Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig

Farber, Charles R.; Raney, Nancy E.; Rilington, V. D.; Venta, Patrick J.; Ernst, Catherine W.

doi:10.1159/000075739

Cited by 10 publications

(11 citation statements)

References 28 publications

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“…In this paper, we report the gene structure of the open reading frame exons and confirm previous physical and linkage mapping of the KITLG gene to SSC5 (Farber et al. 2003; Okumura et al.…”

Section: Introductionsupporting

confidence: 85%

Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits

Hadjiconstantouras¹,

Sargent²,

Skinner³

et al. 2008

Animal Genetics

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Kit ligand (KITLG) is the ligand for the type III receptor tyrosine kinase KIT. Studies of the KIT/KITLG pathway in a number of mammalian species have shown that it is important for the development of stem cell populations in haematopoietic tissues, germ cells in reproductive organs and the embryonic migrating melanoblasts that give rise to melanocytes. Consequently, mutations in the pathway may result in a range of defects including anaemia, sterility and de-pigmentation. The cDNA sequence of the porcine KITLG gene has been reported previously, and is an attractive candidate locus for moderating coat colour in pigs. In this paper we report the gene structure and physical mapping of the porcine gene. We also report the identification of polymorphisms in the gene, one of which was used to confirm linkage to chromosome 5. Preliminary RNA expression studies using a panel of tissues have shown that in addition to the known variant lacking exon 6, there is alternative splicing of exon 4. However, little evidence was found for the KITLG gene being linked to variation in colour in a Meishan x Large White cross.

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“…In this paper, we report the gene structure of the open reading frame exons and confirm previous physical and linkage mapping of the KITLG gene to SSC5 (Farber et al. 2003; Okumura et al.…”

Section: Introductionsupporting

confidence: 85%

Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits

Hadjiconstantouras¹,

Sargent²,

Skinner³

et al. 2008

Animal Genetics

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“…The assignments of EDNRB to SSC11 and KITLG to SSC5 has been reported previously. 2,3 We confirmed these locations using linkage analysis of microsatellite markers and one SNP from each gene in two experimental F2 families, including a Japanese Wild Boar · LW pedigree 4 and a Duroc · Jinhua (DJ) pedigree. SNPs at nucleotide 344 of EDNRB, nucleotide 177 of SLC45A2, nucleotide 548 of MITF (Table S2) and nucleotide 323 of MYO5A (AB222082) in 192 DNA samples of the DJ resource family were genotyped using primer sets EDNRB-2, SLC45A2-3, MITF-4 and MYO5A-5 respectively.…”

Section: Linkage Mappingmentioning

confidence: 65%

“…2 Exon and intron numbers of each gene are followed by their designations as they appear in the Ensembl browser (http://www.ensembl.org/ Homo_sapiens/) transcript ID: ENST00000334286 (EDNRB), ENST00000228280 (KITLG), ENST00000296589 (SLC45A2), ENST00000314557 (MITF), ENST00000356338 (MYO5A), ENST00000336787 (RAB27A) and ENST00000329835 (SILV). 3 The KITLG transcript obtained in this study is a variant showing alternative splicing within the 3¢-UTR.…”

Section: Commentmentioning

confidence: 80%

“…1 The ribosome protein L6 (RPL6) and L10 (RPL10) genes encode for members of the ribosomal 60S subunit proteins that play an important role in protein synthesis. 2,3 In this study, full-length cDNAs of the porcine K-ALPHA-1, TUBB, MAPRE1, RPL6 and RPL10 genes were isolated. Protein sequences were deduced, and the molecular characteristics were analysed.…”

Section: Supplementary Materialsmentioning

confidence: 99%

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Sequencing, mapping and nucleotide variation of porcine coat colour genes EDNRB, MYO5A, KITLG, SLC45A2, RAB27A, SILV and MITF

Okumura¹,

Hayashi

Sekikawa

et al. 2006

Animal Genetics

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Description: In this study, we report the DNA sequences of the coding regions, single nucleotide polymorphisms (SNPs) and chromosomal assignments of seven porcine coat colour-related genes: endothelin receptor type B (EDNRB), KIT ligand (KITLG), solute carrier family 45, member 2 (SLC45A2, formerly known as MATP or membrane-associated transporter protein), microphthalmia-associated transcription factor (MITF), myosin VA (heavy polypeptide 12, myoxin) (MYO5A), RAB27A, member RAS oncogene family (RAB27A) and silver homolog (mouse) (SILV). These are genes responsible for piebald spotting (S), steel (Sl), underwhite (uw), microphthalmia (mi), dilute (d), ashen (ash) and silver (si), respectively, in mice

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“…Comparative analyses by Goureau et al (2001) and Lahbib-Mansais et al (2003) revealed conserved synteny but gene order differences between HSA12 and segments of SSC5. Farber et al (2003) localized an evolutionary breakpoint within the region HSA12q23.3 ] q24.11 by mapping genes from this human region to SSC5 and 14, respectively. Fine mapping of ESTs (Rink et al, 2006) and BAC-end sequences (Meyers et al, 2005) confirmed these findings and provided a detailed physical map of this region.…”

mentioning

confidence: 99%

Exclusion of <i>NFYB </i>as candidate gene for congenital splay leg in piglets and radiation hybrid mapping of further five homologous porcine genes from human chromosome 12 (HSA12)

Boettcher

Paul²,

Bennewitz³

et al. 2007

Cytogenet Genome Res

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Nuclear transcription factor Y, beta (NFYB) was evaluated as candidate gene for congenital splay leg in piglets based on data from differential display and QTL analysis. We mapped NFYB to pig chromosome 5 (SSC5). By assigning further five porcine genes from the corresponding region on human chromosome (HSA) 12q23.3→ q24.11 to SSC5 and 14 we could confine an evolutionary breakpoint from an interval of more than 10 Mb to less than 400 kb. Comparative sequence analysis of the coding region of NFYB in healthy and splay leg piglets revealed no polymorphism. Inter-species conservation of the codons ranges from 87% to 95% between pig, human, cow, dog, rat and mouse, respectively. The expression of NFYB in M. biceps femoris was not different between healthy and splay leg piglets. However, healthy male piglets had a significantly higher expression than females. Our results exclude NFYB as candidate gene for congenital splay leg but provide a basis for selection of further candidates for the disease from SSC5.

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Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig

Cited by 10 publications

References 28 publications

Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits

Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits

Sequencing, mapping and nucleotide variation of porcine coat colour genes EDNRB, MYO5A, KITLG, SLC45A2, RAB27A, SILV and MITF

Exclusion of <i>NFYB </i>as candidate gene for congenital splay leg in piglets and radiation hybrid mapping of further five homologous porcine genes from human chromosome 12 (HSA12)

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