Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models

Mora, Mónica; Velasco-Galilea, María; Sánchez, Juan Pablo; Ramayo-Caldas, Yuliaxis; Piles, M.

doi:10.1186/s12711-022-00770-2

Cited by 3 publications

(2 citation statements)

References 41 publications

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“…The application of SEM animal breeding dates to the landmark paper by Gianola and Sorensen (2004), who extended the quantitative genetic theory to situations with linear recursiveness between phenotypes and established their parametric equivalence to MTM. Once the theory was put forward, several authors used it to study causal relationships between phenotypes, evaluating the impact of local interventions in livestock species, such as dairy goats (de los Campos et al, 2006), dairy cattle (Wu et al, 2007), pigs (Peñagaricano et al, 2015), broilers (Texeira et al, 2021) and rabbits (Mora, Velasco-Galilea, et al, 2022). The use of SEM in animal breeding has been recently reviewed by Varona and González-Recio (2023).…”

Section: Introductionmentioning

confidence: 99%

Conditioning on the causal network prevents indirect response to selection

Bonamy,

Fernández,

Giovambattista

et al. 2023

J Animal Breeding Genetics

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Multiple trait animal models (MTM) allow to estimate the breeding values (BV) of several traits simultaneously while accounting for genetic and environmental correlations among them. However, relationships among traits may not be reciprocal but rather causal in nature. In these cases, and given a causal network, structural equations models (SEM) arise as a more appropriate methodology. Although MTM and SEM have been shown to be parametrically equivalent, the estimated breeding value (EBV) obtained from either one or the other should be interpreted differently. In this study, we investigated the impact of using these estimates on the response to selection for a causal network comprising five different traits through a stochastic simulation experiment. Three different selection targets were assayed, involving traits located upstream, midstream and downstream this causal network. We first considered the case in which traits were causally related but not genetically correlated. The current results support our hypothesis that MTM will absorb causal relationships as genetic correlations and, consequently, change the response to selection achieved as compared with SEM. We found no differences on the response to selection when the target trait was located at the top of the causal network, but noticeable differences were detected on upstream traits when selection pressure was placed on midstream or downstream traits. We also assayed a scenario in which causal effects and genetic correlations act simultaneously and found that selection based on BVs estimated using SEM diminished the indirect response in traits upstream the causal network.

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Section: Introductionmentioning

confidence: 99%

Conditioning on the causal network prevents indirect response to selection

Bonamy,

Fernández,

Giovambattista

et al. 2023

J Animal Breeding Genetics

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“…A few genome‐wide association studies (GWAS) for several production traits have been recently carried out in rabbit after, also for this livestock species, genomic tools, including a single nucleotide polymorphism (SNP) array and a reference genome, have been made available to the scientific community (Bovo et al., 2021; Casto‐Rebollo et al., 2020; Fontanesi et al., 2021; Laghouaouta et al., 2020; Liao et al., 2021; Mora et al., 2022; Sánchez et al., 2020; Sosa‐Madrid, Hernández, et al., 2020; Sosa‐Madrid, Santacreu, et al., 2020; Wang, Xie, et al., 2022; Yang et al., 2020). However, thus far, no GWAS have been carried out in this livestock species to identify DNA markers associated with resistance to any enteropathies.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Bovo,

Ribani,

Schiavo

et al. 2023

J Animal Breeding Genetics

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Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. Clostridium genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome‐wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with FST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome‐wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19–0.21 (s.e. 0.09–0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the FST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.

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