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QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.)

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Abstract

Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site–associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)–controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.

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Abbreviations

ASIP:

agouti signaling protein precursor

ddRAD-seq:

double-digest restriction site–associated DNA sequencing

DO:

dissolved oxygen

dph:

days post-hatch

GLM:

general linear model

GWAS:

genome-wide association studies

MAS:

marker-assisted selection

MLM:

mixed linear model

QQ:

quantile-quantile

QTL:

quantitative trait locus

SLC45A1:

solute carrier family 45 member 1

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Acknowledgements

We thank the two anonymous reviewers for their comments on the manuscript.

Funding

This work was supported by the Science and Technology Program of Guangzhou, China (No. 201803020043); the National Natural Science Foundation of China (No. 31572612); and the Science and Technology Planning Project of Guangdong Province, China (No. 2017A030303008).

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Authors and Affiliations

  1. State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People’s Republic of China

    Bi Jun Li, Zong Xian Zhu, Xiao Hui Gu, Hao Ran Lin & Jun Hong Xia

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  1. Bi Jun Li
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  2. Zong Xian Zhu
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  3. Xiao Hui Gu
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  4. Hao Ran Lin
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Contributions

JHX and HRL contributed to the project conception. The experiment and data analysis were conducted by BJL, JHX, ZXZ, and XHG. The manuscript was prepared by JHX and BJL. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jun Hong Xia.

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Ethics Statement

All experiments in this study were approved by the Animal Care and Use Committee of the School of Life Science at the Sun Yat-sen University and were performed according to the regulations and guidelines established by this committee.

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Supplementary Table 1

The primer information of 9 microsatellite markers on chrLG5 and chrLG15. (DOCX 14 kb)

Supplementary Table 2

The primer information of RT-qPCR in this study. (DOCX 13 kb)

Supplementary Table 3

The body color scores for the 192 tilapia in this study. (XLSX 20 kb)

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Li, B.J., Zhu, Z.X., Gu, X.H. et al. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.). Mar Biotechnol 21, 384–395 (2019). https://doi.org/10.1007/s10126-019-09888-9

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