Segregation patterns and inheritance rate of copy number variations regions assessed in a Gochu Asturcelta pig pedigree

Arias, Katherine D.; Gutiérrez, Juan Pablo; Fernández, I.; Menéndez‐Arias, Nuria A.; Álvarez, Isabel

doi:10.1016/j.gene.2022.147111

Cited by 4 publications

(13 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, a total of 177 LB, gathering 804 different alleles (4.7% of the total number of alleles identified; 4.5 alleles per LB) overlapped with 72 different CNV regions (Supplementary Table S2 ) previously identified in Gochu Asturcelta pig [ 38 ]. These 177 LB lengthened 78.3 ± 115.2 kb on average and their mean number of alleles per locus was 4.7 ± 3.6.…”

Section: Resultsmentioning

confidence: 99%

“…Since the wrongly called SNPs are in low frequency [ 27 ], ADI haplotypes are likely to appear in frequencies consistent with putatively harmful alleles, potentially darkening this kind of studies. Furthermore, since calling errors can be caused by genomic alterations such as Copy Number Variations, which can be inherited from parents to offspring [ 38 ], the calling errors could also be “inherited” in a relatively high frequency (Fig. 2 ).…”

Section: Discussionmentioning

confidence: 99%

“…Following previous analyses [ 38 ], candidate haplotypes were subject to enrichment analyses using the BioMart tool [ 39 ]. Protein-coding genes found within these candidate haplotypes identified were retrieved from the Ensembl Genes 91 database, based on the Sscrofa v11.1 porcine reference genome.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Population dynamics of potentially harmful haplotypes: a pedigree analysis

Arias,

Fernández,

Gutiérrez

et al. 2024

BMC Genomics

Self Cite

View full text Add to dashboard Cite

Background 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.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Population dynamics of potentially harmful haplotypes: a pedigree analysis

Arias,

Fernández,

Gutiérrez

et al. 2024

BMC Genomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…This problem was solved when F L&H was adjusted for the mean inbreeding coefficient of the first generation of selection (Ne L&H0 ). Arias et al (2023) described that the adjustment of the inbreeding coefficients by the mean of the reference population did not allow a complete correction of the estimates, however, the use of the allele frequencies of the RP to estimate the IBD evolution in the population studied hides some assumptions, as the reference population is in Hardy-Weinberg equilibrium or that the RP have no molecular…”

Section: Generation Of Selectionmentioning

confidence: 99%

Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance

Ojeda-Marín,

Cervantes,

Formoso-Rafferty

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (FNEJ), Li and Horvitz (FL&H), Van Raden method 1 (FVR1) and method 2 (FVR2), and Yang (FYAN). Inbreeding based on runs of homozygosity (FROH) and pedigree inbreeding (FPED) were also computed. FROH, FNEJ, and FL&H were also adjusted for their average values in the first generation of selection and named FROH0, FNEJ0, and FL&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆FPEDt) and individual increases in inbreeding (∆FPEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆FNEJ0, ∆FL&H, ∆FL&H0, ∆FVR1, ∆FVR2, ∆FYAN, and ∆FROH0). The Ne was obtained from different ∆F, such as NePEDt, NePEDi, NeNEJ0, NeL&H, NeL&H0, NeVR1, NeVR2, NeYAN, and NeROH0. Comparing with FPED, FROH, FNEJ and FVR2 overestimated inbreeding while FNEJ0, FL&H, FL&H0, FVR1 and FYAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. FROH had the highest correlation with FPED (0.89); FYAN had correlations >0.95 with all the other molecular inbreeding coefficients. NePEDi was more reliable than NePEDt and presented similar behaviour to NeL&H0 and NeNEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation NePEDi was 42.20, NeL&H0 was 45.04 and NeNEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively FROH presented the highest correlation with FPED, which addresses the identity by descent probability (IBD). The evolution of NeL&H0 and NeNEJ0 was the most similar to that of NePEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.

show abstract

“…Immediately thereafter, a strict mating policy prohibiting matings between close relatives and prolonging the reproductive career of the founders and their direct descendants as much as possible was implemented to keep founder contributions balanced across generations and to preserve their genetic background in the present population [ 32 ]. The mating policies generated a complex pedigree useful for testing different hypotheses on the relationship between pedigree and genomic information and the preservation of genetic diversity [ 32 , 33 , 35 ].…”

Section: Introductionmentioning

confidence: 99%

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs

Arias,

Gutiérrez,

Fernández

et al. 2023

Genet Sel Evol

Self Cite

View full text Add to dashboard Cite

Background In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz’s, FLH; and Yang and colleague’s FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents’ mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons. Results The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors. Conclusions Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.

show abstract

Segregation patterns and inheritance rate of copy number variations regions assessed in a Gochu Asturcelta pig pedigree

Cited by 4 publications

References 39 publications

Population dynamics of potentially harmful haplotypes: a pedigree analysis

Population dynamics of potentially harmful haplotypes: a pedigree analysis

Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs

Contact Info

Product

Resources

About