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Genetic diversity of Bubalus bubalis in Germany and global relations of its genetic background

Citation

Hoeflich, Andreas; Noce, Antonia (2021), Genetic diversity of Bubalus bubalis in Germany and global relations of its genetic background, Dryad, Dataset, https://doi.org/10.5061/dryad.9cnp5hqgc

Abstract

This is the first study aimed to explore the genetic diversity and population structure of domestic water buffalo (Bubalus bubalis) in Germany and their potential relations to herds in other parts of Europe or worldwide. To this end, ear tissue samples of 285 animals from four different herds, including Brandenburg (n=27), Mecklenburg-Western Pomerania (n=28), Lower Saxony (n=26), and Saxony (n=28), together with animals from herds in Bulgaria (n=58), Romania (n=63), and Hungary (n=55) were collected and genotyped using the Axiom Buffalo Single Nucleotide Polymorphism (SNP) Array (90K). This dataset was then merged with 220 genotypes from Brazil, Colombia, Egypt, Turkey, India, Pakistan, Iran, and Italy obtained from public repositories. The multidimensional scaling based on identity by state matrix distances followed by a model-based estimation of population structure revealed a mixed genetic make-up of German buffalos with contribution from Bulgaria (Murrah breed), Romania, and Italy. This analysis was confirmed with a phylogenetic tree based on the fixation index (FST) between populations. Moreover, we performed an analysis for run of homozygosity (ROH) distribution in the genome with our own data. By using ROH, we calculated the inbreeding coefficient (FROH) and identified genomic regions that are potentially under historical selection pressure for German populations. A high degree of genetic diversity and a low inbreeding level was identified in German buffalos, suggesting familiar relations to buffalos in Italy, Romania, and Bulgaria. We further demonstrate that European buffalos stand out from other buffalo populations worldwide, supporting the idea that buffalos not completely disappeared from the European continent during the late Pleistocene. In addition, a novel genotype was identified in Hungarian buffalos, also clearly separate from other buffalo populations included in this study. The high genetic diversity in European buffalos seems to be an excellent prerequisite for the establishment of local breeds characterized by unique traits and features. This study may also be considered as an initial step on the way to genome characterization for the sustainable development of the buffalo economy in Germany and other parts of Europe in the future.

Methods

Genomic DNA, Axiom Buffalo Single Nucleotide Polymorphism (SNP) Array (90K),

Usage Notes

Plink files, raw data. ReadMe file uploaded