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.
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。.
Keywords: Candidate gene; Genetic linkage map; Genomic synteny analysis; SNP.