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The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation.

Cattle are among the most important domesticated bovid species in the world, of which Ethiopia possesses large populations adapted to different agro-ecologies and production systems. Though several molecular population genetic studies have been done on Ethiopian indigenous cattle, genomic diversity and selection signatures pertinent to adaptation to the different local environments have yet to be comprehensively characterized. Here, the whole genome sequences of 151 samples from 14 Ethiopian indigenous cattle populations were analyzed to assess genomic diversity and differentiation as well as signatures of positive selection (using Hp, iHS, FST, and XP-CLR) in comparison to Sudanese zebu, Asian zebu, Ankole, and African and European taurine cattle. High genomic differentiation was observed between Ethiopian and non-Ethiopian cattle populations, while low genomic differentiation and inbreeding were present between and within Ethiopian cattle populations. Sixteen genome regions overlapping with 40 candidate genes were commonly identified by at least three genome scan methods. High frequencies of missense SNPs in ITPR2, CHADL, GNAS, STING1, and KIT genes with high haplotype differentiations were observed in Ethiopian cattle compared to non-Ethiopian cattle. The candidate genes were significantly associated with several biological functions and molecular pathways responsible for nutrient metabolism, skeletal development, immune response, reproduction, water balance, coat color pigmentation, and circulatory homeostasis. Our results provide new insights into the adaptation of the Ethiopian indigenous cattle to the country’s diverse environments.

Cirneco dell’Etna is an old Italian breed of scent hunting dogs. Commonly used genomic measures such as heterozygosity, fixation indexes, and runs of homozygosity can help to improve knowledge about its genetic diversity. This study aimed to: (i) investigate Cirneco’s genomic background, (ii) quantify its genomic inbreeding, and (iii) detect genomic regions differentiating the Cirneco’s two allowed coat colours, self-coloured fawn and tan and white. Canine 230K SNP BeadChips was used to investigate 24 Cirneco (19 self-coloured fawn, and 5 tan and white) and other 106 dogs from eight phylogenetically and historically related breeds. The genetic distance, ancestry, and relationship among breeds were explored by multidimensional scaling, Reynolds distances, phylogenetic tree, and admixture analysis. The genomic inbreeding (FROH) was calculated for each breed. Averaged Wright’s fixation index FST was used to identify the genes that most differentiated the two groups of Cirneco. All analyses highlighted that Segugio Italiano and Kelb tal Fenek are the closest breeds to Cirneco. Within the breed, tan and white subjects showed a more heterogeneous genetic background and a lower inbreeding in comparison with self-coloured fawn ones, even though more than half of the latter presented a superimposable admixture. The gene that most differentiated these two groups is Microphthalmia-Associated Transcription Factor (MITF), previously associated with white spotting in other breeds. Given the small size of the Cirneco population and its open registry, its management should carefully combine morphological and genealogical evaluations with genetic tools to identify the best breeders while maintaining an acceptable genetic pool., peer-reviewed

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright’s F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d’Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species.

Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population., This work was supported by Ministerio de Economia y Competividad grants AGL2013-41834-R (MEC, Spain), AGL2016-78709-R (MEC, Spain) and by the CERCA Programme/Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533). Genotyping of the CHCU samples was funded by the Animal Genetics Division of INRAE, as part of the CHACUBA project. Y. Rodriguez-Valera was funded by the French Embassy in Havana (Cuba) and INRAE. Y. Ramayo-Caldas was funded by the European Union H2020 Research and Innovation programme under Marie Skłodowska-Curie grant (P-Sphere) agreement No 6655919.

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25–50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25–51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

The availability of dense single nucleotide polymorphism (SNP) assays allows for the determination of autozygous segments based on runs of consecutive homozygous genotypes (ROH). The aim of the present study was to investigate the occurrence and distribution of ROH in 21 Italian sheep breeds using medium-density SNP genotypes in order to characterize autozygosity and identify genomic regions that frequently appeared in ROH within individuals, namely ROH islands. After filtering, the final number of animals and SNPs retained for analyses were 502 and 46 277 respectively. A total of 12 302 ROH were identified. The mean number of ROH per breed ranged from 10.58 (Comisana) to 44.54 (Valle del Belice). The average length of ROH across breeds was 4.55 Mb and ranged from 3.85 Mb (Biellese) to 5.51 Mb (Leccese). Valle del Belice showed the highest value of inbreeding on the basis of ROH (FROH= 0.099), whereas Comisana showed the lowest (FROH= 0.016), and high standard deviation values revealed high variability in autozygosity levels within each breed. Differences also existed in the length of ROH. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were 25 Mb. The levels of ROH that we estimated here reflect the inbreeding history of the investigated sheep breeds. These results also highlight that ancient and recent inbreeding have had an impact on the genome of the Italian sheep breeds and suggest that several animals have experienced recent autozygosity events. Comisana and Bergamasca appeared as the less consanguineous breeds, whereas Barbaresca, Leccese and Valle del Belice showed ROH patterns typically produced by recent inbreeding. Moreover, within the genomic regions most commonly associated with ROH, several candidate genes were detected.

