Identification and Classification of Genome Variants of Khuzestan River Buffalos Using Sequencing Technology

The rapid development of sequencing technologies and bioinformatic tools has made it possible to sequence the entire genome of many species, providing a starting point for exploring the genome-wide genetic diversity of organisms. The buffalo is one of the most important domesticated animals in the world and has great economic value for humans, being used for milk, meat, leather and most importantly as labor. Khuzestani buffalo are among the most important buffalo in Iran. These animals are scattered in western and southwestern Iran. The largest population of this breed is in the Khuzestan province and they are fully adapted to the geographical features of this region

In this study, whole genome sequencing of the Khuzestan buffalo was performed in paired-end format using Illumina technology. Quality control of the readings obtained met all quality parameters and processing of the readings showed that all samples were of high quality. The BWA-MEM software package was then used to match the data to the reference genome. Genome variants were obtained with the Freebayes software. The final filtering of the variant file then took place. This filtering serves to increase the quality of the analysis and to sort out inferior variants.

The alignment percentage for all samples was over 97.44% and also the coverage in the sequenced samples ranged from x 4.3 to x 9.12, indicating reasonable quality of the reads. Also, in this study we identified 76,676,529 million variants fairly evenly distributed on the chromosomes of the Khuzestan buffalo. The highest and the lowest number of variants were observed on chromosome 1 chromosome 28, repectively. In this study, the total number of translocation and inversion mutations in the genome level was 298,193,017 and 135,694,466, respectively. In addition, the ratio of transitions to transversion was estimated at 2.1989 (Ts/Tv).

The presence of genetic diversity in the native population of Iranian buffalos are valuable parameters that can be studied to evaluate the genetic potential of economic traits in these populations in order to design suitable breeding programs.