- It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. - Conclusions: This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. - The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo ’ s natural adaptive history together to a recent selection for milk used as primary food source from this species.. - the swamp ( Bubalus bubalis carabanensis 2n = 48) buf- falo, occurred about 3000–6000 years before present in the Indo–Pakistani area and in the vicinity of borders of China, respectively [2, 3]. - According to the FAOSTAT data (http://www.fao.org/. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Beldman et al. - In the developing countries including Iran, river buffalo breeding is nowadays recognized of great import- ance because of (i) the ability of buffalo to convert low- quality feed to valuable milk, (ii) adaptation to harsh climate conditions and resistance to local parasites, (iii) long productive lifespan [6], and (iv) their potential in milk and meat production performances [7]. - As de- scribed by Safari et al. - Davoudi et al. - Additionally, Ghoreishifar et al. - [6] identified ROH in the Azeri and Khuzestani breeds.. - Redon et al.. - gains) on all 24 autosomes were detected in the 361 samples (Supplementary Table S1). - The largest loss/gain ratio was found in the MAZ breed (1.32) while the KHU showed a value close to the unit.. - The total number of regions identified, as reported in Table 1, is possibly linked to the sample’s population size, especially for singleton_CNVRs that in the MAZ breed result to be a very large proportion (73%) of identified CNVRs: it is more likely, in fact, to identify singleton_CNVRs in small populations as they are those not in common among individuals.. - Table 1 Summary of statistics for CNV detected in the three Buffalo populations Breed N samples N. - Table 2 Summary of all CNVRs identified in the three Buffalo populations. - 3 (A) in the Venn diagram.. - In Iran, breeding of river buffaloes plays an important role in the economy of the country, also impacting on social and cultural activities [7]. - well adapted to different environments proper of the geographical areas of the country in which they are reared: Azari – the north-west-north of Iran (70. - Khu- zestani – west and south-west (22%) of the Country while the Mazandarani is farmed in the north (8%) re- gion (http://www.fao.org/3/ah847e/ah847e00.pdf).. - The genetic variability in Iranian buffalo breeds have been recently studied and findings based on the Linkage Disequilibrium (LD) obtained from the Affymetrix 90 K SNP genotypes [19] showed a close genetic relation be- tween AZE and KHU due to a high LD consistency across the two populations and a lower similarity when the comparison involved MAZ with both AZE and KHU due to variability in the LD trend within breed. - A genome wide CNVs detection has been here per- formed resulting in a total of 9550 CNVs and 2.995 CNVRs in the three breeds. - Excluding singleton_CNVRs the CNVRs re- sulted 1605 in the three breeds. - This result suggest that the moderate level of admixture identified for MAZ and AZE by [6], is confirmed here and graphically visualizable in the PCA (Fig. - 4 is also showing that CNVs are not the same across the three breeds as they do partially overlap: in fact only 22 CNVRs are in com- mon among the three breeds, while 31, 65 and 30 were found only in the AZE, KHU and MAZ respectively, as showed by Venn diagram in Fig. - CNVs are in fact a different class of markers respect to SNP and it is ex- pected that PCA is discriminating the population not in the same exact manner.. - A fur- ther evidence is provided in the avian species as for strongly selected populations, as in chicken, where a very low proportion of complex CNVRs, 0 to 5% was found, while in a the non-selected Mexican creole poultry population the proportion of complex CNVRs was up to 14% [14].. - The knowledge of genomic variation in the water buffalo species is still very limited and most of the recent find- ings still rely on comparison with cattle species. - This work provides a step forward in the biological interpret- ation of genomic variation in the buffalo species. - We may speculate that the presence of the set of genes and QTL traits harbored in the CNVRs here mapped could be linked with the buffalo ’ s natural adaptive history, i.e. - As extensively described in [4] and in [19], the SNPs data comes from populations sampled with the aim to be representative of each breed. - A quality control of raw intensity files using the stand- ard protocol in the Affymetrix Power Tools package (www.affymetrix.com) was performed in order to guar- antee a high quality of obtained data. - A total of 70,230 SNPs was then retained in the analysis mapped on the Bubalus bubalis (UOA_WB_1) genome assembly.. - As the Quantitative Trait Loci (QTL) database for the buffalo species is not available, the QTL associated to the genes here found in the CNVRs were identified in t h e c a t t l e Q T L d a t a b a s e ( Q T L d b : ht t p s. - animalgenome.org/cgi-bin/QTLdb/BT/search) by gene name, using the “Search by associated gene” option of QTLdb.. - states for each of the identified CNVRs and used in the PCA analysis.. - org/10.1186/s . - https://www.animalgenome.org/cgi-bin/QTLdb/BT/search. - http://www.fao.org/faostat/en/?#data/QA accessed . - The datasets supporting the results and conclusions of our study are included within the article and in the additional files.. - https://doi.org/1 0.1371/journal.pone.0185220.. - 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