Genome-wide runs of homozygosity (ROH) are suitable for understanding population history, calculating genomic inbreeding, deciphering genetic architecture of complex traits and diseases as well as identifying genes linked with agro-economic traits. Autozygosity and ROH islands, genomic regions with elevated ROH frequencies, were characterized in 112 animals of seven Indian native cattle breeds (B. indicus) using BovineHD BeadChip. In total, 4138 ROH were detected. The average number of ROH per animal was maximum in draft breed, Kangayam (63.62 ± 22.71) and minimum in dairy breed, Sahiwal (24.62 ± 11.03). The mean ROH length was maximum in Vechur (6.97 Mb) and minimum in Hariana (4.04 Mb). Kangayam revealed the highest ROH based inbreeding (FROH>1Mb = 0.113 ± 0.059), whereas Hariana (FROH>1Mb = 0.042 ± 0.031) and Sahiwal (FROH>1Mb = 0.043 ± 0.048) showed the lowest. The high standard deviation observed in each breed highlights a considerable variability in autozygosity. Out of the total autozygous segments observed in each breed except Vechur, > 80% were of short length (< 8 Mb) and contributed almost 50% of the genome proportion under ROH. However, in Vechur cattle, long ROH contributed 75% of the genome proportion under ROH. ROH patterns revealed Hariana and Sahiwal breeds as less consanguineous, while recent inbreeding was apparent in Vechur. Maximum autozygosity observed in Kangayam is attributable to both recent and ancient inbreeding. The ROH islands were harbouring higher proportion of QTLs for production traits (20.68% vs. 14.64%; P≤ 0.05) but lower for reproductive traits (11.49% vs. 15.76%; P≤ 0.05) in dairy breeds compared to draft breed. In draft cattle, genes associated with resistant to diseases/higher immunity (LYZL1, SVIL, and GPX4) and stress tolerant (CCT4) were identified in ROH islands; while in dairy breeds, for milk production (PTGFR, CSN1S1, CSN2, CSN1S2, and CSN3). Significant difference in ROH islands among large and short statured breeds was observed at chromosome 3 and 5 involving genes like PTGFR and HMGA2 responsible for milk production and stature, respectively. PCA analysis on consensus ROH regions revealed distinct clustering of dairy, draft and short stature cattle breeds.

