How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

Doekes, Harmen P.; Bijma, P.; Windig, J.J.

doi:10.3390/genes12060926

Cited by 59 publications

(64 citation statements)

References 164 publications

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“…Inbreeding depression or heterosis occurs due to directional dominance ( Falconer and Mackay 1996 ). A trait should be influenced by dominance effects resulting in dominance variance to exhibit inbreeding depression ( Howard et al 2017 ; Doekes et al 2021 ). Directional dominance is when the phenotypes of heterozygous individuals differ from homozygous individuals in a consistent direction.…”

Section: Discussionmentioning

confidence: 99%

Genomic studies with preselected markers reveal dominance effects influencing growth traits in Eucalyptus nitens

Thumma¹,

Joyce²,

Jacobs³

2021

G3 Genes|Genomes|Genetics

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Genomic selection (GS) is being increasingly adopted by the tree breeding community. Most of the GS studies in trees are focused on estimating additive genetic effects. Exploiting the dominance effects offers additional opportunities to improve genetic gain. To detect dominance effects, trait-relevant markers may be important compared to nonselected markers. Here, we used preselected markers to study the dominance effects in a Eucalyptus nitens (E. nitens) breeding population consisting of open-pollinated (OP) and controlled-pollinated (CP) families. We used 8221 trees from six progeny trials in this study. Of these, 868 progeny and 255 parents were genotyped with the E. nitens marker panel. Three traits; diameter at breast height (DBH), wood basic density (DEN), and kraft pulp yield (KPY) were analyzed. Two types of genomic relationship matrices based on identity-by-state (IBS) and identity-by-descent (IBD) were tested. Performance of the genomic best linear unbiased prediction (GBLUP) models with IBS and IBD matrices were compared with pedigree-based additive best linear unbiased prediction (ABLUP) models with and without the pedigree reconstruction. Similarly, the performance of the single-step GBLUP (ssGBLUP) with IBS and IBD matrices were compared with ABLUP models using all 8221 trees. Significant dominance effects were observed with the GBLUP-AD model for DBH. The predictive ability of DBH is higher with the GBLUP-AD model compared to other models. Similarly, the prediction accuracy of genotypic values is higher with GBLUP-AD compared to the GBLUP-A model. Among the two GBLUP models (IBS and IBD), no differences were observed in predictive abilities and prediction accuracies. While the estimates of predictive ability with additive effects were similar among all four models, prediction accuracies of ABLUP were lower than the GBLUP models. The prediction accuracy of ssGBLUP-IBD is higher than the other three models while the theoretical accuracy of ssGBLUP-IBS is consistently higher than the other three models across all three groups tested (parents, genotyped, and nongenotyped). Significant inbreeding depression was observed for DBH and KPY. While there is a linear relationship between inbreeding and DBH, the relationship between inbreeding and KPY is nonlinear and quadratic. These results indicate that the inbreeding depression of DBH is mainly due to directional dominance while in KPY it may be due to epistasis. Inbreeding depression may be the main source of the observed dominance effects in DBH. The significant dominance effect observed for DBH may be used to select complementary parents to improve the genetic merit of the progeny in E. nitens.

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Section: Discussionmentioning

confidence: 99%

Genomic studies with preselected markers reveal dominance effects influencing growth traits in Eucalyptus nitens

Thumma¹,

Joyce²,

Jacobs³

2021

G3 Genes|Genomes|Genetics

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“…Smallholder farmers keep a small sheep population size (<10 sheep per flock) [10], making it impossible for animals to mate randomly and avoid inbreeding [48]. Repeated inbreeding over generations can lead to inbreeding depression [49]. Inbreeding depression refers to the decrease in mean phenotypic value with the increased level of inbreeding [49].…”

Section: Inbreedingmentioning

confidence: 99%

“…Repeated inbreeding over generations can lead to inbreeding depression [49]. Inbreeding depression refers to the decrease in mean phenotypic value with the increased level of inbreeding [49].…”

