Fine decomposition of the inbreeding and the coancestry coefficients by using the tabular method

García-Cortés, Luis Alberto; Martínez-Ávila, J. C.; Toro, M. Á.

doi:10.1007/s10592-010-0084-x

Cited by 18 publications

(26 citation statements)

References 22 publications

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“…It will be interesting to analyse how well f SEG correlates with genealogical coancestry, should the data be available, and exploring whether in cases of bottlenecks or population expansion the cumulative distribution of lengths of ROHs can be scaled to the corresponding cumulative contribution of each cohort to inbreeding (Garcia‐Cortes et al . ). Our results suggests the need to explore the consequences of using this IBD segment‐based measure of coancestry in selection programmes where the populations may have some inbreeding depression, as shown recently in Holstein cattle (Bjelland et al .…”

Section: Discussionmentioning

confidence: 97%

Using genomic tools to maintain diversity and fitness in conservation programmes

Cara¹,

Villanueva²,

Toro

et al. 2013

Molecular Ecology

100

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Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.

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Section: Discussionmentioning

confidence: 97%

Using genomic tools to maintain diversity and fitness in conservation programmes

Cara¹,

Villanueva²,

Toro

et al. 2013

Molecular Ecology

100

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show abstract

“…As noted by Casellas (2018), d predicted infinitesimal IDL inherent to the genome of each individual, whereas their realization in terms of inbreeding depression of inbred offspring was linked by Z 4 . This was a lower-triangular matrix where each non-zero element was a partial inbreeding coefficient obtained by Mendelian decomposition from the standard pedigree file (Caballero and Toro, 2000;García-Cortés et al, 2010). This approach split the overall inbreeding coefficient of each individual (F i ) into the specific contribution of each relevant ancestor (F j ') in terms of identity-by-descent.…”

Section: Operational Modelmentioning

confidence: 99%

Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties1

Casellas

Ibáñez‐Escriche

Varona

et al. 2019

Journal of Animal Science

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“…Slightly larger variability and fitness may be maintained if we applied strategies that distinguish between those individuals that contribute the most to inbreeding (Garcia-Cortes et al, 2010), or ancestral inbreeding from recent inbreeding (Ballou, 1997). The harmful effects of inbreeding are due to recent inbreeding, as the population has overcome ancestral inbreeding (Swindell and Bouzat, 2006).…”

Section: Small Population Sizementioning

confidence: 99%

Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings

Cara¹,

Villanueva²,

Toro

et al. 2013

Heredity

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Conservation programmes aim at minimising the loss of genetic diversity, which allows populations to adapt to potential environmental changes. This can be achieved by calculating how many offspring every individual should contribute to the next generation to minimise global coancestry. However, an undesired consequence of this strategy is that it maintains deleterious mutations, compromising the viability of the population. In order to avoid this, optimal contributions could be combined with inbred matings, to expose and eliminate recessive deleterious mutations by natural selection in a process known as purging. Although some populations that have undergone purging experienced reduced inbreeding depression, this effect is not consistent across species. Whether purging by inbred matings is efficient in conservation programmes depends on the balance between the loss of diversity, the initial decrease in fitness and the reduction in mutational load. Here we perform computer simulations to determine whether managing a population by combining optimal contributions with inbred matings improves its long-term viability while keeping reasonable levels of diversity. We compare the management based on genealogical information with management based on molecular data to calculate coancestries. In the scenarios analysed, inbred matings never led to higher fitness and usually maintained lower diversity than random or minimum coancestry matings. Replacing genealogical with molecular coancestry can maintain a larger genetic diversity but can also lead to a lower fitness. Our results are strongly dependent on the mutational model assumed for the trait under selection, the population size during management and the reproductive rate.

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Fine decomposition of the inbreeding and the coancestry coefficients by using the tabular method

Cited by 18 publications

References 22 publications

Using genomic tools to maintain diversity and fitness in conservation programmes

Using genomic tools to maintain diversity and fitness in conservation programmes

Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties1

Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings

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