A robust linkage map of the porcine autosomes based on gene-associated SNPs

Vingborg, R. K. K.; Gregersen, Vivi Raundahl; Zhan, Bin; Panitz, Frank; Høj, Anette; Sørensen, Kirsten Kørup; Madsen, Lone Bruhn; Larsen, Knud; Hornshøj, Henrik; Wang, Xuefei; Berthou, Christian

doi:10.1186/1471-2164-10-134

Cited by 27 publications

(23 citation statements)

References 100 publications

(99 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2009). This part of chromosome 2 in pig corresponds to a region of the human chromosome 5 (Vingborg et al. 2009), where the IL9 gene is located to 5q31.1.…”

Section: Resultsmentioning

confidence: 99%

Genomic regions associated with ventro-cranial chronic pleuritis in pig

Sørensen¹,

Gregersen²,

Christensen³

et al. 2011

Journal of Animal Breeding and Genetics

View full text Add to dashboard Cite

Ventro-cranial chronic pleuritis can be a result of pleuropneumonia and enzootic pneumonia. These diseases cause severe losses in intensive pig production worldwide, but host resistance is difficult to breed for. It could be beneficial to use marker-assisted selection, and a step towards this is to identify genomic regions associated with the trait. For this purpose, 7304 pigs from 11 boar families were analysed for associations between single nucleotide polymorphisms and ventro-cranial chronic pleuritis. The pigs were genotyped by the use of the iSelect Custom 7 K porcine SNP Chip. Quantitative trait loci (QTL), significant at the chromosome-wide level, were identified on Sus scrofa chromosomes (SSC) 2, 4, 11, 12 and 13 in four different boar families. The QTL on SSC 4 in family G was also significant at the genome-wide threshold according to Bonferroni correction. We have identified a number of candidate genes, but the causative mutations still need to be identified. Markers closely associated with the resistance traits have a strong potential for use in breeding towards animals with improved characteristics concerning ventro-cranial chronic pleuritis.

show abstract

“…2009). This part of chromosome 2 in pig corresponds to a region of the human chromosome 5 (Vingborg et al. 2009), where the IL9 gene is located to 5q31.1.…”

Section: Resultsmentioning

confidence: 99%

Genomic regions associated with ventro-cranial chronic pleuritis in pig

Sørensen¹,

Gregersen²,

Christensen³

et al. 2011

Journal of Animal Breeding and Genetics

View full text Add to dashboard Cite

show abstract

“…Most of the putative SNP were novel SNP that were not included in the list of gene-associated SNP or any other recently reported SNP data set on the pig genome Vingborg et al, 2009). The BAG clones were completely sequenced by manual finishing up to a quality score of 30 in phrap (data not shown).…”

Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 61

Lee

Byun

Kang

et al. 2012

Journal of Animal Science

View full text Add to dashboard Cite

This study was carried out to identify SNP associated with fatness traits on pig chromosome 6. In total, 11,067 putative genomic variations were detected in 125 complete bacterial artificial chromosome sequences corresponding to the region between SW2098 and SW1881, which harbors multiple QTL affecting intramuscular fat content (IMF) and backfat thickness (BFT). Among 173 putative SNP validated by MassArray, 120 SNP were used in an association study on 541 offspring produced by a cross of Korean native pig and Landrace breeds. The significance level of each SNP was determined using single marker regression analysis. Further, significant threshold values were determined using a false discovery rate. Nine out of 120 SNP showed significant effects on BFT or IMF or both. Of the 9 significant SNP, 4 were significantly associated with IMF, 7 were significantly related to BFT, and 2 SNP (Kps8172 and Kps6413) showed significant effects on both traits. Moreover, multiple regression analysis considering all significant SNP was used to correct spurious false positives due to linkage disequilibrium. Consequently, only 1 SNP (Kps6413) was significant for IMF, whereas 4 SNP including Kps6413 showed significant effects on BFT. The significant SNP had generally additive effects and on average explained 1.72% of the genetic variation for IMF and 3.92% for BFT, respectively. These markers can potentially be applied in pig breeding programs for improving IMF and BFT traits after validation in other populations.

show abstract

“…Indeed linkage maps have been assembled for many species including a broad range of markers (cattle [8], pig [26], sheep [27], mouse [28], chicken [29] and human [30]). In the case of mouse [31] was able to place SNP markers at a resolution and accuracy of 0.3 Mb by linkage mapping.…”

Section: Discussionmentioning

confidence: 99%

Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates

et al. 2010

View full text Add to dashboard Cite

BackgroundRecent developments of high-density SNP chips across a number of species require accurate genetic maps. Despite rapid advances in genome sequence assembly and availability of a number of tools for creating genetic maps, the exact genome location for a number of SNPs from these SNP chips still remains unknown. We have developed a locus ordering procedure based on linkage disequilibrium (LODE) which provides estimation of the chromosomal positions of unaligned SNPs and scaffolds. It also provides an alternative means for verification of genetic maps. We exemplified LODE in cattle.ResultsThe utility of the LODE procedure was demonstrated using data from 1,943 bulls genotyped for 73,569 SNPs across three different SNP chips. First, the utility of the procedure was tested by analysing the masked positions of 1,500 randomly-chosen SNPs with known locations (50 from each chromosome), representing three classes of minor allele frequencies (MAF), namely >0.05, 0.010.05), for validating and checking the quality of a genome assembly, and offers a means for positioning of unordered scaffolds containing SNPs. The LODE procedure will be helpful in refining genome sequence assemblies, especially those being created from next-generation sequencing where high-throughput SNP discovery and genotyping platforms are integrated components of genome analysis.

show abstract

A robust linkage map of the porcine autosomes based on gene-associated SNPs

Cited by 27 publications

References 100 publications

Genomic regions associated with ventro-cranial chronic pleuritis in pig

Genomic regions associated with ventro-cranial chronic pleuritis in pig

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 61

Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates

Contact Info

Product

Resources

About