Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations
Dimitris PapachristouPanagiota KoutsouliGeorge P. LaliotisElisabeth KunzMaulik UpadhyayDoris SeichterIngolf RußGjoko BunevskiNikolaos KostarasIosif BizelisIvica Međugorac
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Abstract Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.Keywords:
Introgression
Runs of Homozygosity
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Summary Using genome‐wide SNP data, we calculated genomic inbreeding coefficients ( F ROH > 1 Mb , F ROH > 2 Mb , F ROH > 8 Mb and F ROH > 16 Mb ) derived from runs of homozygosity ( ROH ) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity ( F HOM ). We compared these values of inbreeding coefficients with those calculated from pedigrees ( F PED ) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients F ROH > 8 Mb and F ROH > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh ( F PED = 0.014, F ROH > 8 Mb = 0.019 and F ROH > 16 Mb = 0.008); the highest, for Brown Swiss ( F PED = 0.048, F ROH > 8 Mb = 0.074 and F ROH > 16 Mb = 0.037). In contrast, inbreeding estimates based on the genomic coefficients F ROH > 1 Mb and F ROH > 2 Mb were considerably higher than pedigree‐derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3–1.7‐fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.
Runs of Homozygosity
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Runs of Homozygosity
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Summary Runs of homozygosity (ROH) are recognized as potential inbreeding measure in studies on humans. Inbreeding coeffi cients derived from ROH (F ROH ) measure proportion of the genome arranged in long homozygous segments and highly correlate with those derived from pedigree (F ped ). From that we assumed that ROH represent an alternative to pedigree inbreeding levels in studies on animals too, because pedigree can be incorrect, incomplete and can not fully explain what happened in meiosis. To confi rm our premise we used pedigree and genotype data from 500 Austrian dual purpose Simmental bulls to determine correlation between F ROH and F ped . ROH were obtained using Fortran 90 soft ware created by the authors. Proportions of genome in ROH were calculated for lengths of ROH of >1, >2, >4, >8 and >16 Mb. Pedigree data were analyzed and inbreeding coeffi cients for complete pedigree (FpedT) and fi ve generations (F ped5 ) were calculated using ENDOG soft ware. We found low F pedT and F ped5 (means of 1.5% and 0.9%) while FROH for segments >1Mb suggested much higher values (9.0%) indicating old inbreeding that can not be traced using pedigree. Th e highest correlations were found between FROH calculated from ROH of length >4Mb and F pedT (0.68) that is consistent with studies on humans. We conclude that inbreeding coeffi cients derived from ROH are useful for measuring levels of inbreeding in cattle, because ROH are not subject to mistakes as pedigrees and calculations made from those.
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Single nucleotide polymorphism (SNP) genotyping tools, which can analyse thousands of SNPs covering the whole genome, have opened new opportunities to estimate the inbreeding level of animals directly using genome information. One of the most commonly used genomic inbreeding measures considers the proportion of the autosomal genome covered by runs of homozygosity (ROH), which are defined as continuous and uninterrupted chromosome portions showing homozygosity at all loci. In this study, we analysed the distribution of ROH in three commercial pig breeds (Italian Large White, n = 1968; Italian Duroc, n = 573; and Italian Landrace, n = 46) and four autochthonous breeds (Apulo-Calabrese, n = 90; Casertana, n = 90; Cinta Senese, n = 38; and Nero Siciliano, n = 48) raised in Italy, using SNP data generated from Illumina PorcineSNP60 BeadChip. We calculated ROH-based inbreeding coefficients (FROH) using ROH of different minimum length (1, 2, 4, 8, 16 Mbp) and compared them with several other genomic inbreeding coefficients (including the difference between observed and expected number of homozygous genotypes (FHOM)) and correlated all these genomic-based measures with the pedigree inbreeding coefficient (FPED) calculated for the pigs of some of these breeds. Autochthonous breeds had larger mean size of ROH than all three commercial breeds. FHOM was highly correlated (0.671 to 0.985) with FROH measures in all breeds. Apulo-Calabrese and Casertana had the highest FROH values considering all ROH minimum lengths (ranging from 0.273 to 0.189 and from 0.226 to 0.152, moving from ROH of minimum size of 1 Mbp (FROH1) to 16 Mbp (FROH16)), whereas the lowest FROH values were for Nero Siciliano (from 0.072 to 0.051) and Italian Large White (from 0.117 to 0.042). FROH decreased as the minimum length of ROH increased for all breeds. Italian Duroc had the highest correlations between all FROH measures and FPED (from 0.514 to 0.523) and between FHOM and FPED (0.485). Among all analysed breeds, Cinta Senese had the lowest correlation between FROH and FPED. This might be due to the imperfect measure of FPED, which, mainly in local breeds raised in extensive production systems, cannot consider a higher level of pedigree errors and a potential higher relatedness of the founder population. It appeared that ROH better captured inbreeding information in the analysed breeds and could complement pedigree-based inbreeding coefficients for the management of these genetic resources.
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The main objective of this study was to leverage genomic information to ascertain patterns of inbreeding and selection in five North American dairy cattle populations. We obtained genotypes for over 4 million individuals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Inbreeding based on runs of homozygosity was calculated in each population. The average inbreeding ranged from 0.11 for Ayrshire to 0.17 for Jersey. We calculated a coefficient of homozygosity for each marker. Highly homozygous markers were joined into larger genomic segments of interest that ranged from 0.08 to 7.83 Mb in length and spanned 14 chromosomes across breeds. Annotation of genes and QTLs in the highly homozygous regions revealed selection for economically important traits, notably for udder and cow health, productive life, and reproductive traits. We found differences across breeds on inbreeding load, genomic regions of high inbreeding, and selection signatures.
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Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH = 0.0798) was higher than that of BY_R1 (FROH = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.
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Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.
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While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters. The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection. Using ROH with a minimum window size of 20 to 50 using SNP1101 provided the closest estimates to true inbreeding in simulation study. Pedigree inbreeding tended to underestimate true inbreeding, and results for genomic inbreeding varied depending on assumptions about base allele frequencies. Using an ROH approach also made it possible to assess the effect of population structure and selection on distribution of runs of autozygosity across the genome. In the simulation, the longest individual ROH and the largest average length of ROH were observed when selection was based on best linear unbiased prediction (BLUP), whereas genomic selection showed the largest number of small ROH compared to BLUP estimated breeding values (BLUP-EBV). In North American Holsteins, the average number of ROH segments of 1 Mb or more per individual increased from 57 in 1990 to 82 in 2016. The rate of increase in the last 5 years was almost double that of previous 5 year periods. Genomic selection results in less autozygosity per generation, but more per year given the reduced generation interval. This study shows that existing software based on the measurement of ROH can accurately identify autozygosity across the genome, provided appropriate threshold parameters are used. Our results show how different selection strategies affect the distribution of ROH, and how the distribution of ROH has changed in the North American dairy cattle population over the last 25 years.
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The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two "pure" lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
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