GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish
The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method...
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MDPI AG
2025-01-01
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| author | Yunfeng Zhao Jin Gao Hong Feng Li Jiang |
| author_facet | Yunfeng Zhao Jin Gao Hong Feng Li Jiang |
| author_sort | Yunfeng Zhao |
| collection | DOAJ |
| description | The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method to perform a genome-wide association study analysis on loci related to head size in catfish. Compared with traditional GWAS methods, the GRAMMAR-Lambda method offers higher computational efficiency, statistical power, and stability, especially in complex population structures. This research identifies many candidate genes closely related to cranial morphology in terms of head length, width, and depth in catfish, including <i>bmpr1bb</i>, <i>fgfrl1b</i>, <i>nipbl</i>, <i>foxp2</i>, and <i>pax5</i>, etc. Based on the results of gene–gene interaction analysis, we speculate that there may be frequent genetic interactions between chromosome 19 and chromosome 29 in bone development. Additionally, many candidate genes, gene families, and mechanisms (such as SOCE mechanisms) affecting skeletal development and morphology have been identified. These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits. |
| format | Article |
| id | doaj-art-d47a31697f9d4020ac99cb98969e1092 |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-01-01 |
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| series | Biology |
| spelling | doaj-art-d47a31697f9d4020ac99cb98969e10922025-01-24T13:23:29ZengMDPI AGBiology2079-77372025-01-011416310.3390/biology14010063GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in CatfishYunfeng Zhao0Jin Gao1Hong Feng2Li Jiang3Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572024, ChinaHainan Academy of Ocean and Fisheries Sciences, Haikou 571126, ChinaDepartment of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, ChinaKey Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaThe shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method to perform a genome-wide association study analysis on loci related to head size in catfish. Compared with traditional GWAS methods, the GRAMMAR-Lambda method offers higher computational efficiency, statistical power, and stability, especially in complex population structures. This research identifies many candidate genes closely related to cranial morphology in terms of head length, width, and depth in catfish, including <i>bmpr1bb</i>, <i>fgfrl1b</i>, <i>nipbl</i>, <i>foxp2</i>, and <i>pax5</i>, etc. Based on the results of gene–gene interaction analysis, we speculate that there may be frequent genetic interactions between chromosome 19 and chromosome 29 in bone development. Additionally, many candidate genes, gene families, and mechanisms (such as SOCE mechanisms) affecting skeletal development and morphology have been identified. These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits.https://www.mdpi.com/2079-7737/14/1/63linear mixed modelEMMAX<i>Ictalurus punctatus</i>morphologygenome-wide association study |
| spellingShingle | Yunfeng Zhao Jin Gao Hong Feng Li Jiang GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish Biology linear mixed model EMMAX <i>Ictalurus punctatus</i> morphology genome-wide association study |
| title | GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish |
| title_full | GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish |
| title_fullStr | GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish |
| title_full_unstemmed | GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish |
| title_short | GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish |
| title_sort | grammar lambda delivers efficient understanding of the genetic basis for head size in catfish |
| topic | linear mixed model EMMAX <i>Ictalurus punctatus</i> morphology genome-wide association study |
| url | https://www.mdpi.com/2079-7737/14/1/63 |
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