Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

AbstractBackgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.ResultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.ConclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

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Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

10.21203/rs.3.rs-318745/v1 ◽

2021 ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection ◽

Genomic Inbreeding

Abstract Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

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Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

10.1101/2021.03.11.434987 ◽

2021 ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection ◽

Genomic Inbreeding

AbstractBackgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.ResultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FSTanalyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.ConclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

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The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.669 ◽

2020 ◽

Vol 24 (7) ◽

pp. 747-754

Author(s):

V. R. Kharzinova ◽

N. A. Zinovieva

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Molecular Genetic ◽

Genetic Material ◽

Animal Husbandry ◽

Molecular Genetic Analysis ◽

Fixation Index ◽

Large White ◽

Black And White ◽

The Republic

One of the main tasks of genetics and animal breeding is the assessment of genetic diversity and the study of genetic relationships between different breeds and populations using molecular genetic analysis methods. We analysed the polymorphism of microsatellites and the information on the state of genetic diversity and the population structure of local breeds in Russia: the Kemerovo, the Berkshire, the Liven, the Mangalitsa, and the Civilian; in the Republic of Belarus: the Large White and the Black-and-White; and in Ukraine: the White Steppe, as well as commercial breeds of imported origin of domestic reproduction: the Large White, the Landrace, and the Duroc. The materials used for this study were the tissue and DNA samples extracted from 1,194 pigs and DNA of the UNU “Genetic material bank of domestic and wild animal species and birds” of the L.K. Ernst Federal Research Center for Animal Husbandry. Polymorphisms of 10 microsatellites (S0155, S0355, S0386, SW24, SO005, SW72, SW951, S0101, SW240, and SW857) were determined according to the previously developed technique using DNA analyser ABI3130xl. To estimate the allele pool of each population, the average number of alleles (NA), the effective number of alleles (NE ) based on the locus, the rarified allelic richness (AR), the observed (HO ) and expected (HE ) heterozygosity, and the fixation index (FIS) were calculated. The degree of genetic differentiation of the breeds was assessed based on the pairwise values of FST and D. The analysis of the allelic and genetic diversity parameters of the local breeds showed that the maximum and minimum levels of polymorphism were observed in pigs of the Ukrainian White Steppe breed (NA = 6.500, NE = 3.709, and AR = 6.020) and in pigs of the Duroc breed (NA = 4.875, NE = 2.119, and AR = 3.821), respectively. The highest level of genetic diversity was found in the Large White breed of the Republic of Belarus (HO = 0.707 and NE = 0.702). The minimum level of genetic diversity was found in pigs of the imported breeds – the Landrace (HO = 0.459, HE = 0.400) and the Duroc (HO = 0.480, HE = 0.469) – indicating a high selection pressure in these breeds. Based on the results of phylogenetic analysis, the genetic origin of Large White pigs, the breeds, from which the Berkshire pigs originated, and the genetic detachment of the Landrace from the Mangalitsa breeds were revealed. The cluster analysis showed a genetic consolidation of the Black-and-White, the Berkshire, and the Mangalitsa pigs. Additionally, the imported breeds with clustering depending on the origin were characterised by a genetic structure different from that of the other breeds. The information obtained from these studies can serve as a guide for the management and breeding strategies of the pig breeds studied, to allow their better use and conservation.

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The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽

10.1186/s12864-020-07270-x ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

N. Z. Gebrehiwot ◽

E. M. Strucken ◽

H. Aliloo ◽

K. Marshall ◽

J. P. Gibson

Keyword(s):

Genetic Diversity ◽

Bos Taurus ◽

Large Population ◽

Bos Indicus ◽

Principal Component ◽

Effective Population ◽

Indigenous Cattle ◽

Cattle Breeds ◽

African Cattle ◽

Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

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Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers

Animals ◽

10.3390/ani11082381 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2381

Author(s):

Mohammad Shamsul Alam Bhuiyan ◽

Soo-Hyun Lee ◽

Sheikh Mohammad Jahangir Hossain ◽

Gautam Kumar Deb ◽

Most Farhana Afroz ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Snp Markers ◽

Gene Pools ◽

Effective Population ◽

Phylogenetic Tree Analysis ◽

Indigenous Cattle ◽

Geographic Separation ◽

First Time ◽

North Bengal

Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations.

