Efficient use of genomic information for sustainable genetic improvement in small cattle populations

Obšteter, Jana; Jenko, Janez; Hickey, John M.

doi:10.3168/jds.2019-16853

Cited by 17 publications

(19 citation statements)

References 31 publications

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“…Populations can also alleviate the loss of genetic variability and increase sustainability by implementing optimum contribution selection. In our previous study we tested the effect of varying the use of sires in a population equal to the one simulated here (Obšteter et al, 2019). We showed that small populations can increase the genetic gain of genomic selection by 25% by rapidly turning over elite sires.…”

Section: Discussionmentioning

confidence: 94%

“…We simulated two populations with overlapping generations that mimicked a domestic and a foreign breeding program and differed in selection intensity and accuracy. The simulation included genomes, genetic values, and phenotypes for a polygenic trait with heritability 0.25, and a whole cattle breeding program as described previously (Obšteter et al, 2019). In short, both breeding programs started from the same base population.…”

Section: Simulation Of the Base Population And Historical Breedingmentioning

confidence: 99%

“…For computational simplicity, each breeding program included ~22,500 active animals but differed in the selection parameters to reflect their size and resources. The simulated trait represented a polygenic net merit encompassing many traits influenced by 10,000 causal loci (Obšteter et al, 2019). To generate genetic difference between the two breeding programs due to genetic drift and selection, we ran each breeding program for 20 years of random mating followed by a 10 year burn-in period with conventional selection with progeny testing in both populations.…”

Section: Simulation Of the Base Population And Historical Breedingmentioning

confidence: 99%

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The benefits and perils of import in small cattle breeding programs

Obšteter

Jenko²,

Pocrnić

2022

Preprint

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Small breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the benefit of import depends on the strength of genotype by environment interaction. It also also diminishes the relevance of domestic selection and the use of domestic breeding animals. Introduction of genomic selection has potentially execerbated this issue, but is also opening the potential for smaller breeding program. The aim of this paper was to determine when and to what extent do small breeding programs benefit from import. We simulated two cattle breeding programs differing in selection parameters representing a large foreign and a small domestic breeding program that differ in the initial genetic mean and annual genetic gain. We evaluated a control scenario without the use of foreign sires in the domestic breeding program and 20 scenarios that varied the percentage of domestic dams mated with foreign sires, the genetic correlation between the breeding programs (0.8 or 0.9), and the time of implementing genomic selection in the domestic compared to the foreign breeding program (concurrently or with a 10-year delay). We compared the scenarios based on the genetic gain and genic standard deviation. Finally, we partitioned breeding values and genetic trends of the scenarios to quantify the contribution of domestic selection and import to the domestic genetic gain. The simulation revealed that when both breeding programs implemented genomic selection simultaneously, the use of foreign sires increased domestic genetic gain only when genetic correlation was 0.9. In contrast, when the domestic breeding program implemented genomic selection with a 10-year delay, genetic correlation of 0.8 sufficed for a positive impact of import. In that scenario, domestic genetic gain increased with the increasing use of foreign sires but with a diminishing return. The partitioning analysis revealed that the contribution of import expectedly increased with the increased use of foreign sires. However, the increase did not depend on the genetic correlation and was not proportional to the increase in domestic genetic gain. This means that a small breeding program could be overly relying on import with diminishing returns for the genetic gain and marginal benefit for the genetic variability.

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Section: Discussionmentioning

confidence: 94%

Section: Simulation Of the Base Population And Historical Breedingmentioning

confidence: 99%

Section: Simulation Of the Base Population And Historical Breedingmentioning

confidence: 99%

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The benefits and perils of import in small cattle breeding programs

Obšteter

Jenko²,

Pocrnić

2022

Preprint

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“…In addition, 1,000 QTL per chromosome was considered to be the causal loci of a polygenetic trait influenced by many genes, each of them with minor effects. The chosen number of QTL per chromosome is consistent with many published studies (e.g, Obšteter et al, 2019Obšteter et al, , 2021Selle et al, 2020). The simulated haplotypes were used to establish the founder population of 5,000 animals with 1:1 sex ratio.…”

Section: Burn-in Phasementioning

confidence: 99%

Development of a breeding program for improving the milk yield performance of Butana cattle under smallholder production conditions using a stochastic simulation approach

