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A Brief Review on Aquaculture Genetics, Machine Learning, and Their Convergence
Thisarani Ediriweera,Prabuddha Manjula 한국동물유전육종학회 2021 한국동물유전육종학회지 Vol.5 No.3
This concise account on aquaculture, aquaculture genetics, and emerging trends of its convergence with machine learning, a sub-class of artificial intelligence provides, succinct overviews for each of the disciplines separately, their basics, and machine learning approaches in aquaculture genetics, in a consolidative manner to brief their status, applications and prospects.
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.
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.