SINE indel polymorphism of AGL gene and association with growth and carcass traits in Landrace × Jeju black pig F2 population

Han, Sang‐Hyun; Shin, Kwang-Yun; Lee, Sung-Soo; Ko, Moon-Suck; Jeong, Dong Kee; Oh, Hong Shik; Yang, Byoung-Chul; Cho, In-Cheol

doi:10.1007/s11033-009-9644-x

Cited by 14 publications

(12 citation statements)

References 22 publications

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“…Functional deficiency of AGL activity leads to an autosomal recessive human disease called glycogen storage disease type II, characterized by a variety of symptoms, one of which is growth retardation. In pigs, the AGL gene is associated with traits such as growth, carcass weight and backfat thickness (Han et al. 2010).…”

Section: Resultsmentioning

confidence: 99%

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT‐PCR tools

et al. 2011

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Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopolitan breeds, Large White (LW) and a crossbreed (CB; Duroc × Landrace × Large White). The results were validated by real-time PCR. All animals were of the same age and were raised under the same environmental conditions. Muscle tissues were collected at 3, 6, 9 and 11 months of age, and a total of 173 genes showed significant differential expression between CT and the cosmopolitan genetic types at 3 months of age. Time series cluster analysis indicated that the CT breed had a different pattern of gene expression compared with that of the LW and the CB. Four of the eight clusters highlighted the gene differences between CT and the other two breeds, which were further supported by statistical analyses: clusters 4 and 5 contained a total of 71 genes that were underexpressed at 3 months of age, and cluster 3 and cluster 7 included 28 and 42 genes respectively that were overexpressed at 3 months of age. As expected, differentially expressed genes belonged to the category of genes coding for contractile fibres and transcription factors involved in muscle development and differentiation. These findings highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates.

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Section: Resultsmentioning

confidence: 99%

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT‐PCR tools

et al. 2011

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“…The F 2 population was generated via reciprocal intercrosses between Landrace and JBPs. In a previous study, the authors reported in detail on F 2 animal production (Han et al, 2010); blood, muscle, and tail samples were collected from F 2 animals. All experimental procedures were conducted at the Subtropical Animal Experiment Station of the National Institute of Animal Science, Rural Development Administration of South Korea.…”

Section: Methodsmentioning

confidence: 99%

3’-UTR polymorphisms of SETD7 gene associate with economic traits in an F2 population between Landrace and Jeju (Korea) Black pigs

Cho

Han

Kang

et al. 2017

IJAR

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In order to reveal the association between genotypes of SET domain-containing protein 7; Histone H3-lysine 4-specific methyltransferase (SETD7) gene and economic traits in pigs, this study tested the association between SNP (single nucleotide polymorphism) genotypes of 3'-untranslated region of SETD7 g.1354C>T and growth and carcass traits in a resource population of the crossbred Landrace × Jeju Black pig (JBP). SETD7 T-pigs showed significantly thicker back fat levels than those of CC homozygotes (P<0.05). However, the levels of average daily gains, body weights, loin muscle area, marbling score, and meat colors did not show significant association (P>0.05). These results reveal faster growth rates in the late period of production, especially backfat deposition at the subcutaneous region according to genotypes of the SETD7 gene. These findings indicate that SETD7 genotypes may involve fat deposition or adipocyte differentiation and assist as molecular genetic markers for improving the JBP-related crossbreeding systems.

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“…The copy number variation regions CADM2-CNV1 and CADM2-CNV2 are located at 33,143,512-33,379,427 bp and 33,569,316-33,629,746 bp from the reference genome sequence NC_037328.1, respectively ( Figure 1). Animals 2019, 9,1008 3 of 11 LIHPS-CAAS-2017-115). Blood sample collection and body measurements were performed in strict accordance with the guide for the Care and Use of Laboratory Animals.…”

Section: Genomic Dna Extraction and Copy Number Identificationmentioning

confidence: 99%

“…More than 99% of indels are less than 50 bp in length [6,7], and some long insertions and deletions are returned into the concept of structural variation [8]. As a genetic marker, indels have great potential whether in growth and reproduction traits or the treatment of disease [9][10][11]. However, CNVs include duplication and/or deletions of DNA fragments ≥50 kb, and can cause a greater number of differences than SNPs and indels [12], which can be discovered by clone-based array comparative genome hybridization (array-CGH) [13].…”

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confidence: 99%

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Chen

et al. 2019

Animals

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Simple Summary: Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss-or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects.Abstract: Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.Animals 2019, 9, 1008 2 of 11 polymorphisms (RFLP), single nucleotide polymorphisms (SNP), indels (Insertion/Deletion) and structural variations, such as inversions, duplications and deletions. To date, SNPs are used extensively for complex economic disease traits in livestock [2][3][4][5]. More than 99% of indels are less than 50 bp in length [6,7], and some long insertions and deletions are returned into the concept of structural variation [8]. As a genetic marker, indels have great potential whether in growth and reproduction...

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SINE indel polymorphism of AGL gene and association with growth and carcass traits in Landrace × Jeju black pig F2 population

Cited by 14 publications

References 22 publications

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT‐PCR tools

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT‐PCR tools

3’-UTR polymorphisms of SETD7 gene associate with economic traits in an F2 population between Landrace and Jeju (Korea) Black pigs

Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

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