Development of a single nucleotide polymorphism map of porcine chromosome 2

Jungerius, B.J.; Rattink, A.P.; Crooijmans, R.P.M.A.; Poel, J.J. van der; Oost, B.A. van; Pas, M.F.W. te; Groenen, Martien A. M.

doi:10.1046/j.0268-9146.2003.01056.x

Cited by 20 publications

(15 citation statements)

References 31 publications

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“…Composition of the 39 new SNPs identified in this study was: 74% C/T or A/G, 21% A/T or G/C or A/C or G/T, and 5% others. This observation is comparable with previous studies [5,9].…”

Section: Discussionsupporting

confidence: 93%

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Development of a genetic traceability test in pig based on single nucleotide polymorphism detection

Goffaux

China

Dams

et al. 2005

Forensic Science International

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In order to assure traceability along the meat transformation chain, a powerful system is required. The administrative traceability shows limits that the use of genetic markers could overcome. The individual genome contains sequence differences, basis of the genetic polymorphism of which the genetic markers are the witnesses. Among them, two classes seem to dominate on the traceability field: the microsatellites and the single nucleotide polymorphisms (SNP). The aim of this work was to develop a genetic traceability test in pig based on SNPs mainly located in 5' and 3' untranslated regions. We selected a set of 21 SNP markers including new SNPs identified in this study and SNPs previously described. A genotyping assay was performed on 96 individuals from the major crossbred pig population in Belgium. Results showed that all individuals tested presented a different genotype. We concluded that such a genetic treaceability approach might help the administrative system. Pig / SNP / traceability

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“…Composition of the 39 new SNPs identified in this study was: 74% C/T or A/G, 21% A/T or G/C or A/C or G/T, and 5% others. This observation is comparable with previous studies [5,9].…”

Section: Discussionsupporting

confidence: 93%

“…This value is low compared with a similar study [9]. By directly sequencing PCR amplification products from genes on the porcine SNPs were already described in others porcine genes [1,7].…”

Section: Discussionmentioning

confidence: 65%

Development of a genetic traceability test in pig based on single nucleotide polymorphism detection

Goffaux

China

Dams

et al. 2005

Forensic Science International

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“…A forthcoming paper that focuses on millions of SNP in the chicken genome will be available soon in Nature. In the pig, a recently developed SNP map of chromosome 2 showed that the SNP density is much higher [18], which is in accordance with the present study.…”

Section: Discussionsupporting

confidence: 93%

“…In humans, several high resolution SNP maps have been created for several chromosomes or even the whole genome, providing useful resources for studies on haplotypes associated with human diseases [2,23,28]. Furthermore, an SNP map of porcine chromosome 2 has been reported [18], however such studies have not been performed in the chicken yet. Nevertheless the results of the Chicken Genome Project, which ended in February of 2004, (http://genome.wustl.edu/projects/chicken/) enable the utilization of the draft sequence to identify SNP.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Nie¹,

Lei²,

Ouyang³

et al. 2005

Genet. Sel. Evol.

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-The genes that are part of the somatotropic axis play a crucial role in the regulation of growth and development of chickens. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, 75 pairs of primers were designed and four chicken breeds, significantly differing in growth and reproduction characteristics, were used to identify single nucleotide polymorphisms (SNP) using the denaturing high performance liquid chromatography (DHPLC) technology. A total of 283 SNP were discovered in 31 897 base pairs (bp) from 12 genes of the growth hormone (GH), growth hormone receptor (GHR), ghrelin, growth hormone secretagogue receptor (GHSR), insulin-like growth factor I and II (IGF-I and -II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin, leptin receptor (LEPR), pituitary-specific transcription factor-1 (PIT-1), somatostatin (SS), thyroid-stimulating hormone beta subunit (TSH-β). The observed average distances in bp between the SNP in the 5'UTR, coding regions (non-and synonymous), introns and 3'UTR were 172, 151 (473 and 222), 89 and 141 respectively. Fifteen non-synonymous SNP altered the translated precursors or mature proteins of GH, GHR, ghrelin, IGFBP-2, PIT-1 and SS. Fifteen indels of no less than 2 bps and 2 poly (A) polymorphisms were also observed in 9 genes. Fifty-nine PCR-RFLP markers were found in 11 genes. The SNP discovered in this study provided suitable markers for association studies of candidate genes for growth related traits in chickens.chickens / genes / SNP / DHPLC * Corresponding author: xqzhang@scau.edu.cn 340 Q. Nie et al.

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“…PCR amplification and sequencing were performed essentially as described in Jungerius et al (2003) except that PCR reactions were done in 12 l and sequences were analysed on an ABI3730 automated sequencer.…”

Section: Bac Cloning and Sequencingmentioning

confidence: 99%

Sequencing and genomic annotation of the chicken <i>(Gallus gallus)</i> Hox clusters, and mapping of evolutionarily conserved regions

Richardson

Crooijmans

Groenen

2007

Cytogenet Genome Res

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Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken HOX genes have been extensively studied in the chick limb and other developmental models. To date while the chicken HOXA cluster has been completely sequenced many other chicken HOX genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the HOXA cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available HOX sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the HOX complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken HOX clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.

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Development of a single nucleotide polymorphism map of porcine chromosome 2

Cited by 20 publications

References 31 publications

Development of a genetic traceability test in pig based on single nucleotide polymorphism detection

Development of a genetic traceability test in pig based on single nucleotide polymorphism detection

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Sequencing and genomic annotation of the chicken <i>(Gallus gallus)</i> Hox clusters, and mapping of evolutionarily conserved regions

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