Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats.

The analysis of the genomic landscape of inbreeding using runs of homozygosity (ROH) patterns is becoming an interesting tool to partially understand phenotypic differences among individuals. In this study, we analysed genome-wide ROH patterns in two groups of Florida goats. We first determined the inbreeding levels of each individual by calculating ROH-based inbreeding coefficients (FROH ). Then, the individuals were divided into two groups based on FROH : high inbreeding (HI, FROH  >0.1) and low inbreeding (LI, FROH  <0.03). Finally, we performed an extensive in-depth analysis of ROH distribution in each group separately. We found a higher abundance of short ROH in LI, whereas long ROH was more frequent in HI. Furthermore, ROH abundance was not evenly distributed among chromosomes within groups, with some chromosomes showing larger numbers of ROH, like CHI6, CHI7 and CHI27. A different landscape was observed in recent inbreeding (ROH >8 Mb), with significant increases in CHI6, CHI11 and CHI28. Determination of genomic regions with significantly increased ROH (ROH islands-ROHi) showed 13 ROHi related to whole inbreeding and five ROHi associated with recent inbreeding analysis. Within these genomic regions, 123 and 101 genes were identified in HI and LI, respectively, including 10 and seven candidate genes previously related to production, fertility and heat resistance in goats and livestock species.

[1]  M. Moaeen-Ud-Din,et al.  Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats , 2022, Scientific Reports.

[2]  Manuel Calderón Sánchez,et al.  Genetic Parameters of Somatic Cell Score in Florida Goats Using Single and Multiple Traits Models , 2022, Animals : an open access journal from MDPI.

[3]  J. Jordana,et al.  Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats , 2022, Journal of animal science and biotechnology.

[4]  M. Ramón,et al.  Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares , 2022, Frontiers in Veterinary Science.

[5]  C. Drögemüller,et al.  Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection , 2022, Genetics, selection, evolution : GSE.

[6]  Samuele Bovo,et al.  Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. , 2021, Journal of dairy science.

[7]  A. Talenti,et al.  Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems , 2021, Genetics, selection, evolution : GSE.

[8]  Huijiang Gao,et al.  Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle , 2021, Frontiers in Genetics.

[9]  E. Hay,et al.  Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford , 2021, Animals : an Open Access Journal from MDPI.

[10]  Jiazhong Guo,et al.  Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats , 2021, BMC genomics.

[11]  J. Windig,et al.  How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock , 2021, Genes.

[12]  R. Di Gerlando,et al.  Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations , 2021, Animals : an open access journal from MDPI.

[13]  Fergal J. Martin,et al.  Accessing Livestock Resources in Ensembl , 2021, Frontiers in Genetics.

[14]  R. Lôbo,et al.  Prediction of genomic breeding values of milk traits in Brazilian Saanen goats. , 2021, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.

[15]  A. Molina,et al.  Selection Criteria for Improving Fertility in Spanish Goat Breeds: Estimation of Genetic Parameters and Designing Selection Indices for Optimal Genetic Responses , 2021, Animals : an open access journal from MDPI.

[16]  S. Janssens,et al.  A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species , 2021, Genetics, selection, evolution : GSE.

[17]  T. Kunieda,et al.  FGF5 and EPAS1 gene polymorphisms are associated with high-altitude adaptation in Nepalese goat breeds. , 2021, Animal science journal = Nihon chikusan Gakkaiho.

[18]  E. E. Cunha,et al.  Population structure and effect of inbreeding on milk yield of Saanen goats in Brazilian production systems , 2020 .

[19]  L. Varona,et al.  Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse , 2020, Genetics, selection, evolution : GSE.

[20]  T. Sonstegard,et al.  Comparative analyses of copy number variations between Bos taurus and Bos indicus , 2020, BMC Genomics.

[21]  Samuele Bovo,et al.  Runs of homozygosity islands in Italian cosmopolitan and autochthonous pig breeds identify selection signatures in the porcine genome , 2020 .

[22]  M. Chu,et al.  Combined approaches to reveal genes associated with litter size in Yunshang black goats. , 2020, Animal genetics.

[23]  M. Bonnet,et al.  Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data. , 2020, Physiological genomics.

[24]  F. Silva,et al.  GWAS and gene networks for milk-related traits from test-day multiple lactations in Portuguese Holstein cattle , 2020, Journal of Applied Genetics.

[25]  N. Larios-Sarabia,et al.  Genetic diversity and population structure of Boer and Nubian goats in Mexico , 2020 .

[26]  A. Stella,et al.  Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed , 2020, bioRxiv.

[27]  I Misztal,et al.  Current status of genomic evaluation , 2020, Journal of animal science.

[28]  S. Janssens,et al.  How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species , 2020, BMC Genomics.

[29]  H. Zhu,et al.  InDels within caprine IGF2BP1 intron 2 and the 3'-untranslated regions are associated with goat growth traits. , 2020, Animal genetics.

[30]  Yuehui Ma,et al.  Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds , 2019, Genes.

[31]  C. Drögemüller,et al.  Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds. , 2019, Animal genetics.

[32]  Kyoung Hyoun Kim,et al.  Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds , 2019, Front. Genet..

[33]  K. Yuan,et al.  Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders , 2019, National science review.

[34]  Tamar Sofer,et al.  Genetic association testing using the GENESIS R/Bioconductor package , 2019, Bioinform..

[35]  J. Noguera,et al.  Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties1. , 2019, Journal of animal science.

