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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)

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

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

滇池金线鲃染色体水平基因组构建及生长相关QTLs识别

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)

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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  • 摘要: 滇池金线鲃为云南传统“四大名鱼”之首,是一种具有较高经济价值的珍稀濒危鱼类。该物种于2007年人工繁殖成功,后经历4代群体选育,于2018年获得生长速度快,肌间刺弱化的滇池金线鲃“鲃优一号”国家水产新品种。对该物种的进一步利用虽然仍面临诸多问题,但利用分子标记辅助育种技术(MAS)继续提高品种的生长速度、抗病能力和野外适应性等,是未来产业化利用的重要攻关方向。鉴于此,本研究构建了滇池金线鲃染色体水平的基因组,其大小约1.49Gb,包含48条染色体。基于该组装基因组,通过分别对一个全同胞家系和一个随机群体进行极端大小样本的QTL-seq分析,我们筛选到两个生长相关的主要QTLs (Chr3, 14.9–39.1Mb; Chr17, 4.1–27.4Mb);同时,也筛选到一些生长相关候选基因,如map2k5, stat1, phf21a, sox6, smad6等,这些基因主要调控细胞分化、神经元发育、骨骼肌发育、软骨形成和免疫应答等。本研究结果为未来滇池金线鲃生长性状的分子辅助育种等相关研究奠定了坚实的基础。
    #Authors contributed equally to this work
  • Figure  1.  Chromosome-level genome and growth-related QTLs of S. grahami

    A: Living specimen of S. grahami. B: Chromosome-level genome assembly showing length of each chromosome (I), density of SNP distribution in each 100 kb genomic interval (II), density of gene distribution in each 100 kb genomic interval (III), GC content in each 100 kb genomic interval (IV), and schematic of major inter-chromosomal relationships (V). C: General 2:1 syntenic relationship between S. grahami and D. rerio. D, E: Major significant QTL intervals identified by QTL-seq in sibling and random populations, respectively. X-axis represents different chromosomes (labeled with different colors); y-axis indicates Fst values between two compared bulks. Each point represents Fst value within a sliding window, with a=0.001 used as the threshold (calculated as Fst=0.085 and 0.098 in sibling and random populations, respectively). F, G: Distribution of SNPs with high BFR (BFR≥4) in chromosome-level genome in sibling and random populations, respectively. X-axis represents different chromosomes; y-axis indicates number of SNPs identified in each chromosome. H, I: Overlapping QTL intervals between the two populations in Chr3 and Chr17, respectively. X-axis indicates localization in each chromosome; y-axis represents Fst values between two groups. Double-sided arrow indicates the most overlapped QTL interval.

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出版历程
  • 收稿日期:  2020-11-03
  • 录用日期:  2021-03-23
  • 网络出版日期:  2021-03-24
  • 刊出日期:  2021-05-18

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