滇池金线鲃染色体水平基因组构建及生长相关QTLs识别

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

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

殷艳慧^{1, 2, 3, 4, #},
张新辉^{5, 6, #},
王晓爱^{1, 2, 3, #},
李蕊晗^{5, 6, #},
张源伟^{1, 2, 3},
单鑫鑫^{5, 6},
游欣欣^{5, 6},
黄新迪^{1, 2, 3, 4},
吴安丽^{1, 2, 3},
王茉⁷,
潘晓赋^{1, 2, 3},
卞超^{5, 6},
蒋万胜^8, ,,
石琼^{5, 6, ,},
杨君兴^{1, 2, 3, ,}

1.
中国科学院昆明动物研究所遗传资源与进化国家重点实验室，中国科学院种子创新研究院，云南昆明650224，中国
2.
云南省高原鱼类育种重点实验室，云南昆明650224，中国
3.
云南省高原湖泊健康与修复工程研究中心，云南昆明650224，中国
4.
中国科学院大学，北京100049，中国
5.
深圳市华大海洋研究院，广东省海洋经济动物分子育种重点实验室，深圳市海洋生物基因组学重点实验室，广东深圳518083，中国
6.
中国科学院大学华大基因教育中心，广东深圳518083，中国
7.
西南林业大学生物多样性保护学院，云南省高校极小种群野生动物保育重点实验室，云南昆明 650224，中国
8.
吉首大学大鲵资源保护与综合利用湖南省工程实验室&林产化工工程湖南省重点实验室，湖南张家界427000，中国

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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

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^{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

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

#Authors contributed equally to this work

摘要

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。
- 遗传连锁图谱 /
- 基因组共线性分析 /
- 候选基因 /
- SNP
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
注释:

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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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