Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>)
Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nuc...
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2022-10-01
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| author | Zhiwei Zhang Zhijie Lin Mingliang Wei Ziqiang Chen Mingjun Shen Guangyong Cao Yue Wang Zhiyong Zhang Dianchang Zhang |
| author_facet | Zhiwei Zhang Zhijie Lin Mingliang Wei Ziqiang Chen Mingjun Shen Guangyong Cao Yue Wang Zhiyong Zhang Dianchang Zhang |
| author_sort | Zhiwei Zhang |
| collection | DOAJ |
| description | Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (<i>p</i> < 0.05) or extremely significant correlations (<i>p</i> < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process. |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T19:03:58Z |
| publishDate | 2022-10-01 |
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| series | Genes |
| spelling | doaj.art-ded9c5f2d3914b70a3573bb781f45c1f2023-11-24T04:48:05ZengMDPI AGGenes2073-44252022-10-011311199210.3390/genes13111992Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>)Zhiwei Zhang0Zhijie Lin1Mingliang Wei2Ziqiang Chen3Mingjun Shen4Guangyong Cao5Yue Wang6Zhiyong Zhang7Dianchang Zhang8Jiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaBlack porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (<i>p</i> < 0.05) or extremely significant correlations (<i>p</i> < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.https://www.mdpi.com/2073-4425/13/11/1992black porgytranscriptomeMALDI-TOF MSSNPsgenetics and breeding |
| spellingShingle | Zhiwei Zhang Zhijie Lin Mingliang Wei Ziqiang Chen Mingjun Shen Guangyong Cao Yue Wang Zhiyong Zhang Dianchang Zhang Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) Genes black porgy transcriptome MALDI-TOF MS SNPs genetics and breeding |
| title | Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) |
| title_full | Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) |
| title_fullStr | Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) |
| title_full_unstemmed | Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) |
| title_short | Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (<i>Acanthopagrus schlegelii</i>) |
| title_sort | development of single nucleotide polymorphism and association analysis with growth traits for black porgy i acanthopagrus schlegelii i |
| topic | black porgy transcriptome MALDI-TOF MS SNPs genetics and breeding |
| url | https://www.mdpi.com/2073-4425/13/11/1992 |
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