Genetic Diversity of Bubalus bubalis in Germany and Global Relations of Its Genetic Background - PubMed (original) (raw)

doi: 10.3389/fgene.2020.610353. eCollection 2020.

Saber Qanbari 1, Rayner González-Prendes 2, Julia Brenmoehl 1, María Gracia Luigi-Sierra 3, Michael Theerkorn 4, Marc-André Fiege 5, Heike Pilz 6, Adrian Bota 7, Livia Vidu 8, Csaba Horwath 9, László Haraszthy 10, Pencho Penchev 11, Yordanka Ilieva 11, Tzonka Peeva 11, Wolfgang Lüpcke 12, René Krawczynski 13, Klaus Wimmers 1, Manfred Thiele 14, Andreas Hoeflich 1

Affiliations

Genetic Diversity of Bubalus bubalis in Germany and Global Relations of Its Genetic Background

Antonia Noce et al. Front Genet. 2021.

Abstract

This is the first study 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, animals from different herds in Germany, Bulgaria, Romania, and Hungary were genotyped and compared to genotypes from other populations with worldwide distribution and open to the public. The pilot study analyzed population structure, phylogenetic tree, and inbreeding events in our samples. In buffalos from Germany, a mixed genetic make-up with contributions from Bulgaria (Murrah breed), Romania, and Italy was found. All in all, a high degree of genetic diversity was identified in European buffalos, and a novel genotype was described in Hungarian buffalos by this study. We demonstrate that European buffalos stand out from other buffalo populations worldwide, supporting the idea that buffalos have not completely disappeared from the European continent during the late Pleistocene. 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.

Keywords: Bubalus bubalis; European populations; genetic diversity; genotyping; population structure; run of homozygosity.

Copyright © 2021 Noce, Qanbari, González-Prendes, Brenmoehl, Luigi-Sierra, Theerkorn, Fiege, Pilz, Bota, Vidu, Horwath, Haraszthy, Penchev, Ilieva, Peeva, Lüpcke, Krawczynski, Wimmers, Thiele and Hoeflich.

PubMed Disclaimer

Conflict of interest statement

M-AF, MiT, HP, and RK are employed by the companies Gut Darss GmbH & Co., Hof am Meer GmBH, Wiesenburger Land eG, and Energiequelle GmbH, respectively. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1

FIGURE 1

Geographic map showing the locations with specific coordinates the buffalo samples were collected from, genotyped in the current study. The number of samples for each location are reported in Table 1.

FIGURE 2

FIGURE 2

Methodical workflow chart summarizing the analysis pipeline followed in the current study. QCF = Quality control filters (MAF < 0.05, -geno 0.01, -mind 0.01).

FIGURE 3

FIGURE 3

(A) Multi-Dimensional Scaling (MDS) plot based on genome-wide identity-by-state pairwise inferred with PLINK V1.7, including 36.014 SNPs from 477 individuals. This plot shows the genetic distance between all the 22 populations analyzed worldwide and published in part (Colli et al., 2018a; Deng et al., 2019a). The percentage of variances captured for each dimension is reported in brackets. The dashed circles mark the populations that cluster together. (B) Admixture analysis results at K = 4 and 6, including 22 buffalo populations worldwide. K values indicate the number of ancestries estimation (clusters), K = 6 was the best fitting solution for the lowest cross-validation error reported (CV = 0.61856). Populations are divided by a vertical black line, and it is partitioned into K colored segments that represent the population’s estimated membership fractions in K clusters. The 22 populations are localized in Germany (Ger_Wies, Wiesenburg, n = 28: Ger_Born, Born, n = 28; Ger_Stad, Stadland, n = 26; Ger_Jüt, Jüterbog, n = 27), Italy (Ita_Deng according to Deng et al., 2019a, n = 35; Ita_Colli according to Colli et al., 2018a, n = 15), Mozambique (Mozamb according to Colli et al., 2018a, n = 7), Bulgaria (Bul_Colli according to Colli et al., 2018a, n = 11), Bulgaria (Bul_Noce, n = 58), Hungary (Hun_HT, Földes, n = 19; Hun_Csak, Csákvar, n = 17; Hun_Tisz, Tiszataj, n = 19), Romania (Rom_Colli according to Colli et al., 2018a, n = 9; Rom_Mera, Mera, n = 16; Rom_Serc, Sercaia, n = 47), and also according to Colli et al., 2018a: Brazil (n = 15), Colombia (n = 12), Egypt (n = 15), Turkey (n = 15), Iran (n = 27), India (n = 5), and Pakistan (n = 28). Population labels and the number of individuals of both analyses are reported in Tables 1, 2.

