A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Reproduction traits, such as gestation length (GLE), play an important role in dam line breeding in pigs. The objective of our study was to identify single nucleotide polymorphisms (SNPs) that are associated with GLE in two pig populations. Genotypes and deregressed breeding values were available for 2081 Dutch Landrace-based (DL) and 2301 Large White-based (LW) pigs. We identified two QTL regions for GLE, one in each population. For DL, three associated SNPs were detected in one QTL region spanning 0.52 Mbp on Sus scrofa chromosome (SSC) 2. For LW, four associated SNPs were detected in one region of 0.14 Mbp on SSC5. The region on SSC2 contains the heparin-binding EGF-like growth factor (HBEGF) gene, which promotes embryo implantation and has been described to be involved in embryo survival throughout gestation. The associated SNP can be used for marker-assisted selection in the studied populations, and further studies of the HBEGF gene are warranted to investigate its role in GLE.

show abstract

“…Chen et al . (), using microsatellite markers, have also detected one QTL region on SSC2; however, that peak also does not overlap with ours.…”

Section: Significant Snps Associated With Gestation Length For the Twcontrasting

confidence: 75%

“…; Chen et al . ). These QTL, however, are based on linkage maps with few genetic markers, resulting in large confidence intervals.…”

Section: Significant Snps Associated With Gestation Length For the Twmentioning

confidence: 97%

Genome‐wide association study reveals regions associated with gestation length in two pig populations

et al. 2015

View full text Add to dashboard Cite

show abstract

“…A QTL for ‘plasma FSH concentration’ (QTL #646, [ 26 ]) was found to overlap with CNVR43H and CNVR44H from high fertility group animals. Two low fertility group specific CNVRs (CNVR13L and CNVR39L) overlapped with two different QTLs for ‘gestation length’ (#21837, [ 27 ]; and #452, [ 28 ]). One QTL for ‘testicular weight’ (#6527, [ 29 ]) harboured CNVR5L, a low fertility group CNVR.…”

Section: Resultsmentioning

confidence: 99%

Copy number variations in high and low fertility breeding boars

Révay

Quach

Maignel³

et al. 2015

BMC Genomics

View full text Add to dashboard Cite

BackgroundIn this study we applied the extreme groups/selective genotyping approach for identifying copy number variations in high and low fertility breeding boars. The fertility indicator was the calculated Direct Boar Effect on litter size (DBE) that was obtained as a by-product of the national genetic evaluation for litter size (BLUP). The two groups of animals had DBE values at the upper (high fertility) and lower (low fertility) end of the distribution from a population of more than 38,000 boars. Animals from these two diverse phenotypes were genotyped with the Porcine SNP60K chip and compared by several approaches in order to prove the feasibility of our CNV analysis and to identify putative markers of fertility.ResultsWe have identified 35 CNVRs covering 36.5 Mb or ~1.3% of the porcine genome. Among these 35 CNVRs, 14 were specific to the high fertility group, while 19 CNVRs were specific to the low fertility group which overlap with 137 QTLs of various reproductive traits. The identified 35 CNVRs encompassed 50 genes, among them 40 were specific to the low fertility group, seven to the high fertility group, while three were found in regions that were present in both groups but with opposite gain/loss status. A functional analysis of several databases revealed that the genes found in CNVRs from the low fertility group have been significantly enriched in members of the innate immune system, Toll-like receptor and RIG-I-like receptor signaling and fatty acid oxidation pathways.ConclusionsWe have demonstrated that our analysis pipeline could identify putative CNV markers of fertility, especially in case of low fertility boars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1473-9) contains supplementary material, which is available to authorized users.

show abstract

“…; Chen et al . ) utilized a limited number of DNA markers and employed F 2 populations with large linkage disequilibrium blocks, resulting in large genomic regions associated with GL. Limited genome‐wide association studies have provided more precise locations of potential QTL or have identified variants and candidate genes for GL in swine (Onteru et al .…”

Section: Single Marker Association Results Between Snps That Explainementioning

confidence: 99%

A genome‐wide association study for gestation length in swine

et al. 2019

View full text Add to dashboard Cite

Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska-Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1-GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions. Chromosome:position in number of base pairs. 2 Percentage of additive genetic variance explained. 3Least squares means estimates with matching superscripts differ significantly (P < 0.01). The alleles, 1 or 2, were designated by alphabetical order. 4 P-value for the overall test effect of genotypes.

show abstract

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Cited by 11 publications

References 32 publications

Genome‐wide association study reveals regions associated with gestation length in two pig populations

Genome‐wide association study reveals regions associated with gestation length in two pig populations

Copy number variations in high and low fertility breeding boars

A genome‐wide association study for gestation length in swine

Contact Info

Product

Resources

About