Population dynamics of potentially harmful haplotypes: a pedigree analysis

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dc.contributor.authorArias, Katherine D.
dc.contributor.authorFernández, Iván
dc.contributor.authorGutiérrez García, Juan Pablo
dc.contributor.authorÁlvarez, Isabel
dc.contributor.authorGoyache Goñi, Félix
dc.date.accessioned2024-06-06T17:19:20Z
dc.date.available2024-06-06T17:19:20Z
dc.date.issued2024-05-16
dc.description2024 Acuerdos transformativos CRUE
dc.description.abstractBackground: The identification of low-frequency haplotypes, never observed in homozygous state in a population, is considered informative on the presence of potentially harmful alleles (candidate alleles), putatively involved in inbreeding depression. Although identification of candidate alleles is challenging, studies analyzing the dynamics of potentially harmful alleles are lacking. A pedigree of the highly endangered Gochu Asturcelta pig breed, including 471 individuals belonging to 51 different families with at least 5 offspring each, was genotyped using the Axiom PigHDv1 Array (658,692 SNPs). Analyses were carried out on four different cohorts defined according to pedigree depth and at the whole population (WP) level. Results: The 4,470 Linkage Blocks (LB) identified in the Base Population (10 individuals), gathered a total of 16,981 alleles in the WP. Up to 5,466 (32%) haplotypes were statistically considered candidate alleles, 3,995 of them (73%) having one copy only. The number of alleles and candidate alleles varied across cohorts according to sample size. Up to 4,610 of the alleles identified in the WP (27% of the total) were present in one cohort only. Parentage analysis identified a total of 67,742 parent-offspring incompatibilities. The number of mismatches varied according to family size. Parent-offspring inconsistencies were identified in 98.2% of the candidate alleles and 100% of the LB in which they were located. Segregation analyses informed that most potential candidate alleles appeared de novo in the pedigree. Only 17 candidate alleles were identified in the boar, sow, and paternal and maternal grandparents and were considered segregants. Conclusions: Our results suggest that neither mutation nor recombination are the major forces causing the apparition of candidate alleles. Their occurrence is more likely caused by Allele-Drop-In events due to SNP calling errors. New alleles appear when wrongly called SNPs are used to construct haplotypes. The presence of candidate alleles in either parents or grandparents of the carrier individuals does not ensure that they are true alleles. Minimum Allele Frequency thresholds may remove informative alleles. Only fully segregant candidate alleles should be considered potentially harmful alleles. A set of 16 candidate genes, potentially involved in inbreeding depression, is described.
dc.description.departmentDepto. de Producción Animal
dc.description.facultyFac. de Veterinaria
dc.description.fundingtypeAPC financiada por la UCM
dc.description.refereedTRUE
dc.description.sponsorshipEuropean Commission
dc.description.statuspub
dc.identifier.citationArias, K.D., Fernández, I., Gutiérrez, J.P. et al. Population dynamics of potentially harmful haplotypes: a pedigree analysis. BMC Genomics 25, 487 (2024). https://doi.org/10.1186/s12864-024-10407-x
dc.identifier.doi10.1186/s12864-024-10407-x
dc.identifier.essn1471-2164
dc.identifier.officialurlhttps://doi.org/10.1186/s12864-024-10407-x
dc.identifier.urihttps://hdl.handle.net/20.500.14352/104742
dc.issue.number487
dc.journal.titleBMC Genomics
dc.language.isoeng
dc.publisherSpringer
dc.relation.projectIDPID2019-103951RB/AEI/10.13039/501100011033
dc.relation.projectIDPRE2020-092905
dc.rightsAttribution 4.0 Internationalen
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subject.cdu636.09
dc.subject.keywordLinkage blocks
dc.subject.keywordPopulation genomics
dc.subject.keywordPedigree variation
dc.subject.keywordPotentially harmful alleles
dc.subject.keywordAllele-Drop-In events
dc.subject.ucmVeterinaria
dc.subject.unesco3109 Ciencias Veterinarias
dc.titlePopulation dynamics of potentially harmful haplotypes: a pedigree analysis
dc.typejournal article
dc.type.hasVersionVoR
dc.volume.number25
dspace.entity.typePublication
relation.isAuthorOfPublication775a101d-d1b4-41be-99ec-f8a430157e08
relation.isAuthorOfPublication.latestForDiscovery775a101d-d1b4-41be-99ec-f8a430157e08
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