The overall aim of this research work was to explore strategies that manage genetic variation at the genomic level in the era of powerful genomic selection methods. In paper 1, the role of alternative genomic relationship matrices on the rate of genetic gain at the same rate of true inbreeding in genomic optimum contribution selection breeding schemes were assessed using a stochastic simulation study. For prediction three alternative genomic relationship matrices were calculated based on the genomic information used, i.e. QTL only, markers only, or both markers and QTL. For control of inbreeding, markers only, or both markers and QTL were used. With 7,702 QTL, all genomic relationship matrix combinations used for prediction and control of inbreeding gave similar rates of genetic gain at the same rate of true inbreeding. However, with 1,000 QTL, prediction with QTL and control of inbreeding using markers realized a 29.7% higher rate of genetic gain at a 1% rate of true inbreeding than when using markers for both prediction and control of inbreeding. Hence, the effect of alternative genomic relationship matrices on rates of genetic gain at equal rates of true inbreeding depended on the number of QTL controlling the trait. With a large number of QTL, it is not critical which genomic relationship matrices to use for both prediction and control of inbreeding. However, it is critical with small numbers of QTL, or if few genetic markers can be pinpointed that track (most of) the genetic variance. In paper 2, we evaluated the effect of different prediction methods on rates of genetic gain at equal rates of true inbreeding in genomic optimum contribution breeding schemes, and on the distribution of the genetic drift across the genome. Use of Bayesian variable selection genomic prediction (BayesP) outperformed GBLUP and realized 5.7%, 1.7% and 2.7 % more short-term genetic gain with 180, 1000 and 7702 QTL, respectively, at a short-term rate of inbreeding of 1%. BayesP also had higher accuracies of selection than GBLUP. The difference in accuracies between BayesP and GBLUP were higher with few QTL. Moreover, BayesP resulted in smaller selective sweeps around the QTL region than GBLUP. In conclusion, it is advantageous to use BayesP compared to GBLUP in genomic optimum contribution selection breeding schemes. In paper 3, we compared alternative pedigree and genomic estimators of inbreeding to estimate inbreeding depression in semen quality traits in a Large White pig population. Inbreeding coefficients were measured based on pedigree, average homozygosity (Fhomo), excess of homozygosity (FEx_homo), probability of uniting gametes (Fu), and from the diagonal of genomic relationships matrix (FGRM). Based on Runs of Homozygosity (ROH), three different genomic estimators of inbreeding were obtained: FROH< 5Mb (ROH between 1Mb and 5Mb), FROH>= 5Mb (ROH greater or equal to 5Mb), and FROH> 2Mb (ROH above 2Mb). Significant inbreeding depression effects on semen quality traits were found using FROH> 2Mb, FROH>= 5Mb, FEx_homo, and Fhomo. Moreover, FROH> 2Mb and FROH>= 5Mb showed the strongest association with inbreeding depression in semen quality traits. Hence, we recommend using the ROH based measures of genomic inbreeding to quantify inbreeding depression. Moreover, pig industries should consider implementing control of inbreeding in their breeding plan to maintain high-quality semen in sufficient quantities. In conclusion: The use of genomic prediction methods and genomic relationship matrices for EBV prediction that focus on chromosomal regions with causative effects benefit rates of genetic gain at a controlled rate of inbreeding. Genomic relationship matrices for the control of inbreeding should represent the inbreeding across the entire genome as well as possible. ROH based inbreeding coefficients were best at picking up the inbreeding depression aspect of inbreeding amongst the investigated measures of molecular inbreeding. Additional research is warranted on whether this also holds for other negative aspects of inbreeding, such as genetic drift of detrimental alleles to high frequency, and loss of genetic variation. Det overordna målet for denne avhandlinga var å utforska strategiar som forvaltar genetisk variasjon på genomnivå i vår tid når effektive genomiske seleksjonsmetodar er tilgjengelege. I Paper 1 blir effekten av bruk av ulike genomiske slektskapsmatriser på genetisk framgang ved same sanne innavlsrate samanlikna. Avlsprogram med genomisk optimal seleksjon blei simulerte stokastisk. Tre typar genomiske slektskapsmatriser blei laga for genomisk prediksjon: enten med bare QTL (kvantitativ-eigenskaps-loci), med bare genetiske markørar, eller med både markørar og QTL. For å kontrollera innavl brukte ein enten bare genetiske markørar, eller både markørar og QTL . Med 7702 QTL fekk vi om lag same avlsframgang gitt same sanne innavlsgrad for alle dei tre genomiske slektskapsmatrisene vi prøvde. Men med 1000 QTL ga prediksjon med QTL-slektskap og innavlskontroll med markørar 27,9% større genetisk framgang når det var 1% sann innavlsauke, samanlikna med bruk av markørar for både prediksjon og innavlskontroll. Så avhengig av kor mange QTL som eigenskapen er styrt av kan det spelar ei rolle kva type genomiske slektskapsmatriser ein bruker til genomisk avlsverdiprediksjon av eigenskapen. Når det er mange QTL som styrer eigenskapen spelar det liten rolle kva slag genomisk slektskap ein bruker for prediksjon og innavlskontroll. Men når få QTL styrer eigenskapen, eller når (mesteparten av) den genetiske variansen til eigenskapen kan forklarast av få markørar, blir det viktig kva slag genomiske matriser ein bruker for prediksjon og innavlskontroll. I Paper 2 samanlikna vi ulike avlsverdiprediksjonsmetodar når det gjaldt genetisk framgang og genetisk drift i ulike delar av genomet. Samanlikningane blei gjorde ved lik sann innavlsgrad og med genomisk optimal seleksjon. Bruk av Bayes’ variabelseleksjon genomisk prediksjon (BayesP) var betre enn GBLUP og ga 5,7%, 1,7% og 2,7% høgare kortvarig genetisk framgang med 180, 1000 og 7702 QTL. Den kortvarige innavlsgraden var 1%. Og BayesP ga sikrare seleksjon enn GBLUP, spesielt når det var få QTL. Dessutan ga BayesP kortare seleksjonssveip i QTL-områda enn GBLUP. Konklusjonen er at det svarer seg å bruka BayesP framfor GBLUP i genomisk optimale seleksjonsprogram. I Paper 3 samanlikna vi genomiske og anetavle-estimatorar til å detektera innavlsdepresjon for sædkvalitet hos rånar i ein yorkshire-populasjon. Innavlskoeffisientane blei rekna ut enten med anetavle, gjennomsnittleg homosygoti (Fhomo), overskotshomosygoti (FEx_homo), korelasjonen til foreldregametar (FU), eller frå diagonalane i genomiske slektskapsmatriser (FGRM). Avhengig av homosygositetslengder (ROH) valde ein tre genomiske innavlsestimatorar: FROH< 5Mb (ROH frå 500kb til 5Mb), FROH>= 5Mb (ROH større eller lik 5Mb), og FROH> 2Mb (ROH over 2Mb). Signifikante innavlsdepresjonseffektar på sædkvalitet blei funne med FROH> 2Mb, FROH>= 5Mb, FEx_homo og Fhomo. FROH> 2Mb og FROH>= 5Mb ga høgare assosiasjon med genomisk innavlsdepresjon for sædkvalitet enn dei andre måla. Difor anbefaler vi bruk av ROH-baserte mål for genomisk innavl for kvantifisering av innavlsdepresjon. Elles bør svineproduksjonsselskap vurdera å nytta innavlskontroll i avlsplanane sine for å halda fram med å ha nok høgkvalitets-sæd i framtida. Til konklusjon: Avlsverdiprediksjon med bruk av genomiske prediksjonsmetodar og genomiske slektskapsmatriser som fokuserer på kromosomområde som har effekt på eigenskapen det blir avla for gir høgare avlsframgang ved kontrollert innavslgrad. Genomiske slektskapsmatriser til kontroll av innavl bør visa innavl over heile genomet så godt som muleg. Blant måla for innavl var ROH-baserte best til å måla innavlsdepresjon av dei som blei testa. Det krevst meir forsking for å få veta om dette også gjeld for andre negative effektar av innavl, slik som genetisk drift for øydeleggjande allel til høge genfrekvensar, og tap av genetisk variasjon. The Center for Genomic selection in Animals and Plants (GenSAP)

