Development of 50 gene‐associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4

Fujishima-Kanaya, N.; Toki, Daisuke; Suzuki, Kohei; Sawazaki, T.; Hiraiwa, Hideki; Iida, Masatake; Hayashi, Takeshi; Uenishi, Hirohide; Wada, Yasuhiko; Ito, Yukiyo; Awata, Takashi

doi:10.1046/j.1365-2052.2003.00967.x

Cited by 22 publications

(25 citation statements)

References 17 publications

(17 reference statements)

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“…Furthermore, by exploiting conservation of genome organization between pigs and humans and by improving the pighuman comparative map, comparative positional candidate genes for these traits can be identified from the human genome database. In our recent study (Fujishima-Kanaya et al, 2003), eleven genes in HSA1 have been mapped to SSC4 by linkage analysis using our swine family, which is consistent with earlier studies (Rettenberger et al, 1995, Goureau et al, 1996 al., 2000); this further demonstrated that the HSA1 region with the direction from q arm to p arm was conserved in SSC4 with direction from centromere to q-telomere. In the present study, in order to obtain the precise correspondence between the two regions, swine BAC clones containing 27 genes, including ten genes mapped on the linkage map (Fujishima-Kanaya et al, 2003), were assigned to the IMpRH map.…”

supporting

confidence: 78%

Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Hiraiwa

Sawazaki²,

Suzuki³

et al. 2003

Cytogenet Genome Res

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Loci affecting swine intramuscular fat content, backfat thickness, carcass weight, and daily weight gain were assigned to regions of swine chromosome (SSC) 4, which were shown to correspond to human chromosome (HSA) 1p22→ q25 by ZOO-FISH, bidirectional chromosome painting, as well as by the linkage map of genes. In order to select candidate genes responsible for the above traits from the human genome database, precise correspondence between SSC4 and HSA1 is a prerequisite. In the present study, 27 genes, PTGFR, GBP1, GBP2, GFI1, GCLM, ABCD3, EXTL2, KCNA3, ADORA3, KCND3, WNT2B, NRAS, SYCP1, PTGFRN, IGSF2, NOTCH2, S100A10, SHC1, SSR2, LMNA, CCT3, CD5L, PEA15, FCER1G, EAT2, DDR2, and LAMB3, located in the HSA1 region corresponding to SSC4 or possibly SSC4, were assigned to the IMpRH map. The alignment of genes from centromere to telomere in the SSC4 q arm is basically conserved in HSA1p22→q25 with the direction from the q arm to the p arm, which is in good agreement with results from linkage mapping. In addition, the present study first demonstrated that WNT2B residing in the middle of the HSA1 region was assigned to SSC18 with a high lod score (> 5), and that at least three intrachromosomal rearrangements occurred in the region in the process of swine and human evolution. PTGFR, and LAMB3 localized at both ends of the HSA1 region were assigned to SSC6 and SSC9, respectively, which is consistent with regional correspondence reported earlier. In the course of the above analysis, microsatellite markers were developed in the proximity of eleven genes localized on SSC4, and three genes on other swine chromosomes.

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confidence: 78%

Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Hiraiwa

Sawazaki²,

Suzuki³

et al. 2003

Cytogenet Genome Res

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“…BAC clones (Suzuki et al 2000) were isolated with swine STS and BAC end sequences were used for chromosome walking. Microsatellite sequences were isolated from BAC clones by using a direct sequencing method reported previously (Fujishima-Kanaya et al 2003). Genotyping of microsatellite markers was performed with the ABI Prism 3700 DNA Analyzer and GeneScan analysis software (Applied Biosystems).…”

Section: Isolation Of Bacterial Artificial Chromosomes (Bac) Clones Amentioning

confidence: 99%

Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1)

Mikawa¹,

Morozumi²,

Shimanuki³

et al. 2007

Genome Res.

116

128

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The number of vertebrae in pigs varies and is associated with meat productivity. Wild boars, which are ancestors of domestic pigs, have 19 vertebrae. In comparison, European commercial breeds have 21-23 vertebrae, probably owing to selective breeding for enlargement of body size. We previously identified two quantitative trait loci (QTL) for the number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7. These QTL explained an increase of more than two vertebrae. Here, we performed a map-based study to define the QTL region on SSC1. By using three F 2 experimental families, we performed interval mapping and recombination analyses and defined the QTL within a 1.9-cM interval. Then we analyzed the linkage disequilibrium of microsatellite markers in this interval and found that 10 adjacent markers in a 300-kb region were almost fixed in European commercial breeds. Genetic variation of the markers was observed in Asian local breeds or wild boars. This region encoded an orphan nuclear receptor, germ cell nuclear factor (NR6A1, formerly known as GCNF), which contained an amino acid substitution (Pro192Leu) coincident with the QTL. This substitution altered the binding activity of NR6A1 to its corepressors, nuclear receptor-associated protein 80 (RAP80) and nuclear receptor corepressor 1 (NCOR1). In addition, somites of mouse embryos demonstrated expression of NR6A1 protein. Together, these results suggest that NR6A1 is a strong candidate for one of the QTL that influence number of vertebrae in pigs.

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“…Moreover, we analysed the polymorphism of microsatellites present in the whole genomic DNA sequence of CA3. Previously, microsatellite markers SJ160, SJ158 and SJ159 (associated with the CA3 gene) were located at the position 46.9 cM on the SSC4 linkage map [3]. In our study on the pig CA3 gene representing about 10 kb, we identified only microsatellites SJ160, SJ158 and a novel microsatellite locus within introns but not the SJ159 locus.…”

Section: Discussionmentioning

confidence: 76%

“…backfat thickness, dressing percentage and lean meat percentage. Moreover, the porcine CA3 gene has been assigned to pig chromosome 4 (SSC4) at position 46.9 cM [3,4]. SSC4 encompasses several quantitative trait loci that are economically important in pig breeding.…”

Section: Discussionmentioning

confidence: 99%

Expression pattern and polymorphism of three microsatellite markers in the porcineCA3gene

Zhou

Deng

et al. 2008

Genet. Sel. Evol.

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-Carbonic anhydrase III (CA3) is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibres. In order to further understand the functions of the porcine CA3 protein in muscle, the temporal and spatial distributions of its gene product were analysed and the association between the presence of specific polymorphisms and carcass traits in the pig was also examined. Real-time PCR revealed that the CA3 mRNA expression showed no differences with age in skeletal muscles from Yorkshire pigs at postnatal day-1, month-2, and month-4. We provide the first evidence that CA3 is differentially expressed in the skeletal muscle of Yorkshire and Meishan pig breeds. In addition, the whole pig genomic DNA sequence of CA3 was investigated and shown to contain seven exons and six introns. Comparative sequencing of the gene from three pig breeds revealed the existence of microsatellite SJ160 in intron 5 and microsatellite SJ158 and a novel microsatellite marker that includes a tandem repeat of (TC) n in intron 4. We also determined the allele number and frequencies of the three loci in seven pig breeds and found that they are low polymorphic microsatellite markers. Statistical analysis showed that the CA3 microsatellite polymorphism was associated with dressing percentage, internal fat rate, carcass length, rib number and backfat thickness in the pig.pig / carbonic anhydrase III / expression pattern / microsatellite polymorphism

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Development of 50 gene‐associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4

Cited by 22 publications

References 17 publications

Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Elucidation of correspondence between swine chromosome 4 and human chromosome 1 by assigning 27 genes to the ImpRH map, and development of microsatellites in the proximity of 14 genes

Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1)

Expression pattern and polymorphism of three microsatellite markers in the porcineCA3gene

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