Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing
Weight traits serve as key economic indicators for assessing growth performance and commercial quality in the mud crab <i>Scylla paramamosain</i>, yet the genetic basis of these traits remains poorly characterized. Here, we performed whole-genome resequencing on 323 individuals and condu...
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2025-06-01
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| author | Lin Chen Yaodong Zhang Peitan Jia Siyi Zhou Qionghui Qin Weiren Zhang Kewei Huang Xiaopeng Wang Haihui Ye |
| author_facet | Lin Chen Yaodong Zhang Peitan Jia Siyi Zhou Qionghui Qin Weiren Zhang Kewei Huang Xiaopeng Wang Haihui Ye |
| author_sort | Lin Chen |
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| description | Weight traits serve as key economic indicators for assessing growth performance and commercial quality in the mud crab <i>Scylla paramamosain</i>, yet the genetic basis of these traits remains poorly characterized. Here, we performed whole-genome resequencing on 323 individuals and conducted genome-wide association studies (GWAS) on five weight-related traits: (1) body-related traits, including body weight (BW), trunk weight (TruW), and weight excluding chelae (WEC); (2) appendage-related traits, containing appendage weight (AppW) and cheliped weight (CheW). Significantly associated SNPs were primarily enriched on chromosomes 15, 22, 25, and 36. For body-related traits, we identified 45 shared candidate SNPs and 175 common candidate genes; appendage-related traits revealed 71 shared candidate SNPs, and 229 common genes were identified; and across all five traits, there were 9 shared candidate SNPs and 49 common genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that shared functional terms/pathways among the five traits were mainly related to metabolism, development, and immunity. Body-related traits exhibited more unique GO terms and KEGG pathways associated with metabolism and immunity, whereas appendage-related traits showed some unique GO terms and KEGG pathways involved in development and morphogenesis. Among the candidate genes, we identified multiple genes associated with growth and development, metabolism, and immune responses. For example, the <i>CCHa1R</i> gene, common to carapace-related traits, is linked to feeding; the <i>DCX-EMA</i> gene, which is common to appendage-related traits, is connected to movement, and the <i>MSTO1</i> gene is pertinent to muscle development. Among the candidate genes shared by all five traits, there are a series of genes concerning growth and development (such as <i>NVD</i>, <i>CYP307A1</i>, <i>FGF1</i>, <i>NF2</i>, <i>ANKRD52</i>) and immune responses (<i>RGS10</i>). These findings advance our understanding of the genetic architecture underlying decapod crustacean growth and provide valuable insights for optimizing sustainable breeding strategies in <i>S. paramamosain</i>. |
| format | Article |
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| institution | Kabale University |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-06-01 |
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| spelling | doaj-art-9b7c673fda014624b708c7b5ef5916bd2025-08-20T03:28:29ZengMDPI AGAnimals2076-26152025-06-011513182910.3390/ani15131829Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome ResequencingLin Chen0Yaodong Zhang1Peitan Jia2Siyi Zhou3Qionghui Qin4Weiren Zhang5Kewei Huang6Xiaopeng Wang7Haihui Ye8State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaState Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, ChinaWeight traits serve as key economic indicators for assessing growth performance and commercial quality in the mud crab <i>Scylla paramamosain</i>, yet the genetic basis of these traits remains poorly characterized. Here, we performed whole-genome resequencing on 323 individuals and conducted genome-wide association studies (GWAS) on five weight-related traits: (1) body-related traits, including body weight (BW), trunk weight (TruW), and weight excluding chelae (WEC); (2) appendage-related traits, containing appendage weight (AppW) and cheliped weight (CheW). Significantly associated SNPs were primarily enriched on chromosomes 15, 22, 25, and 36. For body-related traits, we identified 45 shared candidate SNPs and 175 common candidate genes; appendage-related traits revealed 71 shared candidate SNPs, and 229 common genes were identified; and across all five traits, there were 9 shared candidate SNPs and 49 common genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that shared functional terms/pathways among the five traits were mainly related to metabolism, development, and immunity. Body-related traits exhibited more unique GO terms and KEGG pathways associated with metabolism and immunity, whereas appendage-related traits showed some unique GO terms and KEGG pathways involved in development and morphogenesis. Among the candidate genes, we identified multiple genes associated with growth and development, metabolism, and immune responses. For example, the <i>CCHa1R</i> gene, common to carapace-related traits, is linked to feeding; the <i>DCX-EMA</i> gene, which is common to appendage-related traits, is connected to movement, and the <i>MSTO1</i> gene is pertinent to muscle development. Among the candidate genes shared by all five traits, there are a series of genes concerning growth and development (such as <i>NVD</i>, <i>CYP307A1</i>, <i>FGF1</i>, <i>NF2</i>, <i>ANKRD52</i>) and immune responses (<i>RGS10</i>). These findings advance our understanding of the genetic architecture underlying decapod crustacean growth and provide valuable insights for optimizing sustainable breeding strategies in <i>S. paramamosain</i>.https://www.mdpi.com/2076-2615/15/13/1829weight-related traits<i>Scylla paramamosain</i>whole-genome resequencingGWAS |
| spellingShingle | Lin Chen Yaodong Zhang Peitan Jia Siyi Zhou Qionghui Qin Weiren Zhang Kewei Huang Xiaopeng Wang Haihui Ye Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing Animals weight-related traits <i>Scylla paramamosain</i> whole-genome resequencing GWAS |
| title | Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing |
| title_full | Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing |
| title_fullStr | Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing |
| title_full_unstemmed | Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing |
| title_short | Genome-Wide Association Study for Weight-Related Traits in <i>Scylla paramamosain</i> Using Whole-Genome Resequencing |
| title_sort | genome wide association study for weight related traits in i scylla paramamosain i using whole genome resequencing |
| topic | weight-related traits <i>Scylla paramamosain</i> whole-genome resequencing GWAS |
| url | https://www.mdpi.com/2076-2615/15/13/1829 |
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