Istrian (IS) and Pag (PS) sheep breeds are Croatian autochthonous sheep breeds. We analyzed genotypes of 175 animals (96 IS, and 75 PS) using Illumina OvineSNP50 BeadChip array and estimated genomic inbreeding levels (FROH) and linkage disequilibrium effective population size (NeLD). We also defined the genomic position of IS and PS concerning overall 671 animals of 22 Italian, Spanish and some Merino sheep breeds. For this purpose, we used publicly available data from Dryad digital repository. The inbreeding level based on runs of homozygosity (FROH) was higher in IS compared to PS for FROH>2Mb, 0.08 vs. 0.04, FROH>8Mb, 0.04 vs. 0.03, and FROH>16Mb, 0.02 vs. 0.01 respectively. Software NeEstimator was used to estimate Ne from the parental generation of the sample based on the linkage disequilibrium (LD) method. Estimated NeLD for IS was 101 (95% CI= 81-130), while higher NeLD of 222 (95% CI= 161-343) was obtained for PS. Principal Components Analysis of the overall dataset showed separation of both, IS and PS from other breeds. However, PS was placed near to the cluster containing some Italian breeds (Massese, Appenninica, Sardinian White, Comisana, Leccese, and Laticauda) while IS was slightly remote. To our knowledge, this is the first genomic analysis of IS and PS providing valuable insights into their conservation status.

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 &mina 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.

Made available in DSpace on 2018-12-11T17:22:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-09-17 Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results: The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (- 0.01 to - 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho Institute for Animal Breeding and Genetics University of Veterinary Medicine Hannover Departamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho Associação Nacional de Criadores e Pesquisadores (ANCP) Embrapa Cerrados Zoetis Universidade de São Paulo Departamento de Nutrição e Produção Animal Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho Departamento de Ciências Exatas Faculdade de Ciências Agrárias e Veterinárias UNESP Univ Estadual Paulista Júlio de Mesquita Filho

Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level ofr2= 0.09 by around 26 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organisation.

