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

Famed as a high-yield and nutrition-enriched fish, this species contains higher amount of protein, lipids, and essential amino acids than many common market fish, such as Ctenopharyngodon idellus (Valenciennes, 1844) (grass carp) and Hypophthalmichthys nobilis (Richardson, 1845) (bighead carp) (Zhao...

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Published in:Dōngwùxué yánjiū 2021-05, Vol.42 (3), p.262-266
Main Authors: Yin, Yan-Hui, Zhang, Xin-Hui, Wang, Xiao-Ai, Li, Rui-Han, Zhang, Yuan-Wei, Shan, Xin-Xin, You, Xin-Xin, Huang, Xin-Di, Wu, An-Li, Wang, Mo, Pan, Xiao-Fu, Bian, Chao, Jiang, Wan-Sheng, Shi, Qiong, Yang, Jun-Xing
Format: Article
Language:English
Subjects:
Amino acids
Association analysis
Bayous
Bones
Breeding
Carp
Chromosomes
Ctenopharyngodon idella
Deoxyribonucleic acid
DNA
DNA sequences
DNA sequencing
Endangered & extinct species
Fish
Freshwater fishes
Gene mapping
Genomes
Hypophthalmichthys nobilis
Identification
Kinases
Lipids
Nutrition
Population
Proteins
Quality control
Quantitative trait loci
Selective breeding
Single-nucleotide polymorphism
Species extinction
Transcriptomes
Wildlife conservation
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Summary:Famed as a high-yield and nutrition-enriched fish, this species contains higher amount of protein, lipids, and essential amino acids than many common market fish, such as Ctenopharyngodon idellus (Valenciennes, 1844) (grass carp) and Hypophthalmichthys nobilis (Richardson, 1845) (bighead carp) (Zhao et al., 2013). Since 2007, our team has successfully achieved the artificial breeding of S. grahami (Yang et al., 2007), which has not only helped in avoiding its wild extinction, but also opened a new era for its utilization. [...]after four generations of artificial selection, a new national breed ("S. grahami, Bayou No. 1") with accelerated growth and weakened inter-muscular bones was certified in 2018. Commonly used methods for identifying QTLs and candidate genes in fish species studies include genome-wide association analysis (GWAS), QTL analysis, restriction site-associated DNA sequencing (RADseq), and transcriptome sequencing (RNA-seq) (Li et al., 2018; Liu et al., 2017; Salem et al., 2012; Yu et al., 2016). According to the SNP identification procedure in QTL-seq analysis, a total of 282 476 and 281 611 sliding windows were detected in the sibling and random populations, respectively, with more than 15 SNPs in each window.
ISSN:0254-5853
DOI:10.24272/j.issn.2095-8137.2020.321