Investigation of Single Nucleotide Polymorphisms in Porcine Candidate Gene for Growth and Meat Quality Traits in the Berkshire Breed

Kim, Sang Wook; Jung, Ji Hye; Tag, Kyung; Kim, Kwan‐Suk; Hee, Chang Hong; Park, Jun kyu; Joo, Young Kuk; Kim, Tae Suk; Choi, Bong Hwan; Kim, Tae Hun; Song, Ki Duk; Cho, Byung Wook

doi:10.5352/jls.2007.17.12.1622

Cited by 4 publications

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“…Zhou et al [ 77 ] found that COL11A2 was significantly associated with body shape of Large Yellow Croaker. Some research showed that the COL11A2 gene was related to the skeletal system morphogenesis and growth of cartilage [ 78 , 79 ]. Another study revealed that the COL11A2 gene responsible for skeletal system morphogenesis and body growth was differentially expressed in adipose tissue between Jeju native pigs and Berkshire [ 80 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Wang

et al. 2022

Genes

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Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Wang

et al. 2022

Genes

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The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig

et al. 2018

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Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq

et al. 2014

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Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

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Investigation of Single Nucleotide Polymorphisms in Porcine Candidate Gene for Growth and Meat Quality Traits in the Berkshire Breed

Cited by 4 publications

References 1 publication

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq

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