Genomic dissection of inbreeding depression: a gate to new opportunities

Čurik, Ino; Ferenčaković, Maja; Sölkner, Johann

doi:10.1590/s1806-92902017000900010

Cited by 33 publications

(28 citation statements)

References 89 publications

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“…Correlations were lower when both groups were analyzed separately, showing values more consistent with those reported previously [ 14 ]. Three causes were suggested as source of divergence between F ROH and F PED : 1) the persistence of ancestral short ROH through time due to low recombination rates, which are ignored in the estimation of F PED [ 55 ], 2) the depth and reliability of pedigree information [ 18 , 56 ] and 3) the stochastic nature of IBD inheritance [ 57 ]. In this study, pedigree errors were minimized using molecular parentage tests for all individuals.…”

Section: Discussionmentioning

confidence: 99%

Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

et al. 2018

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The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred domestic animals. Here, we analyzed and characterized the occurrence of ROH fragments in highly inbred (HI; average pedigree-based inbreeding coefficient FPED = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average FPED = 0.008; 0 to 0.025). We studied the length of the fragments, their abundance, and genome distribution using high-density microarray data. The number of ROH was significantly higher in the HI group, especially for long fragments (>8Mb). In the LI group, the number of ROH continuously decreased with fragment length. Genome-wide distribution of ROH was highly variable between samples. Some chromosomes presented a larger number of fragments (BTA1, BTA19, BTA29), others had longer fragments (BTA4, BTA12, BTA17), while other ones showed an increased ROH accumulation over specific loci (BTA2, BTA7, BTA23, BTA29). Similar differences were observed in the analysis of 12 individuals produced by a similar inbred event (FPED3 = 0.125). The correlation between the fraction of the genome covered by ROH (FROH) and FPED was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between FPED and the microsatellite-based inbreeding coefficient (FMIC) was only moderate (r = 0.44), suggesting that STR-based inbreeding estimations should be avoided. Similarly, we found a very low correlation (r = -0.0132) between recombination rate and ROH abundance across the genome. Finally, we performed functional annotation analyses of genome regions with significantly enriched ROH abundance. Results revealed gene clusters related to pregnancy-associated proteins and immune reaction. The same analysis performed for regions enriched with recently formed ROH (> 8 Mb) showed gene clusters related to flagellum assembly. In both cases, the processes were related to male and female reproductive functions, which may partially explain the reduced fertility associated with inbred populations.

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Section: Discussionmentioning

confidence: 99%

Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

et al. 2018

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“…Overall, the majority of these strategies rely on either pedigree information or genomic relationships averaged over the genome (for a detailed review of inbreeding management strategies, please refer to Howard et al, 2017a). The use of region-specific metrics that characterize the genetic diversity (i.e., effective population size) and mapping inbreeding depression at specific regions could be used alongside commonly estimated genomewide metrics (Kardos et al, 2016;Curik et al, 2017). These regions can be identified and mapped when only affected individuals have the homozygous haplotypes carrying the causal mutation and also when only heterozygous haplotypes are identified, suggesting the lethality of the homozygous haplotypes (VanRaden et al, 2011;Kardos et al, 2016).…”

Section: Managing Inbreeding Using Genomic Informationmentioning

confidence: 99%

“…For example, Charlier et al (2008) narrowed down the probable cause of congenital muscular dystonia 2 in Belgian Blue cattle to a 3.61-Mb interval on chromosome 29 when present in its homozygous form. In addition, specific chromosomal regions that resulted in the reduction of volume and concentration of ejaculate in Brown Swiss population have been identified (Ferenčaković et al, 2014;Curik et al, 2017). In this way, potential matings of a sire to different dams, with similar haplotypes at the genome-wide level, could be further discriminated by maximizing haplotypic diversity, which is expected to affect the genomic load carried by the resulting offspring.…”

Section: Introductionmentioning

confidence: 99%

Symposium review: The genomic architecture of inbreeding: How homozygosity affects health and performance