The Dalmatian Pramenka (DAL) is the largest autochthonous population of sheep in Croatia that belongs to the long tailed Pramenka type of sheep, which are widespread over South-East Europe. We genotyped 32 DAL individuals on the Illumina Ovine SNP50 K BeadChip, and calculated parameters that are important for the conservation status: observed genome-wide heterozygosity (oHet), effective population size estimated via linkage (NeLD), and gametic (NeGD), disequilibrium and the ROH-based inbreeding level (FROH≤50g and FROH≤10g). A comparison with 24 Appenninica, 24 Arawapa, 24 Australian Merino, 24 Churra, 24 Finnsheep, 21 Merino Landschaf, 24 Massese and 24 Sardinian White revealed that DAL has the highest observed heterozygosity (oHet=0.375) and the second highest NeGD (124), as well as the lowest ROH- based inbreeding levels (FROH≤50g=0.021 and FROH≤10g=0.009). Interestingly, DAL has the highest estimated decline in NeLD (ΔNeLD=13), resulting in an extremely low NeLD of 15-31 (95% CI). Most likely, this notable difference is the consequence of the population growth of DAL in last generations, in contrast to the population decline in the period considered in historical NeLD estimates (12 to 100 generations back).

Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p

The availability of high throughput genotyping has facilitated the quantification of inbreeding by genomic markers in farm animals. Run 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 inbreeding derived from ROH (FROH) in three Italian local cattle breeds. Individuals of Cinisara (71), Modicana (72), Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of the Italian Holstein cattle breed were included in the analysis. The following criteria were used to define a ROH: two missing SNPs; one heterozygous SNP; minimum density of 1 SNP every 100 kb; maximum gap between consecutive SNPs of 1 000 kb. We used a definition of ROH as tracts of homozygous genotypes that were >4 000 kb in length with a minimum number of 40 SNPs included in the run. Across all four breeds, we identified 3,661 ROH. The Modicana breed showed the highest mean number of ROH for individual (11.03) and the highest value of FROH (0.053), whereas the Reggiana showed the lowest values (7.15 and 0.033, respectively). The three most homozygous animals present in our dataset were from the Cinisara (676.9 Mb), Modicana (681.2 Mb) and Reggiana (725.2 Mb), with almost a quarter of their genome classified as ROH. Differences among breeds existed for the ROH length. The individuals of Reggiana and Italian Holstein breeds showed high number of shorter ROH segments, whereas the Sicilian breeds showed ROH characterized by the presence of large segments. In fact, in all breeds, most ROH segment coverage was in the shorter length categories (4-8 Mb), but the Sicilian breeds presented the highest percentage of ROHs (12%) inside the ROH length category >24Mb. Therefore our results showed the presence of inbreeding due to recent consanguineous matings and a lack of gene flow from other herds and breeds. ROH analyses represent an important instrument that may be used in inference of population history and to associate with important production and disease traits. Considering that the increased of inbreeding leads to different negative effects, our results showed the necessity of implementing conservation programs to preserve the local breeds.

The reduction of the population mean for a quantitative trait such as size, fertility, vigour, yield, and fitness is a negative consequence of inbreeding known as inbreeding depression. For the last 100 years, regression of individual performance on the individual pedigree inbreeding coefficients has been the standard procedure used in majority of research related to human, livestock and plant populations. Derived from the high-throughput SNP information, runs of homozygosity (ROH) were recently proposed as accurate estimates of inbreeding. In this study we estimated inbreeding depression on sperm quality traits in several Austrian cattle populations using inbreeding coefficients derived from pedigree (Fped), genomic inbreeding (ROHs of various length: FROH1 , FROH2 , FROH4, FROH8, and FROH16) and individual multilocus heterozygosity (iH). Bull fertility referred to sperm quality of ejaculates (volume, sperm concentration, percentage of viable spermatozoa and motility) collected in several Austrian Artificial insemination centres. Bulls were genotyped with Illumina Bovine 50k SNP chip. We used mixed model with a bull as a random effect and all other effects (age of the bull, semen collector, month and year of collection and number of ejaculates per bull per day), including pedigree and genomic inbreeding coefficients (covariable), as fixed effects. In majority of models we found the presence of inbreeding depression while the strength of models (pedigree versus genomic inbreeding) interchanged depending on a trait or/and population analysed. On the other side, among all predictors tested, iH was the worst predictor of inbreeding depression. Although, genomic inbreeding coefficients have been shown to be powerful, still much work has left for complete understanding of inbreeding depression.

