Development a novel 50 K liquid SNP Array and genome-wide association study of thermotolerance trait in red swamp crayfish (Procambarus clarkii)

Qiujin Wang; Zishuo Bai; Liang Jia; Chuntong Liu; Qizhou Xu; Zhiyi Bai

doi:10.1016/j.aquaculture.2026.743927

journal article Mar 01, 2026

Development a novel 50 K liquid SNP Array and genome-wide association study of thermotolerance trait in red swamp crayfish (Procambarus clarkii)

Qiujin Wang Zishuo Bai Liang Jia Chuntong Liu Qizhou Xu Zhiyi Bai

Aquaculture pp. 743927 · Elsevier BV

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References

104

[1]

Asif "GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size" Mol. Psychiatry (2021) 10.1038/s41380-020-0670-3

[2]

Ballinger "Procambarus clarkii (red swamp crayfish)" CABI Compendium. (2022) 10.1079/cabicompendium.67878

[3]

Barnes "Thermal tolerance and burrowing behaviors of red swamp crayfish (Procambarus clarkii)" Auburn University. (2024)

[4]

Bhattacharya "The Hsp70-Hsp90 co-chaperone hop/Stip1 shifts the proteostatic balance from folding towards degradation" Nat. Commun. (2020) 10.1038/s41467-020-19783-w

[5]

Boroumand "Extensive proteomics characterization of basic proline-rich proteins in human saliva and investigation on their properties as substrates of epithelial transglutaminase 2" Plant Sci. (2019)

[6]

Bowman "Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species" Mol. Ecol. (2018) 10.1111/mec.14704

[7]

Boyd (2017)

[8]

Budhlakoti "Genomic selection: A tool for accelerating the efficiency of molecular breeding for development of climate-resilient crops" Front. Genet. (2022) 10.3389/fgene.2022.832153

[9]

Chang "Genome-wide DNA methylation and transcription analysis reveal the potential epigenetic mechanism of heat stress response in the sea cucumber Apostichopus japonicus" Front. Mar. Sci. (2023) 10.3389/fmars.2023.1136926

[10]

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen, Hao Chen, Hannah R. Thomas et al.

Molecular Plant 2020 10.1016/j.molp.2020.06.009

[11]

Comte "Evolutionary and environmental determinants of freshwater fish thermal tolerance and plasticity" Glob. Chang. Biol. (2017) 10.1111/gcb.13427

[12]

Deng "AquaGWAS: A genome-wide association study pipeline for aquatic animals and its application to reference-required and reference-free genome-wide association study for abalone" Front. Mar. Sci. (2022) 10.3389/fmars.2022.841561

[13]

Ding "Genome-wide association study identified candidate SNPs and genes associated with hypoxia tolerance in large yellow croaker (Larimichthys crocea)" Aquaculture (2022) 10.1016/j.aquaculture.2022.738472

[14]

Ding "Genome-wide association and transcriptome analysis provide the SNPs and molecular insights into the hypoxia tolerance in large yellow croaker (Larimichthys crocea)" Aquaculture (2023) 10.1016/j.aquaculture.2023.739547

[15]

Du "Effect of low water temperature on viral replication of white spot syndrome virus in Procambarus clarkii" AQUACULTURE (2008) 10.1016/j.aquaculture.2008.03.003

[16]

Du "Expression pattern of heat shock protein 90AB (HSP90AB) and stress-inducible protein 1 (Stip1) during spermatogenesis of mudskipper Boleophthalmus pectinirostris" Comp. Biochem. Physiol. B: Biochem. Mol. Biol. (2019) 10.1016/j.cbpb.2019.01.016

[17]

Ehret "Genome-wide association studies: contribution of genomics to understanding blood pressure and essential hypertension" Curr. Hypertens. Rep. (2010) 10.1007/s11906-009-0086-6

[18]

Feng "Time series analysis reveals the environmental variability of Procambarus clarkii cultures under changing meteorological parameters and its potential effect on an important cultivating area in China" Aquaculture (2021) 10.1016/j.aquaculture.2021.736688

[19]

Gao "Multiple testing corrections for imputed SNPs" Genet. Epidemiol. (2011) 10.1002/gepi.20563

[20]

Gao "The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of north American Atlantic salmon. G3: genes, genomes" Genetics (2023)

[21]

Gao "Genome-wide association and transcriptomic analysis and the identification of growth-related genes in Macrobrachium nipponense" BMC Genomics (2024) 10.1186/s12864-024-11105-4

[22]

Guo "Immune response to acute heat stress in the intestine of the red swamp crayfish, Procambarus clarkii" Fish Shellfish Immun. (2020) 10.1016/j.fsi.2020.03.017

[23]

Guo, Z., Yang, Q., Huang, F., Zheng, H., Sang, Z., Xu, Y., Zhang, C., Wu, K., Tao, J., Prasanna, B.M., 2021. Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip. Plant Commun 2(6). https://www.cell.com/plant-communications/fulltext/S2590-3462(21)00132-2. 10.1016/j.xplc.2021.100230

[24]

Gutierrez "Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar)" PLoS One (2015) 10.1371/journal.pone.0119730

[25]

