis)

Meiotic chromosome behaviour and testicular histology were studied in water buffaloes (Bubalus bubalis) including two river (Murrah), two swamp and three F1 (Murrah cross swamp) hybrids aged between two and two and a half years, from testicular biopsies obtained by an open surgical method. Meiotic preparations revealed spermatogonial metaphases, pachytene, diplotene, diakinesis, first and second meiotic metaphases and spermatozoa in all three types of buffalo. Chromosome sets ranging from 22 to 26 (most frequent, 24 and 25) with many cells carrying univalent, bivalent and multivalent configurations were observed in hybrids, whereas the meiotic cells in the Murrah and swamp showed chromosome sets exclusively of 25 and 24 (bivalents) respectively. Histological examination of the hybrid testis revealed a large proportion of degenerating spermatocytes and abnormal spermatids in the process of spermiogenesis suggesting that the various synaptic associations leading to unbalanced gametes may be responsible for the degenerating germ cells in the hybrids. The unbalanced meiotic products will probably lead to selection against such spermatozoa or early embryos after fertilisation. Due to a large percentage of germinal epithelial cells in F1 hybrids being wasted, the fertility of backcross and F2 generations will be subnormal.