Journal of Food, Agriculture & Environment, Vol.12 (2), April 2014 379 www.world-food.net Journal of Food, Agriculture & Environment Vol.12 (2): 379-382. 2014 WFL Publisher Science and Technology Meri-Rastilantie 3 B, FI-00980 Helsinki, Finland e-mail: info@world-food.net Received 12 January 2014, accepted 10 April 2014. Molecular diversity of different chicken populations based on nucleotide sequencing Raed M. Al-Atiyat 1, 2 * and Alaeldein M. Abudabos 1 1 Animal Production Department, King Saud University, P. O. Box 2460, Riyadh 11451, Kingdom of Saudi Arabia. 2 Animal Production Department, Mutah University, Jordan. *e-mail: ralatiyat@ksu.edu.sa, raedatiyat@gmail.com Abstract The aim of this study was to describe molecular genetic diversity of indigenous chickens and Lohmann, Hubbard and Ross broiler chickens based on nucleotide DNA sequencing. Sixteen individuals of the four populations were sequenced for haplotype of 470 bp using T7 promoter. A high level of molecular genetic variation was observed within haplotypes of indigenous chickens from different localities in Jordan. This might be due to no selection practices and production purposes performed assuming that indigenous chickens are more for egg production rather than meat. In fact, haplotypes of broiler chickens only showed low molecular genetic variation within individuals. On the other hand, the results of this study suggest that the haplotypic diversity of chicken DNA sequence was high because different breeds of broiler chickens were used. Broiler chickens shared haplotypes, which were grouped together in the evolutionary trees and had common ancestry origin. The indigenous chickens were separately clustered in one group. The commercial broiler individuals were clustered together in a group as a clade of the three broiler populations. Finally, molecular pairwaise differences coefficients (FST) were significant, allowing one to quickly perceive genetic affinities between the studied populations. The FST for indigenous chickens and Hubbard, Lohmann and Ross broiler chickens were 0.447, 0.430 and 0.571, respectively. Key words: Molecular diversity, DNA sequence, indigenous and broiler chickens. Introduction The first non-mammalian farm animal that had its genome sequenced was chicken 1 . The chicken genome has more than twenty-three thousand genes contained in only 1 billion DNA base pairs 1 . The sequencing regions of DNA are either genes or non-coding regions found to be useful for evolutionary studies. In particular, sequencing regions of DNA was successful in describing evolution of chickens covering genetic distances and phylogeny 2-4 . The common sequences technology has been determined using of bacteriophage T7 promoter 5 . It has commonly applicable with this universal DNA primer to any piece of DNA or nucleotide. The determination of genetic evolution based on DNA sequence provides an accurate information for genetic distance level of phylogenetic distinction 6 . In poultry, establishment of genetic evolution among populations and commercial strains is important for identifying their unique genetic resources 7 . On the other hand, the DNA sequencing technology is also widely used to study the genetic diversity and differentiation within and between populations 3, 8-10 . Biodiversity of chicken has been thoroughly studied at different levels and in different regions and countries around the world. All studies agreed on domestication region and origin in Asia as early as 8000 years BC 11-13 . Furthermore, Asian chickens in general might be in close genetic relatedness to current commercial breeds. In particular, Mediterranean chickens might be more genetically similar to commercial chickens in Europe and the world 14 . Jordan, as a Mediterrian country, has genetically characterized its indigenous chickens at phenotypic 15, 16 and molecular levels 4, 17, 18 . The molecular genetic diversity of indigenous chickens using DNA sequencing technology is still lacking, so far. The main aim of this study was to describe molecular genetic diversity of indigenous chickens based on nucleotide DNA sequence. Materials and Methods Sampling of chicken populations: Sixteen individuals of four chicken populations were sampled from Jordan. Four individuals of indigenous chickens were chosen randomly for sampling based on pre-collected information of their phenotype and history at the rearing facilities of rural and commercial farms in this study. In addition, four individuals were also chosen from each of the most popular three commercial broiler strains, Lohmann ® , Hubbard ® and Ross ® , based on different hatchery supplier in Jordan. Sampling was performed by taking a tissue punch of approximately 0.1 cm of the wattle area using an animal punch applicator. DNA extraction and quantification: Each tissue sample was DNA extracted using a commercial kit of E.Z.N.A ® MicroElute Genomic DNA extraction Kit 19 . DNA concentrations and purification were performed using Nano-Drop DNA spectro- photometer. The extracted DNA was purified at amount of 10 ng/μl. DNA sequencing and PCR reaction: The DNA sequencing was genotyped by Macrogen ® Company utilizing commonly used universal primers, T7promoter (5' -TAATACGACTCACTA TAGGG-3' ) into PCR reactions. Subsequently, PCR products were performed using high throughput Applied Biosystems ® 3730XL automated sequencer. Analysis of DNA sequences: The resulting DNA sequences of 470 bp was made available for molecular genetic variation analyses using Arelquin ® genetic Software 20 . The resulting DNA sequence information was analysed for molecular diversity analyses, Analysis of Molecular Variance (AMOVA), minimum spanning network between haplotypes and molecular pairwaise distances and population differentiation were estimated.