Runs of homozygosity analysis for selection signatures in the Yellow Korean native chicken
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Objective: Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population.Methods: A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population.Results: In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (FROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 111 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus regions with ROH islands were found to be associated with production traits.Conclusion: This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.
Abstract
Objective: Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population. Methods: A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population. Results: In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (FROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 111 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus regions with ROH islands were found to be associated with production traits. Conclusion: This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.
참고문헌 (30)
- Kim KG, "A study on the change of production performance of 5 strains of Korean native chicken after establishment of varieties", Korean J Poult Sci, 46, pp.193~204 (2019)[DOI]
- Jin S, "The breeding history and commercial development of the Korean native chicken", Worlds Poult Sci J, 73, pp.163~174 (2017)[DOI]
- "Domestic animal diversity information system (DAD-IS)" (2024)[URL]
- Cho S, "Comparison of selection signatures between korean native and commercial chickens using 600K SNP array data", Genes, 12, pp.824~ (2021)[DOI]
- Cho E, "Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens", J Anim Sci Technol, 65, pp.912~921 (2023)[DOI]
- Kim K, "Comparison of body weight and egg production ability across nine combinations of Korean indigenous chicken breeds", Korean J Poult Sci, 48, pp.161~168 (2021)[DOI]
- Sohn SH, "Diallel cross combination test for improving the laying performance of Korean native chickens", Korean J Poult Sci, 50, pp.133~141 (2023)[DOI]
- Peripolli E, "Runs of homozygosity : current knowledge and applications in livestock", Anim Genet, 48, pp.255~271 (2017)[DOI]
- Purfield DC, "The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds", PLoS ONE, 12, pp.e0176780~ (2017)[DOI]
- Gorssen W, "A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species", Genet Sel Evol, 53, pp.2~ (2021)[DOI]
- Meyermans R, "How to study runs of homozygosity using PLINK? a guide for analyzing medium density SNP data in livestock and pet species", BMC Genomics, 21, pp.94~ (2020)[DOI]
- Lencz T, "Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia", Proc Natl Acad Sci USA, 104, pp.19942~19947 (2007)[DOI]
- Purfield DC, "Runs of homozygosity and population history in cattle", BMC Genet, 13, pp.70~ (2012)[DOI]
- Mastrangelo S, "Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds", Anim Genet, 49, pp.71~81 (2018)[DOI]
- McQuillan R, "Runs of homozygosity in European populations", Am J Hum Genet, 83, pp.359~372 (2008)[DOI]
- Kinsella RJ, "Ensembl BioMarts: a hub for data retrieval across taxonomic space", Database, 2011, pp.bar030~ (2011)[DOI]
- Fonseca PAS, "GALLO:an R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci", GigaScience, 9, pp.giaa149~ (2020)[DOI]
- Hu ZL, "Animal QTLdb : an improved database tool for livestock animal QTL", association data dissemination in the post-genome era, 2013, pp.41, D871~D879
- Ferenčaković M, "Estimating autozygosity from high-throughput information : effects of SNP density and genotyping errors", Genet Sel Evol, 45, pp.42~ (2013)[DOI]
- Ferenčaković M, "Estimates of autozygosity derived from runs of homozygosity : empirical evidence from selected cattle populations", J Anim Breed Genet, 130, pp.286~293 (2013)[DOI]
- Qanbari S, "Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle", BMC Genomics, 12, pp.318~ (2011)[DOI]
- Guo Y, "Transcriptomic analysis of spleen revealed mechanism of dexamethasone-induced immune suppression in chicks", Genes(Basel), 11, pp.513~ (2020)[DOI]
- Lieber MR, "Mechanism and regulation of human non-homologous DNA end-joining", Nat Rev Mol Cell Biol, 4, pp.712~720 (2003)[DOI]
- Kanakachari M, "Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens", Front Genet, 13, pp.990849~ (2022)[DOI]
- Otaify GA, "Gnathodiaphyseal dysplasia : severe atypical presentation with novel heterozygous mutation of the anoctamin gene(ANO5)", Bone, 107, pp.161~171 (2018)[DOI]
- Zhao J, "HDAC4 regulates the proliferation, differentiation and apoptosis of chicken skeletal muscle satellite cells", Animals(Basel), 10, pp.84~ (2020)
- Liu L, "Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens", BMC Genomics, 20, pp.863~ (2019)[DOI]
- Chen X, "Genetic parameters for yolk cholesterol and transcriptional evidence indicate a role of lipoprotein lipase in the cholesterol metabolism of the Chinese wenchang chicken", Front Genet, 10, pp.902~ (2019)[DOI]
- Luo F, "Analysis of genes that influence sheep follicular development by different nutrition levels during the luteal phase using expression profiling", Anim Genet, 47, pp.354~364 (2016)[DOI]
- Wu X, "Long noncoding RNAs profiling in ovary during laying and nesting in Muscovy ducks(Cairina moschata)", Anim Reprod Sci, 230, pp.106762~ (2021)[DOI]