Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

In this study, genome-wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait-associated peak SNP, were identified. The SNPs within the QTL core regions were subsequently tested for trait association in two outcross Piétrain populations consisting of 771 progeny-tested boars and 210 sows with their own performance records. In the sow (boar) dataset, five (eight) of the 15 mapped QTL were validated. Hence, many QTL mapped in the F2 crosses (with Piétrain as a common founder breed) are still segregating in the current Piétrain breed. This confirms the usefulness of existing F2 crosses for mapping QTL that are still segregating in the recent founder breed generation. The approach utilizes the high power of an F2 cross to map QTL in a breeding population for which it is not guaranteed that they would be found using a GWAS in this population.

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“…Piétrain) were frequently chosen as one of the founder breeds (Grosse‐Brinkhaus et al . ; Rückert & Bennewitz ). Ledur et al .…”

Section: Results Of the Validation Studiesmentioning

confidence: 99%

Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses

et al. 2018

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“…2), be capitalized on, in some way, in the Nile tilapia breeding program? While our estimates of epistasis rely upon anonymous loci, a more direct exploitation of epistasis would require identification of the causal variants showing large epistatic interactions [52,53] for each trait. The latter will require substantial resources, probably an order of magnitude greater than resources required for identifying causal variants with additive effects.…”

Section: Use Of the Additive-by-additive Epistatic Effectsmentioning

confidence: 99%

Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia

et al. 2020

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Background: The availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated genetic variance components based on genomic information and compared these to the variance components estimated from pedigree alone in a population generated to estimate non-additive genetic variance. Furthermore, the study examined the impact of the assumptions of Hardy-Weinberg equilibrium (HWE) on estimates of genetic variance components. For the first time, the magnitude of inbreeding depression for important commercial traits in Nile tilapia was estimated by using genomic data. Results: The study estimated the non-additive genetic variance in a Nile tilapia population of full-sib families and, when present, it was almost entirely represented by additive-by-additive epistatic variance, although in pedigree studies this non-additive variance is commonly assumed to arise from dominance. For body depth (BD) and body weight at harvest (BWH), the proportion of additive-by-additive epistatic to phenotypic variance was estimated to be 0.15 and 0.17 using genomic data (P < 0.05). In addition, with genomic data, the maternal variance (P < 0.05) for BD, BWH, body length (BL) and fillet weight (FW) explained approximately 10% of the phenotypic variances, which was comparable to pedigree-based estimates. The study also showed the detrimental effects of inbreeding on commercial traits of tilapia, which was estimated to reduce trait values by 1.1, 0.9, 0.4 and 0.3% per 1% increase in the individual homozygosity for FW, BWH, BD and BL, respectively. The presence of inbreeding depression but lack of dominance variance was consistent with an infinitesimal dominance model for the traits. Conclusions: The benefit of including non-additive genetic effects for genetic evaluations in tilapia breeding schemes is not evident from these findings, but the observed inbreeding depression points to a role for reciprocal recurrent selection. Commercially, this conclusion will depend on the scheme's operational costs and resources. The creation of maternal lines in Tilapia breeding schemes may be a possibility if the variation associated with maternal effects is heritable.

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“…However, they estimated non-significant epistatic interactions for these characters. On the other hand, some authors (Uemoto et al, 2009;Groβe-Brinkhaus et al, 2010) suggested that epistasis might be an important component of production traits (including meatness) in pigs. It should be noted that the above mentioned considerable interlocus effects were estimated for crossbred populations.…”

Section: Resultsmentioning

confidence: 99%

Associations of fifty single nucleotide polymorphisms within candidate genes with meatness in pigs

Borowska¹,

Szwaczkowski²,

Kocwin-Podsiadla³

et al. 2014

CZECH J ANIM SCI

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ABSTRACT:The objective of the paper was to classify 50 SNPs (from 17 chromosomes) according to their contribution to the meatness of 293 boars of two breeds (Polish Landrace and Polish Large White) using entropy analysis and standard association analysis. The collected data were classified into two groups (according to the official EUROP procedure) and used for entropy analysis. Associations of single genotypes versus their groups (located at single chromosomes) with the trait studied were estimated by the use of the Generalized Linear Model

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Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

Cited by 17 publications

References 71 publications

Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses

Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses

Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia

Associations of fifty single nucleotide polymorphisms within candidate genes with meatness in pigs

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