Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle

2021 ◽  
Author(s):  
Sindy Caivio‐Nasner ◽  
Albeiro López‐Herrera ◽  
Luis G. González‐Herrera ◽  
Juan C. Rincón
Keyword(s):  
Diversity Analysis ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding ◽  
Recent Selection

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genomics ◽  
2021 ◽  
Author(s):  
Maryam Nosrati ◽  
Hojjat Asadollahpour Nanaei ◽  
Arash Javanmard ◽  
Ali Esmailizadeh
Keyword(s):  
World Wide ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding

scholarly journals Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0232436
Author(s):  
Christos Dadousis ◽  
Francesca Cecchi ◽  
Michela Ablondi ◽  
Maria Chiara Fabbri ◽  
Alessandra Stella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cross Validation ◽  
Small Region ◽  
Economic Factors ◽  
Admixture Analysis ◽  
Goat Breed ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding ◽  
Assignment Success ◽  
Integrated Study

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.

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

scholarly journals The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 498 ◽  
Author(s):  
Antonio Boccardo ◽  
Stefano Paolo Marelli ◽  
Davide Pravettoni ◽  
Alessandro Bagnato ◽  
Giuseppe Achille Busca ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Inbreeding Coefficient ◽  
Nucleotide Polymorphisms ◽  
Canis Lupus Familiaris ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
The Mean ◽  
Dog Breed ◽  
Genomic Inbreeding ◽  
Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

scholarly journals A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1024 ◽  
Author(s):  
Tomasz Szmatoła ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Tomasz Ząbek ◽  
Katarzyna Ropka-Molik ◽  
...  
Keyword(s):  
High Frequency ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
White Variety ◽  
Black And White ◽  
Cattle Breeds ◽  
Hereford Cattle ◽  
Holstein Friesian ◽  
Genomic Inbreeding ◽  
The Impact

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.

scholarly journals Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Matteo Cortellari ◽  
Arianna Bionda ◽  
Alessio Negro ◽  
Stefano Frattini ◽  
Salvatore Mastrangelo ◽  
...  
Keyword(s):  
Rural Areas ◽  
Management Practices ◽  
Southern Italy ◽  
Farming Systems ◽  
Small Population ◽  
Runs Of Homozygosity ◽  
Chromosome 11 ◽  
Low Input ◽  
Signatures Of Selection ◽  
Genomic Inbreeding

Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

scholarly journals Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

2020 ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Mohammad Hossein Fallahi ◽  
Ali Jalil Sarghale ◽  
Mohammad Moradi-Shahrbabak ◽  
...  
Keyword(s):  
Muscle Development ◽  
Bone Development ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
River Buffalo ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
A Genome ◽  
Genomic Inbreeding ◽  
Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

scholarly journals Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

2019 ◽  
Author(s):  
Meenu Bhati ◽  
Naveen Kumar Kadri ◽  
Danang Crysnanto ◽  
Hubert Pausch
Keyword(s):  
Whole Genome Sequencing ◽  
Meat Quality ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Genomic Inbreeding ◽  
Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

scholarly journals Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Elisa Peripolli ◽  
Nedenia Bonvino Stafuzza ◽  
Danísio Prado Munari ◽  
André Luís Ferreira Lima ◽  
Renato Irgang ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Bos Indicus ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding

scholarly journals Associations of autozygosity with a broad range of human phenotypes

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
David W Clark ◽  
Yukinori Okada ◽  
Kristjan H S Moore ◽  
Dan Mason ◽  
Nicola Pirastu ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Inbreeding Depression ◽  
Social Factors ◽  
Genetic Variants ◽  
Runs Of Homozygosity ◽  
Sibling Pairs ◽  
Full Sibling ◽  
Inbreeding Coefficients ◽  
Genomic Inbreeding ◽  
Close Relatives

Abstract In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

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