Omer

Hinrichs

Addo

et al. 2022

Journal of Dairy Science

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Butana is one of the local dairy cattle breeds of Sudan commonly kept by smallholder producers. This breed has been strongly promoted to advance the dairy production sector in the country. The main problem, however, is the lack of a systematic breeding program that involves smallholder producers. The aim of the current study was to identify the most promising design for a breeding program to improve the milk yield performance of Butana cattle under smallholder production conditions. In total, 3 breeding scenarios, including (1) the use of farm bulls, (2) the use of village bulls, and (3) the rotational use of village bulls within village groups, were simulated using a stochastic simulation approach. For each breeding scenario, 3 selection methods for bulls were considered, namely random mating, phenotypic selection, and selection based on estimated breeding value (EBV). The results showed that no genetic gain was realized with random mating in all breeding scenarios. In the farm bull breeding scenario, annual genetic gain (standard deviation units) ranged from 0.01 to 0.19 (phenotypic selection) and from 0.01 to 0.39 (selection based on EBV). In the village bull breeding scenarios, the annual genetic gain ranged from 0.01 to 0.21 (phenotypic selection) and 0.01 to 0.45 (selection based on EBV). The lowest genetic gain was realized for the rotational use of village bulls among villages within groups. Through the rotational use of village bulls, however, a higher genetic variance was maintained than in the farm and village bull breeding scenarios. We concluded that a village bull breeding program with selection based on EBV of young bulls was the most promising breeding design for achieving the breeding goal. Further studies are needed to assess the organizational feasibility of such a breeding program to ensure the participation of smallholder producers and its sustainability.

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“…This, however, depends on the genetic correlation between the environments and on the initial reliability of breeding values, that is the current size of the reference population. If the size of the reference population is already large, adding more genomic information does not increase accuracies of GEBVs to a great extent (Cao et al, 2020;Obšteter et al, 2019).…”

Section: Collaboration Across Linesmentioning

confidence: 99%

Short‐ and long‐term consequences of collaboration between Northern European Red dairy and dual‐purpose cattle

Schmidtmann

Slagboom

Sørensen

et al. 2022

J Animal Breeding Genetics

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In Northern European countries, a great variety of Red cattle populations exists which can be broadly categorized in two groups: specialized dairy and dual‐purpose breeds. Collaboration between these breeds (i.e. the exchange of sires across breeds) can be beneficial but is limited so far. The aim of this study was to demonstrate and evaluate consequences of collaboration between Red breeds using stochastic simulations. Two breeding lines (dairy type and dual purpose) were simulated. As a special aspect of this study, differences in genetic levels of breeding traits (milk production, beef production, mastitis resistance, fertility, feed efficiency) have been taken into account. Various scenarios were investigated where across‐breed selection was either restricted or allowed and with different correlations between breeding goals in the two lines. The results of this study were influenced by the different genetic levels in breeding traits only in the first years of simulation. In the long run, the breed differences did not affect the degree of collaboration between lines. When the correlation between breeding goals was close to unity, the selection of external bulls was highly beneficial in terms of genetic gain and total monetary gain. Additionally, the lowest rate of inbreeding was found in that case. With decreasing correlations between environments, degree of cooperation between lines rapidly terminated and lines operated individually. In last years of simulation, cooperation was only found when the correlation between breeding goals was close to unity. From a long‐term perspective, the exchange of breeding sires across lines also caused negative effects. In the dual‐purpose line, deterioration of genetic gain in mastitis resistance and fertility was observed. Additionally, breeding lines genetically converged, which decreased genetic diversity. Collectively, short‐term benefits and long‐term negative effects have to be reconciled if collaboration between Red breeds in Northern Europe is to be pursued.

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Efficient use of genomic information for sustainable genetic improvement in small cattle populations

Cited by 17 publications

References 31 publications

The benefits and perils of import in small cattle breeding programs

The benefits and perils of import in small cattle breeding programs

Development of a breeding program for improving the milk yield performance of Butana cattle under smallholder production conditions using a stochastic simulation approach

Short‐ and long‐term consequences of collaboration between Northern European Red dairy and dual‐purpose cattle

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