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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Scientific Reports ◽

10.1038/s41598-021-93867-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Md Mahmudul Hasan Khan ◽

Mohd Y. Rafii ◽

Shairul Izan Ramlee ◽

Mashitah Jusoh ◽

Md Al Mamun ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Sustainability ◽

Crop Improvement ◽

Principal Component ◽

Issr Markers ◽

Bambara Groundnut ◽

Fixation Index ◽

Vigna Subterranea ◽

Information Index ◽

Issr Primers

AbstractAs a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.

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Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America

Genes ◽

10.3390/genes12071021 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1021

Author(s):

Josue Chinchilla-Vargas ◽

Jonathan R. Meerbeek ◽

Max F. Rothschild ◽

Francesca Bertolini

Keyword(s):

Genetic Diversity ◽

North America ◽

Management Practices ◽

Genetic Difference ◽

Variant Calling ◽

Principal Component ◽

Genomic Diversity ◽

High Rate ◽

Esox Masquinongy ◽

Signatures Of Selection

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

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SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats

Frontiers in Genetics ◽

10.3389/fgene.2021.708740 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tatiana E. Deniskova ◽

Arsen V. Dotsev ◽

Marina I. Selionova ◽

Henry Reyer ◽

Johann Sölkner ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Principal Component ◽

Production Traits ◽

Effective Population ◽

Altai Mountain ◽

Asian Origin ◽

Breeding Programs ◽

Population Sizes ◽

High Level

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.

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Maintenance of genetic diversity in Eucalyptus urophylla S. T. Blake populations with restriction of the number of trees per family

Silvae Genetica ◽

10.2478/sg-2018-0005 ◽

2018 ◽

Vol 67 (1) ◽

pp. 34-40 ◽

Cited By ~ 3

Author(s):

P. H. M. Silva ◽

A. Brune ◽

S. Pupin ◽

M. L. T. Moraes ◽

A. M. Sebbenn ◽

...

Keyword(s):

Genetic Diversity ◽

Fixation Index ◽

Effective Population ◽

Mato Grosso ◽

Management Level ◽

Expected Heterozygosity ◽

Four Levels ◽

Number Of Individuals ◽

Mato Grosso Do Sul ◽

Different Levels

Abstract Our aim was to verify the effect on gain and genetic diversity through the restriction of the number of trees per family in selection, in order to compose an elite population of Eucalyptus urophylla in two trials under distinct management levels. We studied 166 open-pollinated families of E. urophylla in Anhembi, Sao Paulo State, Brazil under commercial practices, and the same families in Selvíria, Mato Grosso do Sul State, Brazil under lower management level (mainly no mineral fertilization). Mortality, height and diameter at breast height (DBH) were measured. DBH was analyzed by the REML/BLUP to select the best 25 trees, with four levels of tree restriction per family (no restriction; 1; 2 and 3 per family). We evaluated heritability; genetic gain and effective size of number of total and private alleles; observed and expected heterozygosity; coancestry and fixation index. A large difference in survival (48 and 83 %) and productivity (MAI of 26 and 44 m3ha-1y-1) was observed between trials due to the different levels of management applied. The highest restriction in number of individuals per family caused a small decrease in gain, corresponding to 7 % in the more productive trial and 3 % in the less productive one. Observed and expected heterozygosity, coancestry and fixation index were not significantly (lower than 5 %) affected by the restriction in both sites. The restriction of one tree per family allowed different alleles to be kept in the selected population and higher effective population size in order to insure variation for the next generations.

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The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle

Animals ◽

10.3390/ani10122233 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2233

Author(s):

Yoel Rodríguez-Valera ◽

Dominique Rocha ◽

Michel Naves ◽

Gilles Renand ◽

Eliecer Pérez-Pineda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Nucleotide Polymorphisms ◽

Runs Of Homozygosity ◽

Effective Population ◽

Single Nucleotide ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Management And Conservation

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.

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