Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows

Dadousis, Christos; Ablondi, Michela; Cipolat‐Gotet, Claudio; Kaam, J.B.C.H.M. van; Marusi, Maurizio; Cassandro, Martino; Sabbioni, A.; Summer, A.

doi:10.3168/jds.2021-21125

Cited by 20 publications

(27 citation statements)

References 79 publications

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“…The latter (called in the software PLINK and GCTA) is almost never used in practice. However, ( in PLINK and GCTA) has been considered on many occasions [ 12 , 41 , 43 , 44 , 50 , 58 ]. Our results argue against the use of both these estimators, as they showed the lowest correlations with and the most biased estimates of ΔID in the majority of scenarios, as summarized in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Here, we used a terminology, as simple as possible, by identifying the abbreviation for the authors who originally proposed the estimators ( VR , YA , LH ) plus a suffix 1 to indicate that the measure is obtained from a ratio of averages over loci ( VR 1, YA 1, LH 1) and a suffix 2 when the same estimator is obtained from the average of the ratios ( VR 2, YA 2, LH 2). This may simplify the existing “Babel tower” [ 44 ] of nomenclature.…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, in most studies, allele frequencies in the current population are used to obtain different marker-based inbreeding estimates and these are compared with each other and with pedigree-based inbreeding estimates, with rather contrasting results. For example, the correlation of coefficients of inbreeding obtained from pedigrees with those obtained from markers is often intermediate ranging from 0.4 to 0.8 [ 13 , 14 , 39 , 41 , 42 , 49 ], but can sometimes be low or even negative [ 39 , 41 , 44 , 50 , 51 ].…”

Section: Introductionmentioning

confidence: 99%

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A comparison of marker-based estimators of inbreeding and inbreeding depression

et al. 2022

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Background The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). Results If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. Conclusions When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A comparison of marker-based estimators of inbreeding and inbreeding depression

et al. 2022

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“…The FPED_FULL and FPED found can be considered to be low when compared to inbreeding coefficients reported in previous studies in Guzerá breed (Pereira et al, 2016), in indicine Gyr cattle (Santana et al, 2014;Peripolli et al, 2018) and taurine breeds (Zhang et al, 2015;Dadousis et al, 2022). An interesting result emerged when comparing our results with the study of .…”

Section: Discussioncontrasting

confidence: 63%

“…FROH values were lower than those reported for Gyr cattle (Peripolli et al, 2018;Mulim et al, 2022) and higher than those reported for Nellore cattle (Mulim et al, 2022) and taurine breeds (Zhang et al, 2015;Dadousis et al, 2022). However, these values may vary even within the same breed (Peripolli et al, 2018;Mulim et al, 2022), as they depend on the number of animals genotyped, the density of markers, and the parameters used to determine ROHs.…”

Section: Discussioncontrasting

confidence: 55%

Genetic study of reproductive, dairy and growth traits in Guzerá cattle

Carrara¹

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The Guzerá breed is an important Brazilian genetic resource and has been widely used as a pure breed and in crossbreeding strategies to produce animals adapted to tropical climatic conditions. In the last 30 years, some breeders have included selection for dairy traits in addition to selection for beef traits to obtain economic benefits from the sale of meat and milk in dual-purpose production systems. Dual-purpose studies in Guzerá cattle are recent and a previous study showed that there is no genetic antagonism between milk production, growth traits, and age at first calving in these animals, allowing joint selection for these traits. Given the advantages of including marker information such as single nucleotide polymorphisms (SNP) in genetic evaluations, efforts were also made to genotype Guzera animals, particularly those selected for milk and dual-purpose. In this sense, the overall objective of this thesis was to perform genetic and genomic evaluations considering the most important traits selected in Guzerá cattle for both dairy and beef in Guzerá cattle. First, the variance components and genetic parameters for the traits were estimated using bi-trait models. The genetic and phenotypic correlations were all favorable. The absence of genetic antagonism between the reproductive, beef and milk traits indicates that joint selection for beef and dairy traits is possible in the studied population without losses in reproductive traits. Genomic predictions were then performed using single- step genomic best linear unbiased prediction (ssGBLUP) using single-trait models. The performance of genomic prediction (in terms of predictive ability, bias, accuracy of breeding values, rank correlations, and genetic trends) using the ssGBLUP approach compared to the traditional BLUP approach was investigated. This study provided interesting insights into the future application of ssGBLUP in genetic evaluation of Guzerá cattle, especially for dairy traits. The results suggest that ssGBLUP is feasible and can be used in national genetic evaluations for reproductive, dairy, and beef traits in Guzera animals to increase the accuracy of breeding values. However, the number of genotyped animals was not yet sufficient to affect the genetic evaluation in terms of predictive ability and bias. In addition, a third study was conducted to determine the runs of homozygosity (ROH) and calculate the inbreeding coefficients of the animals from the ROH (F ROH ). The inbreeding coefficients from pedigree information (F PED ) were also estimated and the effects of F ROH and F PED on reproductive, dairy and beef traits in Guzerá animals were evaluated. Although the Brazilian population of Guzerá animals has experienced historical events such as the bottleneck effect, inbreeding coefficients were low compared to other cattle breeds, even in younger animals. There was no inbreeding depression in the evaluated traits. The results described in this thesis will contribute to the definition of selection criteria for dual-purpose cattle. In addition, this thesis provides the first results on the impact of incorporating information from SNP markers into genetic evaluations of dairy, reproductive and growth traits in Guzerá cattle (in terms of predictive ability, bias, accuracy of breeding values, rank correlations and genetic trends). In summary, our results show that joint selection for beef and dairy traits is feasible in the population studied, that the inclusion of SNP marker information increases the accuracy of animal breeding values, and that the population maintains low levels of inbreeding even during a bottleneck event without significant effects on the most important traits subject to selection. Keywords: Beef cattle. BLUP. Bos indicus. Dairy cattle. Genetic evaluation. Inbreeding. ssGBLUP. Zebu.

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