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Lim KS, Kim HC, Choi BH, Son JW, Lee KT, Choi TJ, Cho YM, Chai HH, Park JE, Park W, Lim C, Kim JM, Lim D. Identification of Monoallelically Expressed Genes Associated with Economic Traits in Hanwoo (Korean Native Cattle). Animals (Basel) 2021; 12:ani12010084. [PMID: 35011190 PMCID: PMC8749587 DOI: 10.3390/ani12010084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Hanwoo, an indigenous Korean cattle breed, has been genetically improved by selecting superior sires called Korean-proven bulls. However, cows still contribute half of the genetic stock of their offspring, and allelic-specific expressed genes have potential, as selective targets of cows, to enhance genetic gain. The aim of this study is to identify genes that have MAEs based on both the genome and transcriptome and to estimate their effects on breeding values (BVs) for economically important traits in Hanwoo. We generated resequencing data for the parents and RNA-sequencing data for the muscle, fat, and brain tissues of the offspring. A total of 3801 heterozygous single nucleotide polymorphisms (SNPs) in offspring were identified and they were located in 1569 genes. Only 14 genes showed MAE (seven expressing maternal alleles and seven expressing paternal alleles). Tissue-specific MAE was observed, and LANCL1 showed maternal allele expression across all tissues. MAE genes were enriched for the biological process of cell death and angiogenesis, which included ACKR3 and PDCL3 genes, whose SNPs were significantly associated with BVs of lean meat production-related traits, such as weight at 12 months of age, carcass weight, and loin eye area. In the current study, monoallelically expressed genes were identified in various adult tissues and these genes were associated with genetic capacity in Hanwoo.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Hyung-Chul Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Ju-Whan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Tae-Jeong Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Yong-Min Cho
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Chiwoong Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
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DNA methylation studies in cattle. J Appl Genet 2021; 62:121-136. [PMID: 33400132 DOI: 10.1007/s13353-020-00604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Investigation of the role of epigenetics in cattle breeding is gaining importance. DNA methylation represents an epigenetic modification which is essential for genomic stability and maintenance of development. Recently, DNA methylation research in cattle has intensified. The studies focus on the definition of methylomes in various organs and tissues in relation to the expression of genes underlying economically important traits, and explore methylome changes under developmental, environmental, disease, and diet influences. The investigations further characterize the methylation patterns of gametes in connection with their quality, and study methylome alterations in the developing naturally or assisted produced zygotes, embryos, and fetuses, considering their viability. A wide array of technologies developed for accurate and precise analysis of DNA methylation patterns is employed for both single-gene and genome-wide studies. Overall, the research is directed towards the identification of single methylation markers or their combinations which may be useful in the selection and breeding of animals to ensure cattle improvement.
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