Genome-Wide Association Study of Spawning Traits and Candidate Gene Mining in Portunus trituberculatus.
- 1State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
- 2National Experimental Teaching Demonstration Center for Aquatic Sciences, Shanghai Ocean University, Shanghai 201306, China.
- 3Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China.
Abstract
Portunus trituberculatus is a commercially crucial marine aquaculture crab species in China, renowned for its high economic value. Spawning performance is one of the most important target traits in selective breeding programs for this species; however, the genetic architecture underlying this trait remains largely uncharacterized. In the present study, 160 artificially cultivated broodstock individuals were subjected to genomic analysis, with high-throughput liquid chip arrays employed for individual SNP genotyping. By combining these data with phenotypic records of spawning traits, the heritability of the target trait was estimated to be 0.065. A genome-wide association study (GWAS) using a mixed linear model detected nine SNP loci suggestively associated with spawning performance, with an average proportion of phenotypic variance explained (PVE) of 1.96%. One-way ANOVA of these suggestive loci revealed significant differences in phenotypic values among genotype groups, supporting the marker-trait associations; however, because this analysis used the same cohort as the GWAS, it should be considered exploratory rather than independent validation. These suggestive loci were distributed across 8 chromosomes including chromosome 24, 26, 30, 31, 32, 33, 36, and 48. The genetic effect analysis revealed that among the 9 suggestive loci, 8 exhibited additive genetic effects and the remaining 1 locus showed dominant effects. Based on the physical position information of these associated SNPs, 38 positional candidate genes were identified in adjacent genomic regions; 15 of these genes had clear annotation information, including three genes previously documented as reproduction-related: MOXD1, NFAT5, and DDX11. These results delineate the preliminary genetic basis of spawning traits in P. trituberculatus and provide important molecular markers and promising candidate genes for breeding improved varieties with high fecundity.
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BibTeX
@article{pan2026genomewide,
title = {{Genome-Wide Association Study of Spawning Traits and Candidate Gene Mining in Portunus trituberculatus.}},
author = {Xiaotong Pan and Shaoting Jia and Dongfang Sun and Yichen Su and Yuchao Huang and Baoquan Gao and Jianjian Lv},
journal = {International journal of molecular sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198670},
url = {https://europepmc.org/article/MED/42883916},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genome-Wide Association Study of Spawning Traits and Candidate Gene Mining in Portunus trituberculatus.
AU - Xiaotong Pan
AU - Shaoting Jia
AU - Dongfang Sun
AU - Yichen Su
AU - Yuchao Huang
AU - Baoquan Gao
AU - Jianjian Lv
PY - 2026
DA - 2026/09/28
JO - International journal of molecular sciences
DO - 10.3390/ijms27198670
UR - https://europepmc.org/article/MED/42883916
AB - Portunus trituberculatus is a commercially crucial marine aquaculture crab species in China, renowned for its high economic value. Spawning performance is one of the most important target traits in selective breeding programs for this species; however, the genetic architecture underlying this trait remains largely uncharacterized. In the present study, 160 artificially cultivated broodstock individuals were subjected to genomic analysis, with high-throughput liquid chip arrays employed for individual SNP genotyping. By combining these data with phenotypic records of spawning traits, the heritability of the target trait was estimated to be 0.065. A genome-wide association study (GWAS) using a mixed linear model detected nine SNP loci suggestively associated with spawning performance, with an average proportion of phenotypic variance explained (PVE) of 1.96%. One-way ANOVA of these suggestive loci revealed significant differences in phenotypic values among genotype groups, supporting the marker-trait associations; however, because this analysis used the same cohort as the GWAS, it should be considered exploratory rather than independent validation. These suggestive loci were distributed across 8 chromosomes including chromosome 24, 26, 30, 31, 32, 33, 36, and 48. The genetic effect analysis revealed that among the 9 suggestive loci, 8 exhibited additive genetic effects and the remaining 1 locus showed dominant effects. Based on the physical position information of these associated SNPs, 38 positional candidate genes were identified in adjacent genomic regions; 15 of these genes had clear annotation information, including three genes previously documented as reproduction-related: MOXD1, NFAT5, and DDX11. These results delineate the preliminary genetic basis of spawning traits in P. trituberculatus and provide important molecular markers and promising candidate genes for breeding improved varieties with high fecundity.
SN - 1422-0067
ER -