Inbriding i selekcija na X kromosomu u populacijama domaćih životinja
Notice bibliographique
Résumé
In domestic animals, genomic studies of inbreeding and selection have mainly focused on autosomes, neglecting the X chromosome. This neglect is significant as the X chromosome influences many important traits and has unique characteristics that may lead to more pronounced effects of inbreeding and positive selection. In addition, in its small part, PAR, inbreeding avoidance might occur. Furthermore, hemizygous haplotypes on nonPAR in males clearly reveal haplotype structure, enabling detection of positive selection signals and investigation of phylogenetic relationships. Therefore, the main objectives of this dissertation were to evaluate and compare F on the X chromosome and autosomes in domestic animal populations with special focus on PAR and to develop a new method for identifying positive selection signals based on the difference in haplotype richness of nonPAR in males. Each population used was represented by high density Illumina genotypes with an adequate number of both males and females. Five different inbreeding coefficients were used on two distinct populations for cattle (Croatian cattle breeds and Nellore), dogs (Labrador Retriever and Patagonian Sheepdog) and sheep (Croatian sheep breeds and Soay). Conversely, a new method called Haplotype Richness Drop (HRiD) was established and tested alongside classical methods (eROHi, iHS, and nSL) in metapopulation of native Croatian sheep breeds. Each identified signal underwent functional characterization, gene annotation and MJN. Higher inbreeding was found on the X chromosome compared to autosomes in all populations using FROH_SVS and FROH_RZooROH (most reliable), while no differences were found using FLH1, FVR1 and FYA2, with greater variability observed using all five coefficients. No difference in F between sexes at PAR or compared to autosomes was found. Using HRiD, four signals were identified and consistently validated, with the same most significant signal across all four methods (from 13.04 to 13.62 Mb). Overall, 14 positive selection signals (12 regions) were identified with 34 genes, with high concordance (86%) with other studies of sheep. The results demonstrate the high accuracy and reliability of HRiD and show that HRiD can be used comprehensively or in scenarios where only male genotypes are available, which is common in livestock where genomic breeding values are predominantly performed for males. Moreover, MJN is shown to provide useful additional information when analysing haplotypes identified as selection signals (derived versus ancestral haplotype or control for population structure-induced disorders). In general, the results emphasize the importance of including the X chromosome in inbreeding estimation and selection identification in domestic animal populations, while the new HRiD method opens up new possibilities in identifying signals using heterogametic sex haplotypes.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,001 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».