Association of an SNP marker in exon 24 of a class 3 phosphoinositide‐3‐kinase (<i>PIK3C3</i>) gene with production traits in Duroc pigs

Hirose, Kensuke; Takizawa, Takeo; Fukawa, Kazuo; Ito, Tetsuya; Ueda, Masayuki; Hayashi, Yuzo; Tanaka, Kazuaki

doi:10.1111/j.1740-0929.2010.00816.x

Cited by 11 publications

(13 citation statements)

References 24 publications

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“…Moreover, CDH19 was evidenced as a copy number alterations (CNAs) target gene to impact central nervous system. ZWINT (ZW10 interacting protein PIK3C3), PIK3C3 (phosphoinositide-3-kinase class 3) and PTGS2 (prostaglandin-endoperoxide synthase 2) were important for cell proliferation [60]–[62], and PIK3C3 and PTGS2 were proved as candidate marker for production and reproductive traits in pigs [63]–[65]. These findings indicated that CNVs may have potential effect on immune response, production and reproductive traits of these pigs.…”

Section: Resultsmentioning

confidence: 88%

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

et al. 2014

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Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.

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Section: Resultsmentioning

confidence: 88%

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

et al. 2014

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“…The data collection method used was that described by Hirose et al . (, ). Population selection traits included average daily gain (ADG), BF, loin EMA, and intramuscular fat content (IMF).…”

Section: Methodsmentioning

confidence: 99%

Association of swine vertnin (VRTN) gene with production traits in Duroc pigs improved using a closed nucleus breeding system

Hirose

Mikawa

Okumura³

et al. 2012

Animal Science Journal

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Vertnin (VRTN) is involved in the variation of vertebral number in pigs and it is located on Sus scrofa chromosome 7. Vertebral number is related to body size in pigs, and many reports have suggested presence of an association between body length (BL) and meat production traits. Therefore, we analyzed the relationship between the VRTN genotype and the production and body composition traits in purebred Duroc pigs. Intramuscular fat content (IMF) in the Longissimus muscle was significantly associated with the VRTN genotype. The mean IMF of individuals with the wild-type genotype (Wt/Wt) (5.22%) was greater than that of individuals with the Wt/Q (4.99%) and Q/Q genotypes (4.79%). In addition, a best linear unbiased predictor of multiple traits animal model showed that the Wt allele had a positive effect on the IMF breeding value. No associations were observed between the VRTN genotype and other production traits. The VRTN genotype was related to BL. The Q/Q genotype individuals (100.0 cm) were longer than individuals with the Wt/Q (99.5 cm) and Wt/Wt genotypes (98.9 cm). These results suggest that in addition to the maintenance of an appropriate backfat thickness value, VRTN has the potential to act as a genetic marker of IMF.

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“…Another candidate gene, acyl-CoA dehydrogenase, C-4 to C-12 straight chain gene [ACADM), was tested, but no association with fat deposition was detected (Kim et al, 2006). Instead, SNP C2604T on exon 24 in phosphoinositide-3-kinase, class 3 gene {PIK3C3) was reported as a candidate DNA marker for fatness traits in an experimental cross of Korean native boars and Landrace breeds (Kim et al, 2005a) and Dtiroc breeds (Hirose et al, 2011). Lee et al (2006) proposed member RAS oncogene family gene {RAB31), vesicle-associated membrane protein, associated protein A gene {VAPA), and 7V-ethylmaleimide-sensitive factor attachment protein ^ gene (NAPG) as candidate genes because these gene loci are close to SW71 and related to the physiological functions of GLUT4.…”

Section: Introductionmentioning

confidence: 98%

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

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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.

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Association of an SNP marker in exon 24 of a class 3 phosphoinositide‐3‐kinase (PIK3C3) gene with production traits in Duroc pigs

Cited by 11 publications

References 24 publications

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

Association of swine vertnin (VRTN) gene with production traits in Duroc pigs improved using a closed nucleus breeding system

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

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