Tracing the breeding farm of domesticated pig using feature selection ()
Objective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2017-11-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-30-11-1540.pdf |
| _version_ | 1818545766846693376 |
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| author | Taehyung Kwon Joon Yoon Jaeyoung Heo Wonseok Lee Heebal Kim |
| author_facet | Taehyung Kwon Joon Yoon Jaeyoung Heo Wonseok Lee Heebal Kim |
| author_sort | Taehyung Kwon |
| collection | DOAJ |
| description | Objective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP) markers strictly selected through least absolute shrinkage and selection operator (LASSO) feature selection. Methods We performed farm tracing of domesticated pig (Sus scrofa) from SNP markers and selected the most relevant features for accurate prediction. Considering multi-breed composition of our data, we performed feature selection using LASSO penalization on 4,002 SNPs that are shared between breeds, which also includes 179 SNPs with small between-breed difference. The 100 highest-scored features were extracted from iterative simulations and then evaluated using machine-leaning based classifiers. Results We selected 1,341 SNPs from over 45,000 SNPs through iterative LASSO feature selection, to minimize between-breed differences. We subsequently selected 100 highest-scored SNPs from iterative scoring, and observed high statistical measures in classification of breeding farms by cross-validation only using these SNPs. Conclusion The study represents a successful application of LASSO feature selection on multi-breed pig SNP data to trace the farm information, which provides a valuable method and possibility for further researches on genetic traceability. |
| first_indexed | 2024-12-12T07:44:20Z |
| format | Article |
| id | doaj.art-27eb98cd1ce342bb9d7988774a492b1b |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-12T07:44:20Z |
| publishDate | 2017-11-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-27eb98cd1ce342bb9d7988774a492b1b2022-12-22T00:32:39ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172017-11-0130111540154910.5713/ajas.17.056123860Tracing the breeding farm of domesticated pig using feature selection ()Taehyung Kwon0Joon Yoon1Jaeyoung Heo2Wonseok Lee3Heebal Kim4 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea Interdisciplinary Program in Bioinformatics Department of Natural Science, Seoul National University, Seoul 08826, Korea International Agricultural Development and Cooperation Center, Chonbuk National University, Jeonju 54896, Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaObjective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP) markers strictly selected through least absolute shrinkage and selection operator (LASSO) feature selection. Methods We performed farm tracing of domesticated pig (Sus scrofa) from SNP markers and selected the most relevant features for accurate prediction. Considering multi-breed composition of our data, we performed feature selection using LASSO penalization on 4,002 SNPs that are shared between breeds, which also includes 179 SNPs with small between-breed difference. The 100 highest-scored features were extracted from iterative simulations and then evaluated using machine-leaning based classifiers. Results We selected 1,341 SNPs from over 45,000 SNPs through iterative LASSO feature selection, to minimize between-breed differences. We subsequently selected 100 highest-scored SNPs from iterative scoring, and observed high statistical measures in classification of breeding farms by cross-validation only using these SNPs. Conclusion The study represents a successful application of LASSO feature selection on multi-breed pig SNP data to trace the farm information, which provides a valuable method and possibility for further researches on genetic traceability.http://www.ajas.info/upload/pdf/ajas-30-11-1540.pdfPigTraceabilityBreed DifferencesSingle Nucleotide Polymorphism |
| spellingShingle | Taehyung Kwon Joon Yoon Jaeyoung Heo Wonseok Lee Heebal Kim Tracing the breeding farm of domesticated pig using feature selection () Asian-Australasian Journal of Animal Sciences Pig Traceability Breed Differences Single Nucleotide Polymorphism |
| title | Tracing the breeding farm of domesticated pig using feature selection () |
| title_full | Tracing the breeding farm of domesticated pig using feature selection () |
| title_fullStr | Tracing the breeding farm of domesticated pig using feature selection () |
| title_full_unstemmed | Tracing the breeding farm of domesticated pig using feature selection () |
| title_short | Tracing the breeding farm of domesticated pig using feature selection () |
| title_sort | tracing the breeding farm of domesticated pig using feature selection |
| topic | Pig Traceability Breed Differences Single Nucleotide Polymorphism |
| url | http://www.ajas.info/upload/pdf/ajas-30-11-1540.pdf |
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