Hamr, P., 2024. The real and potential impacts of invasive crayfish in Ontario Canada: A review. Freshw Crayfish 29(1), 9–22. https://https://doi.org/10.5869/fc.2024.v29-1.9. 10.5869/fc.2024.v29-1.9

[26]

Hansen "Optimum temperature of a northern population of Arctic charr (Salvelinus alpinus) using heart rate Arrhenius breakpoint analysis" Polar Biol. (2017) 10.1007/s00300-016-2033-8

[27]

Hargrove "Assessment of genetic diversity in wild and aquaculture stocks of Mercenaria mercenaria in Florida" J. Shellfish Res. (2015) 10.2983/035.034.0218

[28]

Houston "Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)" BMC Genomics (2014) 10.1186/1471-2164-15-90

[29]

Huang "iTRAQ-based identification of proteins related to muscle growth in the Pacific abalone, Haliotis discus hannai" Int. J. Mol. Sci. (2017) 10.3390/ijms18112237

[30]

Hui "Estimates of heritability based on additive-dominance genetic analysis model in red swamp crayfish, Procambarus clarkii" Aquaculture (2019) 10.1016/j.aquaculture.2019.01.043

[31]

Jiang "Identification and characterization of reference genes for normalizing expression data from red swamp crawfish Procambarus clarkii" Int. J. Mol. Sci. (2015) 10.3390/ijms160921591

[32]

Jin "Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management" PEERJ (2019) 10.7717/peerj.6214

[33]

Jørgensen "Paralysis and heart failure precede ion balance disruption in heat-stressed European green crabs" J. Therm. Biol. (2017) 10.1016/j.jtherbio.2016.08.001

[34]

Joseph "PTPN22 Regulates T Cell Synapse Formation through PSTPIP1-Dependent Actin Remodeling" bioRxiv (2025)

[35]

Ju-Ngam "Functional and stress response analysis of heat shock proteins 40 and 90 of giant river prawn (Macrobrachium rosenbergii) under temperature and pathogenic bacterial exposure stimuli" Biomolecules (2021) 10.3390/biom11071034

[36]

Junprung "HSP70 and HSP90 are involved in shrimp Penaeus vannamei tolerance to AHPND-causing strain of Vibrio parahaemolyticus after non-lethal heat shock" Fish Shellfish Immun (2017) 10.1016/j.fsi.2016.11.049

[37]

Kim "Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency" Mol. Cell. Toxicol. (2022) 10.1007/s13273-021-00171-4

[38]

Kumari "Differential fates of introns in gene expression due to global alternative splicing" Hum. Genet. (2022) 10.1007/s00439-021-02409-6

[39]

Lagarde "Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits" Genet. Sel. Evol. (2023) 10.1186/s12711-023-00811-4

[40]

Genome wide association analysis reveals the genetic sites of heat resistance in largemouth bass (Micropterus salmoides)

Xiang Li, Yan Zhou, Taigang Liu et al.

Aquaculture 2024 10.1016/j.aquaculture.2024.741025

[41]

Lien "A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns" BMC Genomics (2011) 10.1186/1471-2164-12-615

[42]

Liu (2024)

[43]

Liu "Whole-body transcriptome analysis provides insights into the cascade of sequential expression events involved in growth, immunity, and metabolism during the molting cycle in Scylla paramamosain" SCI REP-UK (2022) 10.1038/s41598-022-14783-w

[44]

Liu "Application of the liquid chip" Yellow Sea chip no. 1" in genetic evaluation of the base population with resistance to acute hepatopancreatic necrosis disease in Litopenaeus vannamei" J. Fish. China (2023)

[45]

Lv "Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks" Genomics (2022) 10.1016/j.ygeno.2022.110426

[46]

Ma "AP-3 adaptor complex-mediated vesicle trafficking" Biophys. Rep. (2021) 10.52601/bpr.2021.200051

[47]

Medrano-Mendoza "Genetic diversity, population structure, linkage disequilibrium and GWAS for resistance to WSSV in Pacific white shrimp (Litopenaeus vannamei) using a 50K SNP chip" Aquaculture (2023) 10.1016/j.aquaculture.2022.738835

[48]

Milet "Mixed logistic regression in genome-wide association studies" BMC Bioinformatics (2020) 10.1186/s12859-020-03862-2

[49]

Mogk "Cellular functions and mechanisms of action of small heat shock proteins" Ann. Rev. Microbiol. (2019) 10.1146/annurev-micro-020518-115515

[50]

Mu "Genetic diversity and population structure of different red swamp crayfish (Procambarus clarkii) populations across the north and south of China" Aquaculture and Fisheries. (2025)

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Published: Mar 01, 2026
Pages: 743927
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Cite This Article

Qiujin Wang, Zishuo Bai, Liang Jia, et al. (2026). Development a novel 50 K liquid SNP Array and genome-wide association study of thermotolerance trait in red swamp crayfish (Procambarus clarkii). Aquaculture, 743927. https://doi.org/10.1016/j.aquaculture.2026.743927

Development a novel 50 K liquid SNP Array and genome-wide association study of thermotolerance trait in red swamp crayfish (Procambarus clarkii)

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Development a novel 50 K liquid SNP Array and genome-wide association study of thermotolerance trait in red swamp crayfish (Procambarus clarkii)