FIGURE 4

FIGURE 4

(A) Multidimensional scaling (MDS) plot based on European buffalo populations available in this work. The dashed circles mark the populations that cluster together. (B) Admixture analysis results at K = 4 and 6 exclusively in European buffalo populations. K = 6 was the best fitting solution for the lowest cross-validation error reported (CV = 0.59712). Abbreviations and sample numbers are specified in Figure 3.

FIGURE 5

FIGURE 5

Phylogenetic tree indicating the genetic distance of 22 buffalo populations, analyzed and published in part (Colli et al., 2018a; Deng et al., 2019a), with worldwide distributions based on the fixation index (FST) matrix obtained from 36,014 SNPs in 477 individuals using Arlequine software. Abbreviations and sample numbers are specified in Figure 3.

FIGURE 6

FIGURE 6

The mean sum of runs of homozygosity (ROH) per population within each ROH length category in samples collected from buffalos in Bulgaria (Bul_Noce), Romania (Rom_Mera, Rom_Serc), Hungary (Hun_Csak, Hun_Tisz, Hun_HT), and Germany (Ger_Born, Ger_Jüt, Ger_Stad, Ger_Wies). Data include 61,813 SNPs genotyped in 285 samples (Mb: megabase); all other abbreviations and sample numbers are specified in Figure 3.

FIGURE 7

FIGURE 7

Violin Plot reporting the proportion of autosome covered in run of homozygosity (ROH) aka Genomic inbreeding coefficients (FROH) in Buffalo populations from Bulgaria (Bul_Noce), Romania (Rom_Mera, Rom_Serc), Hungary (Hun_Csak, Hun_Tisz, Hun_HT), and Germany (Ger_Born, Ger_Jüt, Ger_Stad, Ger_Wies). The black line indicates the median of FROH within the breed. Abbreviations and sample numbers are specified in Figure 3.

FIGURE 8

FIGURE 8

Genomic distribution of ROH islands in German buffalo samples. The x-axis represents the SNP genomic coordinate chromosome-wise, and the y-axis visualizes the frequency (%) of overlapping ROH shared among individuals. The red line indicates the threshold to define the regions containing the top 1% of most common ROH-associated SNPs (ROH hotspots or ROH islands). Populations are presented as (A) Mecklenburg-Western Pomerania (Ger_Born), (B) Brandenburg (Ger_Jüt), (C) Lower Saxony (Ger_Stad), and (D) Saxony (Ger_Wies). Abbreviations and sample numbers are specified in Figure 3.

FIGURE 9

FIGURE 9

Venn diagram reporting the number of common and unique genes present in overlapping ROH regions with the highest frequency SNPs in different buffalo populations from Germany (gene names are referred by Table 6).

FIGURE 10

FIGURE 10

Classification of genes with hotspot SNPs in ROH genome regions. Populations are presented as (A) Mecklenburg-Western Pomerania (Ger_Born), (B) Brandenburg (Ger_Jüt), (C) Lower Saxony (Ger_Stad), (D) Saxony (Ger_Wies). Abbreviations and sample numbers are specified in Figure 3.

Similar articles

Cited by

References

    1. Abd El-Salam M. H, El-Shibiny S. (2011). A comprehensive review on the composition and propertiesof buffalo milk. Dairy Sci. Technol. 91 663–699. 10.1007/s13594-011-0029-2 - DOI
    1. Alexander D. H., Novembre J., Lange K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19 1655–1664. 10.1101/gr.094052.109 - DOI - PMC - PubMed
    1. Alexiev A. (1998). The Water Buffalo. Bulgaria: St. Kliment Ohridski University Press.
    1. Bartosiewicz L. (1999). “The emergence of holocene faunas in the carpathian basin: a review,” in The Holocene History of the European Vertebrate Fauna, Ed. Benecke N., (Rahden: Modern Aspects of Research; ) 6 73–90.
    1. Biscarini F., Cozzi P., Gaspa G., Marras G. (2018). detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes. Available at: http://orca.cf.ac.uk/id/eprint/108906 (accessed March 16, 2020).

LinkOut - more resources