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Integrative QTL Mapping and Transcriptomic Profiling to Identify Growth-Associated QTL and Candidate Genes in Hong Kong Catfish (Clarias fuscus)
by
,
Yian Zhu
1,†,
Dayan Zhou
2,†,
Yijun Shen
1,
Chuanhao Pan
1,
Yu Chen
1,
Yulei Zhang
1,
Binlan Yang
2,
Guangli Li
1,
Huapu Chen
1 and 
Changxu Tian
1,*
1
Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
2
Guangxi Introduction and Breeding Center of Aquaculture, Nanning 530001, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2025, 15(12), 1707; https://doi.org/10.3390/ani15121707
Submission received: 5 May 2025
/
Revised: 27 May 2025
/
Accepted: 6 June 2025
/
Published: 9 June 2025
(This article belongs to the Section Animal Welfare)
Simple Summary
The Hong Kong catfish (Clarias fuscus) is a freshwater species commonly cultured in southern China for its high nutritional value. Despite its economic importance, research on the genes associated with growth traits in C. fuscus is limited, hindering the development of effective breeding strategies. In this study, quantitative trait loci (QTL) mapping and RNA-seq were performed to investigate the growth traits of C. fuscus. By combining these two approaches, 27 growth-related candidate genes were identified within 17 QTL intervals, which play important roles in the growth activities of fish. The identification of these QTL regions and candidate genes not only fills the gap in research on growth-related genes in C. fuscus, but also provides valuable data to further elucidate the genetic mechanisms underlying growth traits in this species.
Abstract
Growth traits are critical economic characteristics in aquaculture. This study aimed to identify the candidate genes associated with the growth of C. fuscus by integrating QTL mapping for growth traits and the RNA-seq analysis of differentially expressed genes (DEGs) between two extreme body size groups (big-sized group and small-sized group). QTL mapping was performed on eight growth traits—body weight, body height, body length, body width, orbital diameter, caudal peduncle length, caudal peduncle height, and pre-dorsal length—using 200 individuals from a full-sibling line. Seventeen growth-related QTL were identified across eight linkage groups, explaining phenotypic variance ranging from 8.00% to 11.90%. A total of 162 functional genes were annotated within these QTL intervals. RNA-seq analysis identified 3824 DEGs between the big-sized and small-sized groups, with 2252 genes upregulated and 1572 downregulated in the big group. By integrating QTL mapping and RNA-seq data, 27 candidate genes were identified, including myostatin (mstnb), epidermal growth factor receptor (egfr), and sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (serca1). These findings provide crucial insights into the genetic regulation of growth in C. fuscus and lay a foundation for future genetic selection strategies.
Keywords:
Clarias fuscus; growth traits; transcriptome; QTL mapping; candidate gene
