In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient ( F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH ( F ROH ) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix ( F GRM ), based on the difference between observed v. expected number of homozygous genotypes ( F HOM ) and the genomic homozygosity of individual i ( F MOL i ). The molecular coancestry coefficient ( f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH , whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 ( F MOL i − F ROH ) in Cinisara to 0.17 ( F GRM − F ROH ) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.Keywords: genomic inbreeding, local cattle breeds, runs of homozygosity ImplicationsIn the local breeds with small population size, one of the most important problems is the increase of inbreeding that leads to different negative effects as a reduction in phenotypic values. The current study aims to quantify the genomic inbreeding derived from runs of homozygosity (ROH) (F ROH ) in three Italian local dairy cattle breeds. According to ROH results, recent inbreeding was well detected in the investigated local dairy cattle breeds. Our results showed the necessity of implementing co...

BackgroundBecause very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding () estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies.ResultsWe identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation.ConclusionsThese results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection.Electronic supplementary materialThe online version of this article (10.1186/s12711-017-0360-z) contains supplementary material, which is available to authorized users.

Summary 18The availability of dense single-nucleotide polymorphism (SNP) assays allows for the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 F o r P e e r R e v i e wThe abundance of single-nucleotide polymorphisms (SNPs) throughout the genome and the 44 availability of dense SNP assays, makes these markers particularly suitable for the detection of 45 genomic regions where a reduction in heterozygosity occurred (Kim et al. 2013). Runs of 46 homozygosity (ROH) are contiguous segments of homozygous genotypes that are present in an 47 individual due to parents transmitting identical haplotypes to their offspring (Gibson et al. 2006). 48In animal genetics, ROH are used as predictors of whole genome inbreeding levels (Purfield et 49 al. 2012; Marras et al. 2015; Mastrangelo et al. 2016), to characterize the genomic distribution of 50 inbreeding depression on a phenotype (Biscarini et al. 2014; Pryce et al. 2014), and to identify 51 genes associated with traits of economic interest present in these regions (Zhang et al. 2015; 52 Szmatola et al. 2016; Purfield et al. 2017). Selection pressure and mating schemes can be 53 disentangled by ROH; therefore, ROH detection can also be used to minimize inbreeding and to 54 improve mating systems (Bosse et al. 2012; Zhang et al. 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Runs of homozygosity definition 106Runs of homozygosity were estimated for each animal using PLINK (Purcell et al. 2007). No where L ROH is the total length of all ROH in the genome of an individual, and L aut the specified 118 length of the autosomal genome covered by SNPs on the chip (2 452.06 Mb). 119Each ROH was categorized based on its physical length into 1 to <5 Mb, 5 to <10 Mb, 10 to <15 and averaging this per breed. 123The genomic inbreeding coefficient based on the difference between observed vs. expected 124 number of homozygous genotypes (F HOM ) was also estimated using PLINK (Purcell et al. 2007). 125Pearson's correlation between the two measures of inbreeding was calculated. 127Detection of common runs of homozygosity 128To identify the genomic regions most commonly associated with ROH for the meta-population, 129and for groups on the basis of production purposes (milk, meat, wool and "milk and meat"), the 136Genomic coordinates for all the identified ROH islands were used for the annotation of genes 137 that were fully or partially contained within each selected region using the UCSC Genome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59...

Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).

Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.