Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi)
Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individua...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1088081/full |
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| author | Ling Li Ling Li Shan He Shan He Ming-Hui Lin Ming-Hui Lin Yan-Peng Zhang Yan-Peng Zhang Heiner Kuhl Xu-Fang Liang Xu-Fang Liang |
| author_facet | Ling Li Ling Li Shan He Shan He Ming-Hui Lin Ming-Hui Lin Yan-Peng Zhang Yan-Peng Zhang Heiner Kuhl Xu-Fang Liang Xu-Fang Liang |
| author_sort | Ling Li |
| collection | DOAJ |
| description | Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish. |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T23:31:39Z |
| publishDate | 2023-01-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-5335b77f68994e2e9dde06f9ee3879a22023-01-12T06:04:54ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10880811088081Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi)Ling Li0Ling Li1Shan He2Shan He3Ming-Hui Lin4Ming-Hui Lin5Yan-Peng Zhang6Yan-Peng Zhang7Heiner Kuhl8Xu-Fang Liang9Xu-Fang Liang10Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, ChinaEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, ChinaChinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, ChinaEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, ChinaChinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, ChinaEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, ChinaChinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, ChinaEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, ChinaDepartment of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, GermanyChinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, ChinaEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, ChinaMandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.https://www.frontiersin.org/articles/10.3389/fgene.2022.1088081/fullMandarin fishresequencingwhole-genome bisulfite sequencingfeeding habit domesticationselective sweep |
| spellingShingle | Ling Li Ling Li Shan He Shan He Ming-Hui Lin Ming-Hui Lin Yan-Peng Zhang Yan-Peng Zhang Heiner Kuhl Xu-Fang Liang Xu-Fang Liang Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) Frontiers in Genetics Mandarin fish resequencing whole-genome bisulfite sequencing feeding habit domestication selective sweep |
| title | Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) |
| title_full | Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) |
| title_fullStr | Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) |
| title_full_unstemmed | Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) |
| title_short | Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi) |
| title_sort | whole genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish siniperca chuatsi |
| topic | Mandarin fish resequencing whole-genome bisulfite sequencing feeding habit domestication selective sweep |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1088081/full |
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