Abstract
Common carp (Cyprinus carpio) is one of the most widely studied fish species due to its great economic value and strong environmental adaptability. Scattered scale, a typical phenotype of the mirror carp that is derived from Europe, has never been observed in the Yellow River carp previously. We recently identified approximately one fourth of the F1 progenies displaying scattered scale in a full-sib Yellow River carp family in our breeding program, despite both parents that showed wild type with normal scale patterns. This family provides us unique materials to investigate the genetic basis underlying the abnormal scale mutant in Yellow River carp population. Genome-wide association study (GWAS) and association mapping were performed based on genome-wide single nucleotide polymorphisms (SNP) genotyped with common carp 250 K SNP genotyping array in 82 samples of the Yellow River carp family. We identified a 1.4 Mb genome region that was significantly associated with abnormal scattered scale patterns. We further identified a deletion mutation in fibroblast growth factor receptor 1 a1 (fgfr1a1) gene within this genome region. Amplification and sequencing analysis of this gene revealed a 311-bp deletion in intron 10 and exon 11, which proved that fgfr1a1 could be the causal gene responsible for abnormal scattered scale in the Yellow River carp family. Since similar fragment mutation with 306-bp and 310-bp deletions had been previously reported as causal mutation of scattered scale patterns in the mirror carp, we speculate that either the deletion mutation was introduced from Europe-derived mirror carp or the deletion independently occurred in the mutation hotspot in fgfr1a1 gene. The results provided insights into the genetic basis of scale pattern mutant in Yellow River carp population, which would help us to eliminate the recessive allele of the abnormal scale patterns in Yellow River carp population by molecular marker-assisted breeding.
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Acknowledgements
We acknowledge grant support from the National Natural Science Foundation of China (No. 31422057), the National High-Technology Research and Development Program of China (863 program; 2011AA100401), the Open Project of State Key Laboratory of Large Yellow Croaker Breeding (No. LYC2017RS05), Fundamental Research Funds for the Central Universities, Xiamen University (20720160110), and the Local Science and Technology Development Project Guide by The Central Government (2017L3019).
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PX and JS conceived and supervised the study. ZZ analyzed the data and drafted the manuscript. CD, WP, SK, and BC helped on data analysis. FP helped on manuscript preparation. JF helped with carp family construction and sample collection. PX and LC revised the manuscript. All authors have read and approved the manuscript.
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This study was approved by the Animal Care and Use committee at College of Ocean and Earth Sciences, Xiamen University. All the methods used in this study were carried out in accordance with approved guidelines.
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Zhou, Z., Chen, L., Dong, C. et al. Genome-Scale Association Study of Abnormal Scale Pattern in Yellow River Carp Identified Previously Known Causative Gene in European Mirror Carp. Mar Biotechnol 20, 573–583 (2018). https://doi.org/10.1007/s10126-018-9827-3
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DOI: https://doi.org/10.1007/s10126-018-9827-3