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Golden pompano genome resource enables discovery of valuable gene determining growth traits

Honglin Luo, Yongde Zhang, Changmian Ji, Yongzhen Zhao, Jinxia Peng, Yuhui Xu, Xiuli Chen, Yin Huang, Qingyun Liu, Pingping He, Pengfei Feng, Chunling Yang, Pinyuan Wei, Haiyan Yu, Hongkun Zheng, Yong Lin, Xiaohan Chen
doi: https://doi.org/10.1101/2021.05.20.445047
Honglin Luo
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Yongde Zhang
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Changmian Ji
2Biomarker Technologies, Beijing, 101300, China
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Yongzhen Zhao
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Jinxia Peng
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Yuhui Xu
2Biomarker Technologies, Beijing, 101300, China
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Xiuli Chen
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Yin Huang
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Qingyun Liu
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Pingping He
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Pengfei Feng
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Chunling Yang
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Pinyuan Wei
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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Haiyan Yu
2Biomarker Technologies, Beijing, 101300, China
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Hongkun Zheng
2Biomarker Technologies, Beijing, 101300, China
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  • For correspondence: chnxhn@163.com linnn2005@126.com zhenghk@biomarker.com.cn
Yong Lin
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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  • For correspondence: chnxhn@163.com linnn2005@126.com zhenghk@biomarker.com.cn
Xiaohan Chen
1Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
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  • For correspondence: chnxhn@163.com linnn2005@126.com zhenghk@biomarker.com.cn
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Abstract

One important goal of fish genetic breeding is to identify valuable loci and genes that can facilitate growth and thereby productivity. Few such loci or genes have been identified in golden pompano (Trachinotus ovatus), a species of significant economic value. In this study, we produced a high-quality chromosome-level genome assembly of the golden pompano by de novo sequencing and assemblies for 2 parents and 200 F1 offspring by genome re-sequencing. We exploited these assemblies to identify loci and genes by QTL mapping, Kompetitive Allele Specific PCR (KASP) genotyping, and haplotype-based regional association analysis based on growth records of a 64 biparental and 147 individuals from a naturally occurring population. At a locus 291kb from BSNP21031, we identified a somatostatin receptor type 1-like (designated as gpsstr1) gene in which the BSNP1369 of the promoter region was highly associated with growth. Loss of sstr1a, the homolog of gpsstr1 in zebrafish, caused growth retardation. Sstr1a mediated growth via sstr2 and Wnt-gsk-3β signaling pathways. Our findings provide new insights into the underlying mechanisms controlling growth. Our strategy can serve as an effective way to uncover novel genomic information and facilitate improvement of fish growth.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 22, 2021.
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Golden pompano genome resource enables discovery of valuable gene determining growth traits
Honglin Luo, Yongde Zhang, Changmian Ji, Yongzhen Zhao, Jinxia Peng, Yuhui Xu, Xiuli Chen, Yin Huang, Qingyun Liu, Pingping He, Pengfei Feng, Chunling Yang, Pinyuan Wei, Haiyan Yu, Hongkun Zheng, Yong Lin, Xiaohan Chen
bioRxiv 2021.05.20.445047; doi: https://doi.org/10.1101/2021.05.20.445047
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Golden pompano genome resource enables discovery of valuable gene determining growth traits
Honglin Luo, Yongde Zhang, Changmian Ji, Yongzhen Zhao, Jinxia Peng, Yuhui Xu, Xiuli Chen, Yin Huang, Qingyun Liu, Pingping He, Pengfei Feng, Chunling Yang, Pinyuan Wei, Haiyan Yu, Hongkun Zheng, Yong Lin, Xiaohan Chen
bioRxiv 2021.05.20.445047; doi: https://doi.org/10.1101/2021.05.20.445047

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