Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in <i>Sinocyclocheilus grahami</i> (Cypriniformes, Cyprinidae)

Yan-Hui Yin; Xin-Hui Zhang; Xiao-Ai Wang; Rui-Han Li; Yuan-Wei Zhang; Xin-Xin Shan; Xin-Xin You; Xin-Di Huang; An-Li Wu; Mo Wang; Xiao-Fu Pan; Chao Bian; Wan-Sheng Jiang; Qiong Shi; Jun-Xing Yang

doi:10.24272/j.issn.2095-8137.2020.321

Volume 42 Issue 3

May 2021

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Article Navigation > Zoological Research > 2021 > 42(3): 262-266

Yan-Hui Yin, Xin-Hui Zhang, Xiao-Ai Wang, Rui-Han Li, Yuan-Wei Zhang, Xin-Xin Shan, Xin-Xin You, Xin-Di Huang, An-Li Wu, Mo Wang, Xiao-Fu Pan, Chao Bian, Wan-Sheng Jiang, Qiong Shi, Jun-Xing Yang. Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae). Zoological Research, 2021, 42(3): 262-266. doi: 10.24272/j.issn.2095-8137.2020.321

Citation:

Yan-Hui Yin, Xin-Hui Zhang, Xiao-Ai Wang, Rui-Han Li, Yuan-Wei Zhang, Xin-Xin Shan, Xin-Xin You, Xin-Di Huang, An-Li Wu, Mo Wang, Xiao-Fu Pan, Chao Bian, Wan-Sheng Jiang, Qiong Shi, Jun-Xing Yang. Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae). Zoological Research, 2021, 42(3): 262-266. doi: 10.24272/j.issn.2095-8137.2020.321

Citation:

Yan-Hui Yin, Xin-Hui Zhang, Xiao-Ai Wang, Rui-Han Li, Yuan-Wei Zhang, Xin-Xin Shan, Xin-Xin You, Xin-Di Huang, An-Li Wu, Mo Wang, Xiao-Fu Pan, Chao Bian, Wan-Sheng Jiang, Qiong Shi, Jun-Xing Yang. Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae). Zoological Research, 2021, 42(3): 262-266. doi: 10.24272/j.issn.2095-8137.2020.321

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Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae)

doi: 10.24272/j.issn.2095-8137.2020.321

Yan-Hui Yin^{1, 2, 3, 4, #},
Xin-Hui Zhang^{5, 6, #},
Xiao-Ai Wang^{1, 2, 3, #},
Rui-Han Li^{5, 6, #},
Yuan-Wei Zhang^{1, 2, 3},
Xin-Xin Shan^{5, 6},
Xin-Xin You^{5, 6},
Xin-Di Huang^{1, 2, 3, 4},
An-Li Wu^{1, 2, 3},
Mo Wang⁷,
Xiao-Fu Pan^{1, 2, 3},
Chao Bian^{5, 6},
Wan-Sheng Jiang^{8
,
,},
Qiong Shi^{5, 6
,
,},
Jun-Xing Yang^{1, 2, 3
,
,}

1.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
2.
Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
3.
Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
4.
University of Chinese Academy of Sciences, Beijing 100049, China
5.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China
6.
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
7.
Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan 650224, China
8.
Hunan Engineering Laboratory for Chinese Giant Salamander’s Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest and Chemical Industry Engineering, Jishou University, Zhangjiajie, Hunan 427000, China

#Authors contributed equally to this work

Funds: This study was supported by the National Natural Science Foundation of China (31672282, U1702233, U1902202), Program of the Chinese Academy of Sciences (XDA24030505, XDA23080500, KFJ-STS-QYZD-101), and Program of Yunnan Provincial Science and Technology Department (202003AD150017, 2018FY001-007)

More Information

Corresponding author: E-mail: jiangwschina@163.com; shiqiong@genomics.cn; yangjx@mail.kiz.ac.cn
Received Date: 2020-11-03
Accepted Date: 2021-03-23

Published Online: 2021-03-24

Publish Date: 2021-05-18

Abstract

Abstract

The Dianchi golden-line barbel, Sinocyclocheilus grahami (Regan, 1904), is one of the “Four Famous Fishes” of Yunnan Province, China. Given its economic value, this species has been artificially bred successfully since 2007, with a nationally selected breed (“S. grahami, Bayou No. 1”) certified in 2018. For the future utilization of this species, its growth rate, disease resistance, and wild adaptability need to be improved, which could be achieved with the help of molecular marker-assisted selection (MAS). In the current study, we constructed the first chromosome-level genome of S. grahami, assembled 48 pseudo-chromosomes, and obtained a genome assembly of 1.49 Gb. We also performed QTL-seq analysis of S. grahami using the highest and lowest bulks (i.e., largest and smallest size) in both a sibling and random population. We screened two quantitative trait loci (QTLs) (Chr3, 14.9–39.1 Mb and Chr17, 4.1–27.4 Mb) as the major growth-related locations. Several candidate genes (e.g., map2k5, stat1, phf21a, sox6, and smad6) were also identified, with functions related to growth, such as cell differentiation, neuronal development, skeletal muscle development, chondrogenesis, and immunity. These results built a solid foundation for in-depth MAS studies on the growth traits of S. grahami.
- Genetic linkage map,
- Genomic synteny analysis,
- Candidate gene,
- SNP

#Authors contributed equally to this work

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References(34)

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