Regression of performance (phenotype) on the individual pedigree inbreeding coefficients has been the standard procedure used to quantify inbreeding depression in humans and animals. We have estimated inbreeding depression for the sperm quality traits (volume, sperm concentration, percentage of viable spermatozoa and motility) in Austrian Fleckvieh bulls with emphases on the comparison of models based on pedigree inbreeding versus models based on various genomic estimates of inbreeding [overall and chromosomal (1-29)] derived from BovineSNP50 BeadChip. Linear mixed models were used with a bull as a random effect and all other effects (age of the bull, semen collector, month and year of collection and number of ejaculates per bull per day), including pedigree or genomic (overall and chromosomwise) inbreeding coefficients (co-variable) as fixed effects. Inbreeding depression was found for the volume and percentage of viable spermatozoa, although between two artificial insemination centers some results were heterogeneous. In general, models based on pedigree were comparable to models based on genomic inbreeding (runs of homozygosity) while models based on individual heterozygosity were inferior. In contrast, for all traits analyzed, models with specific chromosomal inbreeding coefficients outperformed models based on overall genomic and pedigree inbreeding coefficients. While genomic inbreeding coefficients have been shown to be powerful, still much work has left to complete our understanding on architecture and modeling of inbreeding depression.

In plant, animal and human genetics the detrimental effect from parental relatedness (inbreeding depression) are well known. Inbreeding depression has traditionally been studied using pedigrees. Pedigree data are usually difficult to obtain, they are potentially unreliable, and do not count for inbreeding arising from distant common ancestors. Recently it is discovered that rates of inbreeding in large outbreed human populations are high enough to have detectable effects. This ancient inbreeding was recorded using “Runs of homozygosity” (ROH). To investigate rates of ancient inbreeding in cattle we used three breeds (Simmental n= 502, Tyrol Grey n = 217, Brown Swiss n = 499) with well known pedigrees (complete generation equivalents 6, 46- 8, 19). We calculated inbreeding from pedigree for whole pedigree (FpedT) and for five generation pedigree (Fped5). Obtained values were highest in Brown Swiss (FpedT = 4, 1%, Fped5 = 2, 1%), and lowest in Simmental (FpedT = 1, 4%, Fped5 = 0, 9%). In order to calculate genomic inbreeding, animals were genotyped with Illumina Bovine 50k SNP chip. From five ROH lengths (>1Mb, >2Mb, >4Mb, >8Mb and >16Mb) inbreeding coefficients (FROH1 , FROH2 , FROH4, FROH8, and FROH16 ) were calculated as sum of all ROHs of specific length divided by length of genome covered with SNPs. Small segments (>1Mb), which represent ancient inbreeding, indicated much higher inbreeding levels than pedigree. Highest was in Brown Swiss (FROH1 = 14, 2) and lowest in Tyrol Grey (FROH1 = 14, 2). Bigger segments (>8Mb and >16Mb), which represent recent inbreeding gave values similar to pedigree coefficients. To conclude we confirmed that pedigree inbreeding coefficients do not detect ancient inbreeding while ROH coefficients do. Insight in ancient inbreeding should help for better quantification of the risk, which is arising from recessive detrimental genetic variants in different populations.

Regression of performance (phenotype) on the individual pedigree inbreeding coefficients has been the standard procedure used to quantify inbreeding depression in humans and animals. In Austrian Fleckvieh bulls we have estimated inbreeding depression for the sperm quality traits (volume, sperm concentration, percentage of viable spermatozoa and motility) with emphases on the comparison of models based on pedigree inbreeding versus models based on various genomic estimates of inbreeding (BovineSNP50 BeadChip). Furthermore, we also analyzed models with chromosomal inbreeding coefficients (1 to 29) as well as models with combination of several chromosomal inbreeding coefficients. Mixed models were used with a bull as a random effect and all other effects (age of the bull, semen collector, month and year of collection and number of ejaculates per bull per day), including pedigree or genomic inbreeding coefficients (covariable) as fixed effects. Inbreeding depression was found for the volume and percentage of viable spermatozoa, although between two artificial insemination centres some results were heterogeneous. In general, models based on pedigree were comparable to models based on genomic inbreeding (runs of homozygosity) while models based on individual heterozygosity were inferior. In contrast, for all traits analyzed, models with various chromosomal inbreeding coefficients outperformed models based on overall genomic inbreeding as well as models based on pedigree. However, while genomic inbreeding coefficients have been shown to be powerful, still much work has left to complete our understanding on architecture of inbreeding depression.