Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)
Abstract Background Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foun...
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-09962-0 |
| _version_ | 1827377460447019008 |
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| author | Jixiang Hua Chunyi Zhong Wenhua Chen Jianjun Fu Jian Wang Qingchun Wang Geyan Zhu Yan Li Yifan Tao Maoyou Zhang Yalun Dong Siqi Lu Wenting Liu Jun Qiang |
| author_facet | Jixiang Hua Chunyi Zhong Wenhua Chen Jianjun Fu Jian Wang Qingchun Wang Geyan Zhu Yan Li Yifan Tao Maoyou Zhang Yalun Dong Siqi Lu Wenting Liu Jun Qiang |
| author_sort | Jixiang Hua |
| collection | DOAJ |
| description | Abstract Background Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. Results We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). Conclusions Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass. |
| first_indexed | 2024-03-08T12:40:29Z |
| format | Article |
| id | doaj.art-85f12a31c4164efd87458ca11b4e54b2 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T12:40:29Z |
| publishDate | 2024-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-85f12a31c4164efd87458ca11b4e54b22024-01-21T12:11:45ZengBMCBMC Genomics1471-21642024-01-0125111510.1186/s12864-024-09962-0Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)Jixiang Hua0Chunyi Zhong1Wenhua Chen2Jianjun Fu3Jian Wang4Qingchun Wang5Geyan Zhu6Yan Li7Yifan Tao8Maoyou Zhang9Yalun Dong10Siqi Lu11Wenting Liu12Jun Qiang13Wuxi Fisheries College, Nanjing Agricultural UniversityWuxi Fisheries College, Nanjing Agricultural UniversitySuzhou Aquatic Technology Extension StationKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesGuangxi Xinjian Investment Group Limited CompanyWuxi Fisheries College, Nanjing Agricultural UniversitySuzhou Aquatic Technology Extension StationKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesSuzhou Aquatic Technology Extension StationKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesWuxi Fisheries College, Nanjing Agricultural UniversityAbstract Background Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. Results We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). Conclusions Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.https://doi.org/10.1186/s12864-024-09962-0Largemouth bassRAD-seqSNPGrowth traitsDominant genotypes |
| spellingShingle | Jixiang Hua Chunyi Zhong Wenhua Chen Jianjun Fu Jian Wang Qingchun Wang Geyan Zhu Yan Li Yifan Tao Maoyou Zhang Yalun Dong Siqi Lu Wenting Liu Jun Qiang Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) BMC Genomics Largemouth bass RAD-seq SNP Growth traits Dominant genotypes |
| title | Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) |
| title_full | Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) |
| title_fullStr | Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) |
| title_full_unstemmed | Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) |
| title_short | Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides) |
| title_sort | single nucleotide polymorphism snp19140160 a c is a potential breeding locus for fast growth largemouth bass micropterus salmoides |
| topic | Largemouth bass RAD-seq SNP Growth traits Dominant genotypes |
| url | https://doi.org/10.1186/s12864-024-09962-0 |
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