Baes

Makanjuola

Miglior

et al. 2019

Journal of Dairy Science

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Inbreeding depression is a growing concern in livestock because it can detrimentally affect animal fitness, health, and production levels. Genomic information can be used to more effectively capture variance in Mendelian sampling, thereby enabling more accurate estimation of inbreeding, but further progress is still required. The calculation of inbreeding for herd management purposes is largely still done using pedigree information only, although inbreeding coefficients calculated in this manner have been shown to be less accurate than genomic inbreeding measures. Continuous stretches of homozygous genotypes, so called runs of homozygosity, have been shown to provide a better estimate of autozygosity at the genomic level than conventional measures based on inbreeding coefficients calculated through conventional pedigree information or even genomic relationship matrices. For improved and targeted management of genomic inbreeding at the population level, the development of methods that incorporate genomic information in mate selection programs may provide a more precise tool for reducing the detrimental effects of inbreeding in dairy herds. Additionally, a better understanding of the genomic architecture of inbreeding and incorporating that knowledge into breeding programs could significantly refine current practices. Opportunities to maintain high levels of genetic progress in traits of interest while managing homozygosity and sustaining acceptable levels of heterozygosity in highly selected dairy populations exist and should be examined more closely for continued sustainability of both the dairy cattle population as well as the dairy industry. The inclusion of precise genomic measures of inbreeding, such as runs of homozygosity, inbreeding, and mating programs, may provide a path forward. In this symposium review article, we describe traditional measures of inbreeding and the recent developments made toward more precise measures of homozygosity using genomic information. The effects of homozygosity resulting from inbreeding on phenotypes, the identification and mapping of detrimental homozygosity haplotypes, management of inbreeding with genomic data, and areas in need of further research are discussed.

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“…The best concept to quantify the level of genomic inbreeding based on true or realized autozygosity was suggested by McQuillan et al (2008). The genomic inbreeding coefficient (F ROH ) is defined as an individual autozygosity reflecting the proportion of the autosomal genome, in which autozygosity is derived from the assumption that very long stretches of homozygosity (ROH) can only result from inbreeding (Curik et al, 2017). The objective of this study was an analysis of the trend of inbreeding in Slovak Spotted cattle by using pedigree-based (F PED ) and genomic (F ROH ) estimates with respect to compare both approaches and to obtain more realistic view on situation in current population.…”

Section: Introductionmentioning

confidence: 99%

Genomic and Pedigree-Based Inbreeding in Slovak Spotted Cattle

Kasarda¹,

Kadlečík²,

Trakovická³

et al. 2019

AGR

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The objective of this study was to evaluate the level of inbreeding in population ofSlovak Spotted cattle and to compare its genomic and pedigree-based estimates.The genomic data have been obtained from in total of 37 AI sires and 50 sire damsgenotyped by using Illumina BovineSNP50v2 BeadChip and ICBF InternationalDairy and Beef v3, respectively. The genealogical information have been obtainedfrom the database of Breeding Services of the Slovak Republic, s. e. The pedigreefile consisted of 109,686 individuals (105,229 dams and 4,457 sires), while thereference population included only living animals, AI sires (129) and dams(36,949). The genomic inbreeding (FROH) was computed as the length of thegenome present in runs of homozygosity (ROH) divided by the total length of theautosomal genome covered by SNPs on the chip and the pedigree-based inbreeding(FPED) was calculated based on assumption that inbreeding of an individual reflectsthe probability that both alleles in one locus are derived from the same ancestor orare identical by descent. The ROH segments greater than 4 Mb (FROH > 4Mb) coveredin average 2.09 % of the genome, while the ROH segments greater than 16 Mb(FROH > 16Mb) achieved 0.43 % which indicated in analysed population recentinbreeding. Similarly, the increase of inbreeding across generation signalized theaverage ΔFPED computed from pedigree information (0.094%). However, thepedigree-based and genomic estimates of inbreeding differ from each other (inaverage FROH>4=0.02; FPED=0.004). In recent generation, the obtained values ofFROH indicated considerably higher degree of inbreeding.

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Genomic dissection of inbreeding depression: a gate to new opportunities

Cited by 33 publications

References 89 publications

Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

Symposium review: The genomic architecture of inbreeding: How homozygosity affects health and performance

Genomic and Pedigree-Based Inbreeding in Slovak Spotted Cattle

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