Evaluation of genetic variation and phylogenetic relationship among north Indian cattle breeds.(Report)

INTRODUCTION

India possesses the largest livestock population in the world including the highest number of 185.18 million cattle (Livestock Census, 2003). The indigenous zebu cattle (Bos indicus) are characterized by prominent hump, a long face, upright horn or drooping ears, dewlap and slender legs. Color varies from white to grey and black (Acharya and Bhat, 1984). Zebus have relatively lower basal metabolic rate and better capacity of heat dissipation. Therefore, they easily adapt to tropical heat and have also developed resistance to diseases, especially tick born diseases.

Potentially there is much unrecognized beneficial genetic variation present in the rare, especially the semi managed breeds and populations, which form important reservoirs of non-exploited resources. There is a tendency for world wide animal production to be based on a few, highly selected breeds which is causing pressure leading to a reduction in number of local breeds (Blott et al., 1998; Barker, 1999). In India, increasing number of cattle breeds is showing the declining trend in population. These breeds were very popular and widespread till first half of last century as draft or dual purpose breeds, but registered a consistent reduction in their number afterwards due to three major factors: mechanization in agriculture, urbanization, and competition from high yielding cross bred cattle populations. Thus, it is essential that the resources (personal and financial) available be best used to ensure that as much valuable genetic diversity as possible survives into the future. Consequently, first step in assessing genetic conservation needs is development of baseline information: evaluation of their genetic variability and their distribution among the populations.

The biological unit for conservation in domesticated animals is usually the breed. When we are selecting breeds for conservation it may be important not just to consider taxonomic distinctness or between population variations but also to take measures of within population diversity. Such measures could be included into a diversity index and population selected for conservation on the basis of this index. Microsatellite markers had been widely used to analyze phylogenetic relationships among various animal groups and different breeds (Bradley et al., 1994; Edwards et al., 2000; Pandey et al., 2006). Microsatellite loci comprise an attractive potential source of information about population histories and evolutionary processes, as these loci permit simple and accurate typing in combination with high levels of polymorphism and widespread distribution in the genome.

In order to develop objective criteria for conservation of the cattle breeds of northern region viz. Ponwar, Kherigarh, Gangatiri and Kenkatha, we collected data for 20 microsatellite loci in these breeds to determine genetic relationship between them.

MATERIALS AND METHODS

Sample collection and DNA extraction Blood samples were collected from total of 181 individuals representing four cattle breeds: 40 samples from Ponwar breed (P) and 47 each of Kherigarh (K), Gangatiri (G) and Kenkatha breeds (Kn), respectively. In Sampling we attempted to avoid closely related animals and sampled the animals that met the standards for each breed. All these breeds were sampled from their breeding tracts in different districts of Uttar Pradesh state of India. Ponwar cattle were sampled from Puranpur and Madhotanda subdivision of Pilibhit district. Kherigarh cattle were sampled from Nihasan and Pallia subdivision of Lakhimpur- Kheri district. Gangatiri cattle were sampled from Ballia district and Kenkatha was sampled from Banda district. DNA was extracted from blood samples as per the standard protocol (Maniatis et al., 1982).

Microsatellite analysis

A set of 20 microsatellite markers (Table 1) recommended for cattle in FAO's DADIS MoDAD programme were utilized for generating microsatellite genotyping data. Since microsatellite markers are co-dominant, 181 samples correspond to 362 alleles for each microsatellite locus. An amalgamation of 20 co-dominant loci and 181 samples were projected to create 7240 allelic data for the population included in this study. Polymerase Chain Reaction (PCR) was performed utilizing 50-100 ng genomic DNA in a 25 [micro]l reaction volume using PTC-200 PCR machine (MJ Research Inc., MA, USA). The PCR reaction cycle was accomplished by denaturation for 1 min at 95[degrees]C, 30 cycles of '95[degrees]C for 1 min, precise annealing temperature of primer for 1 min, 72[degrees]C for 1 min' and finally extension at 72[degrees]C for 5 min. The PCR products were resolved on 6% denaturing polyacrylamide gels (Sequi GT System, Bio-Rad) and silver stained according to protocol given by Bassam et al. (1991). All the microsatellite markers showed reproducible and discernable bands. Exact …