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

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.