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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. 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. doi: 10.24272/j.issn.2095-8137.2020.321

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
#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)
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  • 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.
  • #Authors contributed equally to this work
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