Maulana Mughitz Naji, José Luis Gualdrón Duarte, Natalia Soledad Forneris, Tom Druet
{"title":"近亲繁殖抑制与比利时蓝肉牛最近的同源后裔区段有关。","authors":"Maulana Mughitz Naji, José Luis Gualdrón Duarte, Natalia Soledad Forneris, Tom Druet","doi":"10.1186/s12711-024-00878-7","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.</p><p><strong>Methods: </strong>We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (F<sub>PED</sub>), on the correlation between uniting gametes (F<sub>UNI</sub>), on the genomic relationship matrix (F<sub>GRM</sub>), on excess homozygosity (F<sub>HET</sub>), or on homozygous-by-descent (HBD) segments (F<sub>HBD</sub>).</p><p><strong>Results: </strong>F<sub>UNI</sub> and F<sub>GRM</sub> were sensitive to used allele frequencies, whereas F<sub>HET</sub> and F<sub>HBD</sub> were more robust. We detected significant ID for four traits related to height and length; F<sub>HBD</sub> and F<sub>UNI</sub> presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.</p><p><strong>Conclusions: </strong>Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":3.6000,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10832232/pdf/","citationCount":"0","resultStr":"{\"title\":\"Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.\",\"authors\":\"Maulana Mughitz Naji, José Luis Gualdrón Duarte, Natalia Soledad Forneris, Tom Druet\",\"doi\":\"10.1186/s12711-024-00878-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.</p><p><strong>Methods: </strong>We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (F<sub>PED</sub>), on the correlation between uniting gametes (F<sub>UNI</sub>), on the genomic relationship matrix (F<sub>GRM</sub>), on excess homozygosity (F<sub>HET</sub>), or on homozygous-by-descent (HBD) segments (F<sub>HBD</sub>).</p><p><strong>Results: </strong>F<sub>UNI</sub> and F<sub>GRM</sub> were sensitive to used allele frequencies, whereas F<sub>HET</sub> and F<sub>HBD</sub> were more robust. We detected significant ID for four traits related to height and length; F<sub>HBD</sub> and F<sub>UNI</sub> presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.</p><p><strong>Conclusions: </strong>Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.</p>\",\"PeriodicalId\":55120,\"journal\":{\"name\":\"Genetics Selection Evolution\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.6000,\"publicationDate\":\"2024-01-31\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10832232/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genetics Selection Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s12711-024-00878-7\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genetics Selection Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12711-024-00878-7","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.
Background: Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.
Methods: We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD).
Results: FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.
Conclusions: Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.
期刊介绍:
Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.