Section: Inbreedingmentioning

confidence: 99%

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An Update on South African Indigenous Sheep Breeds’ Extinction Status and Difficulties during Conservation Attempts: A Review

et al. 2022

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South African indigenous breeds’ population is decreasing at a time when their genetic material is mandatory due to the rising climate change and global warming. South African indigenous sheep breeds include Namaqua Afrikaner, Zulu, BaPedi, and Damara sheep. These breeds are the most preferred breeds by rural farmers in South Africa due to their adaptability, low feed, and veterinary requirements. However, since they are characterized by small body sizes, farmers tend to crossbreed them with exotic breeds. An early survey conducted in Kwa-Zulu Natal revealed a 7.5% decline in Zulu sheep between 2008–2011. It has recently been observed that the population left is genotypically mixed with exotic genetic material due to uncontrolled breeding techniques that rural farmers apply. Therefore, the aim of this review is to address the present status, difficulties, and conservation approaches applied to save these breeds. However, this review will be limited to the current extinction status as it appears in the Food and Agriculture Organization (FAO) system, data from recent studies, difficulties limiting the conservation success of these breeds, and the current conservation approaches in use to conserve these breeds.

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“…Традиционно расчёт коэффициента инбридинга осуществляют с использованием родословных записей. Однако современная молекулярная генетика позволяет идентифицировать в геноме животных протяжённые гомозиготные районы (ROH), свидетельствующие о наличии родственных спариваний в родословной [9,10,11]. Использование подхода ROH, по мнению M. Forutan и др.…”

Section: Inbreeding Is An Integral Part Of Breeding Work Today Howeve...unclassified

Evaluation of the inbreeding effect on the milk productivity of Holstein cows

Rudenko

2022

Аграрная наука Евро-Северо-Востока

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Inbreeding is an integral part of breeding work today. However, its effect on the economically valuable traits of animals is not identical. The research was carried out in LLC "Вreeding plant «Pushkinskoe» Bolsheboldinsky district of the Nizhny Novgorod region. The data have been obtained from the primary zootechnical records and database «SELEX» – Dairy cattle (n = 950). The animals were divided into 4 groups depending on the degree of inbreeding. Cows with the close degree of inbreeding had the maximum milk yield (9877.9 kg), those with the mild degree had minimal milk yield (9338.11 kg). An increase in the degree of inbreeding had a negative effect on the fat content in milk, which led to its decrease from 3.85 % in the group with outbred animals to 3.64 % in the group with the close degree of inbreeding. There were no significant differences in the protein content in milk between the groups. The lactation stability coefficient decreases as the degree of inbreeding increases. The variability coefficient of milk yield in animals with the close degree of inbreeding is lower than the other groups (10.53 %), the coefficient varies within 5 % according to the fat content in all groups and in terms of protein content in milk within 1.3-2.2 %. Distant and mild inbreeding has a weak positive relationship with milk yield (r = +0.015 and +0.028), close inbreeding leads to its decrease (r = -0.098). Inside the groups, having inbred connections, аn increase in the inbreeding degree leads to a very slight increase in fat content (r = +0.016-0.129) and the lactation stability coefficient (r = +0.063-0.164), the influence of the degree of inbreeding on the protein content in milk is not identical. The relationship between milk yield and fat content in outbred animals is weakly positive (r = +0.26), in cows with mild and distant degree of inbreeding is weakly negative (r = +0.057-0.121), in the group with a close degree it becomes closely negative (r = - 0.677).

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How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

Cited by 59 publications

References 164 publications

Genomic studies with preselected markers reveal dominance effects influencing growth traits in Eucalyptus nitens

Genomic studies with preselected markers reveal dominance effects influencing growth traits in Eucalyptus nitens

An Update on South African Indigenous Sheep Breeds’ Extinction Status and Difficulties during Conservation Attempts: A Review

Evaluation of the inbreeding effect on the milk productivity of Holstein cows

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