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Thisarani Kalhari Ediriweera,Jun Heon Lee 한국동물유전육종학회 2022 한국동물유전육종학회지 Vol.6 No.4
Whole Genome Sequencing (WGS) provides high throughput sequencing data that reveals the true nature of the complete genome of an individual. The present study has used Ogye chicken WGS data to technically adduce the consensus sequence recovery and visualization of their assembly. Accordingly, they were mapped to NCBI accession: NC_052547.1 (of GRCg7b) using the Geneious mapper of Geneious Prime® software package. The mapping procedure was described step by step with the settings used, and visualizations were illustrated. This technique can effectively be applied in the Geneious Prime® platform to consensus sequence recovery coupled with appealing and elaborative visualizations.
Identification of new major histocompatibility complex-B Haplotypes in Bangladesh native chickens
Ediriweera Thisarani Kalhari,Manjula Prabuddha,Kim Jaewon,Kim Jin Hyung,Nam Seonju,Kim Minjun,Cho Eunjin,Bhuiyan Mohammad Shamsul Alam,Rashid Md. Abdur,이준헌 아세아·태평양축산학회 2024 Animal Bioscience Vol.37 No.5
Objective: The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck.Methods: These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program.Results: A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes.Conclusion: The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations. Objective: The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck. Methods: These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program. Results: A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes. Conclusion: The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.
조은진,Sunghyun Cho,김민준,Thisarani Kalhari Ediriweera,Dongwon Seo,Seung-Sook Lee,Jihye Cha,진대혁,Young-Kuk Kim,이준헌 한국축산학회 2022 한국축산학회지 Vol.64 No.5
Genetic analysis has great potential as a tool to differentiate between different species andbreeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism(SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus)breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198chicken breeds, SNP markers specific to the target population were discovered through acase-control genome-wide association study (GWAS) and filtered out based on the linkagedisequilibrium blocks. Significant SNP markers were selected by feature selection applyingtwo machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machinelearning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the YeonsanOgye chicken population demonstrated 100% accuracy. Hence, the GWAS and machinelearning models used in this study can be efficiently utilized to identify the optimal combinationof markers for discriminating target populations using multiple SNP markers.
Minjun Kim,Eunjin Cho,Jean Pierre Munyaneza,Thisarani Kalhari Ediriweera,Jihye Cha,진대혁,Sunghyun Cho,Jun Heon Lee 한국축산학회 2023 한국축산학회지 Vol.65 No.1
Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.