[36]  C. Robert-Granié,et al.  Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits, udder type traits, and somatic cell scores in French dairy goats. , 2019, Journal of dairy science.

[37]  X. Lan,et al.  Relationship between SNPs of POU1F1 Gene and Litter Size and Growth Traits in Shaanbei White Cashmere Goats , 2019, Animals : an open access journal from MDPI.

[38]  B. Servin,et al.  Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation , 2018, Animal genetics.

[39]  The Gene Ontology Consortium,et al.  The Gene Ontology Resource: 20 years and still GOing strong , 2018, Nucleic Acids Res..

[40]  P. Uimari,et al.  Estimation of intrachromosomal inbreeding depression on female fertility using runs of homozygosity in Finnish Ayrshire cattle. , 2018, Journal of dairy science.

[41]  M. Rothschild,et al.  Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats , 2018, Genetics Selection Evolution.

[42]  J. Lenstra,et al.  Patterns of homozygosity in insular and continental goat breeds , 2018, Genetics Selection Evolution.

[43]  N. Yang,et al.  Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations , 2018, Animal genetics.

[44]  M. Groenen,et al.  Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds , 2018, Front. Genet..

[45]  Jiazhong Guo,et al.  Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds , 2018, Scientific Reports.

[46]  Hao Cheng,et al.  Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns , 2018, PloS one.

[47]  Huijiang Gao,et al.  Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. , 2018, Physiological genomics.

[48]  M. Calus,et al.  Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed , 2018, Genetics.

[49]  F. Zhao,et al.  Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry , 2018, BMC Genomics.

[50]  I. David,et al.  Genome-wide association mapping for type and mammary health traits in French dairy goats identifies a pleiotropic region on chromosome 19 in the Saanen breed. , 2018, Journal of dairy science.

[51]  S. Krawetz,et al.  Current status of sperm functional genomics and its diagnostic potential of fertility in bovine (Bos taurus) , 2018, Systems biology in reproductive medicine.

[52]  Peter K. Joshi,et al.  Runs of homozygosity: windows into population history and trait architecture , 2018, Nature Reviews Genetics.

[53]  Manuel Ramón,et al.  Goat genomic selection: Impact of the integration of genomic information in the genetic evaluations of the Spanish Florida goats , 2017, Small Ruminant Research.

[54]  M. Coffey,et al.  Genome-wide association study of conformation and milk yield in mixed-breed dairy goats. , 2016, Journal of dairy science.

[55]  R. Ventura,et al.  Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle , 2018, BMC Genomics.

[56]  R. Di Gerlando,et al.  Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep , 2017, Genetics Selection Evolution.

[57]  C. Baes,et al.  Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability. , 2017, Journal of dairy science.

[58]  R. Sullivan,et al.  Impact of male fertility status on the transcriptome of the bovine epididymis , 2017, Molecular human reproduction.

[59]  G. T. Sharma,et al.  Influence of follicular fluid and gonadotropin supplementation on the expression of germ cell marker genes during in-vitro maturation of caprine (Capra hircus) oocytes , 2016 .

[60]  M. Goddard,et al.  Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture , 2016, Proceedings of the Royal Society B: Biological Sciences.

[61]  J. Jordana,et al.  A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds , 2016, Genetics Selection Evolution.

[62]  C. Visser,et al.  Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data , 2016, PloS one.

[63]  H. Kadarmideen,et al.  Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare , 2016, Genetics Selection Evolution.

[64]  R. Randel,et al.  Bovine dopamine receptors DRD1, DRD4, and DRD5: genetic polymorphisms and diversities among ten cattle breeds. , 2016, Genetics and molecular research : GMR.

[65]  Qianjun Zhao,et al.  Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus) , 2016, BMC Genomics.

[66]  W. Jing,et al.  Cytokine-Like Protein 1(Cytl1): A Potential Molecular Mediator in Embryo Implantation , 2016, PloS one.

[67]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[68]  R. C. Gomes,et al.  Genome-wide association with residual body weight gain in Bos indicus cattle. , 2015, Genetics and molecular research : GMR.

[69]  T. Sonstegard,et al.  Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions , 2015, BMC Genomics.

[70]  G. Luikart,et al.  Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees , 2015, Heredity.

[71]  Jun Wang,et al.  Design and Characterization of a 52K SNP Chip for Goats , 2014, PloS one.

[72]  Johann Sölkner,et al.  Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors , 2013, Genetics Selection Evolution.

[73]  J. Dekkers,et al.  Application of Genomics Tools to Animal Breeding , 2012, Current genomics.

[74]  Matthew C Keller,et al.  Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms , 2011, BMC Genomics.

[75]  S. Lien,et al.  Fine mapping of quantitative trait Loci on bovine chromosome 6 affecting calving difficulty. , 2008, Journal of dairy science.

[76]  Igor Rudan,et al.  Runs of homozygosity in European populations. , 2008, American journal of human genetics.

[77]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[78]  K. Weigel,et al.  Changes in conception rate, calving performance, and calf health and survival from the use of crossbred Jersey x Holstein sires as mates for Holstein dams. , 2006, Journal of dairy science.

[79]  N. Morton,et al.  Extended tracts of homozygosity in outbred human populations. , 2006, Human molecular genetics.

[80]  M. Matzuk,et al.  Zygote arrest 1 (Zar1) is a novel maternal-effect gene critical for the oocyte-to-embryo transition , 2003, Nature Genetics.

[81]  R. Fisher,et al.  A fuller theory of “Junctions” in inbreeding , 1954, Heredity.