QTL for microstructural and biophysical muscle properties and body composition in pigs

Wimmers, Klaus; Fiedler, I.; Hardge, T.; Muráni, Eduard; Schellander, K.; Ponsuksili, Siriluck

doi:10.1186/1471-2156-7-15

Cited by 76 publications

(19 citation statements)

References 64 publications

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“…We assigned these genes to porcine regions 5q24‐q25, 9p21, 5p15, 9p12 and 6q11–22 respectively, which are in agreement with comparative mapping results 11 . There are several putative QTL for pig backfat thickness, 12 loin eye area 13 and diameter of muscle fibre 14 in the chromosomal regions where these genes mapped. In addition, BTG1 and TOB2 have significant effects on muscle development 15–18 …”

supporting

confidence: 78%

Mapping of porcine BTG1, BTG4, TOB2, USP2 and PEG3 using somatic cell and radiation hybrid panels

Zheng

Zhou

et al. 2007

Animal Genetics

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supporting

confidence: 78%

Mapping of porcine BTG1, BTG4, TOB2, USP2 and PEG3 using somatic cell and radiation hybrid panels

Zheng

Zhou

et al. 2007

Animal Genetics

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“…Multiple regions were found that had a high frequency of ROH across both the maternal breeds whereas one region was detected across all three breeds. The regions on SSC1 (248.7–264.2 Mb), SSC4 (42.1–61.3 Mb) and SSC14 (98.0–111.7 Mb) detected in LW and LA were previously shown to impact meat and carcass quality [48–51], multiple production and meat quality traits [52, 53], and reproduction [54], respectively. Four regions were found to have a higher frequency of ROH5 and/or ROH10 across the terminal DU breed and both the maternal breeds.…”

Section: Discussionmentioning

confidence: 99%

Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

Howard

Tiezzi

Huang³

et al. 2016

Genet Sel Evol

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BackgroundIn nucleus populations, regions of the genome that have a high frequency of runs of homozygosity (ROH) occur and are associated with a reduction in genetic diversity, as well as adverse effects on fitness. It is currently unclear whether, and to what extent, ROH stretches persist in the crossbred genome and how genomic management in the nucleus population might impact low diversity regions and its implications on the crossbred genome.MethodsWe calculated a ROH statistic based on lengths of 5 (ROH5) or 10 (ROH10) Mb across the genome for genotyped Landrace (LA), Large White (LW) and Duroc (DU) dams. We simulated crossbred dam (LA × LW) and market [DU × (LA × LW)] animal genotypes based on observed parental genotypes and the ROH frequency was tabulated. We conducted a simulation using observed genotypes to determine the impact of minimizing parental relationships on multiple diversity metrics within nucleus herds, i.e. pedigree-(A), SNP-by-SNP relationship matrix or ROH relationship matrix. Genome-wide metrics included, pedigree inbreeding, heterozygosity and proportion of the genome in ROH of at least 5 Mb. Lastly, the genome was split into bins of increasing ROH5 frequency and, within each bin, heterozygosity, ROH5 and length (Mb) of ROH were evaluated.ResultsWe detected regions showing high frequencies of either ROH5 and/or ROH10 across both LW and LA on SSC1, SSC4, and SSC14, and across all breeds on SSC9. Long haplotypes were shared across parental breeds and thus, regions of ROH persisted in crossbred animals. Averaged across replicates and breeds, progeny had higher levels of heterozygosity (0.0056 ± 0.002%) and lower proportion of the genome in a ROH of at least 5 Mb (−0.015 ± 0.003%) than their parental genomes when genomic relationships were constrained, while pedigree relationships resulted in negligible differences at the genomic level. Across all breeds, only genomic data was able to target low diversity regions.ConclusionsWe show that long stretches of ROH present in the parents persist in crossbred animals. Furthermore, compared to using pedigree relationships, using genomic information to constrain parental relationships resulted in maintaining more genetic diversity and more effectively targeted low diversity regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0269-y) contains supplementary material, which is available to authorized users.

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“…Collecting muscle fiber type phenotypic data is a very laborious and complicated process; thus only 120 out of 1,912 F 2 individuals were phenotyped. Until now, little research has been done regarding the identification of QTLs or SNPs associated with these traits [7][8][9]11,12]. In our previous study, the following QTLs were identified within the same sample population: 3 QTLs associated with IIB_A on SSC7, SSC8, and SSC15; 3 QTLs associated with IIA_A on SS7 and SSC11; 1 QTL associated with FN on SSC7; and 1 QTL associated with I_NP on SSCX.…”

Section: Discussionmentioning

confidence: 98%

“…Fifteen significant QTLs were associated with muscle fiber traits in a Japanese wild boar ×Large White population [7]. Thirteen QTLs for muscle fiber composition were identified in a Duroc×Berlin Miniature cross population [8]. Estellé et al [9] detected 20 significant genome regions associated with muscle fiber traits in an Iberian× Landrace F 2 pig population.…”

Section: Introductionmentioning

confidence: 99%

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Guo

Gao

Yang

et al. 2020

Asian-Australas J Anim Sci

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Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

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QTL for microstructural and biophysical muscle properties and body composition in pigs

Cited by 76 publications

References 64 publications

Mapping of porcine BTG1, BTG4, TOB2, USP2 and PEG3 using somatic cell and radiation hybrid panels

Mapping of porcine BTG1, BTG4, TOB2, USP2 and PEG3 using somatic cell and radiation hybrid panels

Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

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