Cattle are the most common type of large domesticated ungulates of the subfamily Bovinae and belong to the genus Bos. Generally, cattle are raised as livestock for meat, milk leather, dung and draft purposes. It has been estimated that there were 1.3 billion cattle in the world (Bruford et al., 2003) whereas Bangladesh had 24 million cattle, out of which 6 million were dairy cattle of local and crossbreds (Bhuiyan, 1993). The available breeds in Bangladesh are Red Chittagong, local Pabna, Sahiwal cross breed, Holstein Frisian cross breeds etc. It is speculated that the Red Chittagong evolved through interbreeding among the local cattle on the basis of natural selection. Sahiwal are a breed of zebu cattle, primarily used in dairy production, from the Sahiwal district of Pakistan, a dry region of Punjab which lies along the Indian-Pakistani border (Mason, 1996). The Bangladeshi indigenous cattle breed (Pabna) and Red Chittagong breed, are of particular importance because of their favorable meat, milk, leather and draft quality although their productivity is relatively low in general. Dairying is considered a strong tool to develop village micro economy in Bangladesh (Shamsuddin et al., 2006) to improve rural livelihoods and to alleviate rural poverty. But, like other developing countries, breed substitution and crossbreeding programs have been practiced indiscriminately in Bangladesh for many years with exotic breeds and as a result valuable genetic resources are being lost or diluted.

Genetic diversity or similarity can be measured through genetic markers. These have been used to determine evolutionary relationships within and between species, genera or higher taxonomic categories (Cornuet et al., 1999). RAPD markers, generated by the Polymerase Chain Reaction (PCR) have been widely used since the 1990’s to assess intra-specific genetic variation at the nuclear level (Garrigan et al., 2002). This procedure detects nucleotide sequence polymorphisms in a DNA amplification-based assay using only a single primer of an arbitrary nucleotide sequence. The polymorphism between individuals results from sequence differences in one or both of the primer binding sites and is visible as the presence or absence of a particular RAPD band. Therefore, in order to determine the genetic variability of selective native, exotic and cross cattle populations of Bangladesh, the research was undertaken using RAPD-PCR.

The experimental cattle showed variability in genetical characteristics and the results indicated the effectiveness of RAPD analysis in detecting the level of polymorphism. Randomly 12 primers were tested among them three primers (Table 1) were matched and found polymorphic (Figures 1, 2 and 3).

From the figures, it was observed that primer OPA-03 and OPA-07 were more reproducible and produced a more distinct RAPD profile than primer OPA-09. Three different primers generated various banding patterns and out of the 21 bands scored, 14 bands (66.67%) were found to be polymorphic and 7 bands (33.33%) were found to be monomorphic in nature. Different RAPD patterns generated using the primers in the present experiment are shown in Figure 1 to 3.

Table 2 shows that the frequencies of polymorphic bands varied from primer to primer in which primer OPA-03, OPA-07 and OPA-09 produced 80%, 42.85% and 75% polymorphic loci respectively. Primer OPA-03 produced 10 bands where one at 400 bp and the other 700 bp were monomorphic in all samples. The polymorphic fragments for primer OPA-03 ranged from 900 bp to 2,000 bp. Furthermore, primer OPA-07 and OPA-09 produced 7 and 4 bands, respectively. The range of monomorphic bands for primer OPA-07 and OPA-09 were 700 bp to 1,000 bp, 1,600 bp, respectively. Where as, the range of polymorphic bands were 400 bp to 600 bp and 800 bp to 1,200 bp, respectively. As the number of bands common in all animals produced by primer OPA-07 was (4) greater than the other two primers (2 for OPA-03 and 1 for OPA-09), it can be concluded that OPA-07 may be specific for species or for greater zoological classes (gender, family etc.). This point needs to be clarified in the future by a comparison with other species. Sharma et al. (2009) reported, the size of polymorphic bands ranged between 200 bp and 2,500 bp using 17 operon series random primers to characterize the Malvi and Sahiwal breeds of cattle in Madhya Pradesh, India. In another study involving indigenous African cattle, Gwakisa et al. (1994) used RAPD markers to characterize the local Zebu (Bos indicus) cattle breeds of Tanzania (using ILO 1127 primer) and showed 61% polymorphism which are almost similar to the present study. The degree of polymorphism 66.67% is higher compared to 28% in taurine cattle (Talle et al., 2005) and 18% in zebu cattle (Marle-Koster et al., 2003). Estimation of higher level of genetic variation in the breeds might be consistent with the fact that they are highly polymorphic animals. Polymorphisms at the level of individual, breed, species or gender can be produced by RAPD-PCR but it is difficult to identify the bands. No breed- or sex-specific RAPD bands were detected in this study. Nevertheless, by mean of their monomorphic band profiles, some of the investigated primers can give the information that animals not having these monomorphic bands may not be related to these cattle. More studies should be performed on this matter in comparative genome studies.

This study demonstrated that the short random oligonucleotides of arbitrary sequences can be used to successfully differentiate cattle by variation of RAPD fingerprints in breed-specific DNA pools and subsequently can be used to produce prominent fingerprints in individual animals. The polymorphism of the experimental cattle was 66.67% and suggests that the gene segregation rate has recently increased in these animals. The genetic variation in the experimental cattle populations was high and therefore, there is scope of selective breeding (like ONBS) for future improvement of Red Chittagong, Sahiwal and local cattle. Gradual genetic erosion and extinction is threatening an increasing number of animal species; the major consequence being a loss of global genetic diversity. Sets of genetic markers are required to identify distinct populations so that they can be preserved. The local Bangladeshi Pabna cattle and Red Chittagong cattle are of particular importance because of their favourable meat, milk, leather and draft quality although their productivity is relatively low in general. Like other developing countries, breed substitution and crossbreeding programs with exotic breeds have been practiced indiscriminately in Bangladesh for many years and as a result valuable genetic resources are being lost or diluted. In addition, genetic assessment is also of interest for the design of genetic improvement programs including appropriate choice of breeds for crossbreeding. Thus, it is important to identify molecular characteristics of these breed/populations for undertaking proper breeding programmes and conservation strategy.