Coilia nasus, a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China, possesses considerable aquacultural and economic potential. However, the species faces challenges due to significant variation in the gonadal development rate among females, resulting in inconsistent ovarian maturation times at the population level, an extended reproductive period, and limitations on fish growth rate due to ovarian prematurity. In the present study, we combined genome-wide association study (GWAS) and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms (SNPs) and candidate genes associated with population-asynchronous ovarian development in C. nasus. Genotyping of the female population based on whole-genome resequencing yielded 2 120 695 high-quality SNPs, 39 of which were suggestively associated with ovarian development. Of note, a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified, with cpne5a determined as the causal gene of the peak. Therefore, single-marker and haplotype association analyses were performed on cpne5a, revealing four genetic markers ( P<0.05) and seven haplotypes (r 2>0.9) significantly associated with the phenotype. Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary, respectively, between individuals of different body sizes. Integrating the GWAS and transcriptome analysis results, this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion, extracellular matrix, angiogenesis, and gap junctions involved in population-asynchronous ovarian development. The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C. nasus strains exhibiting population-synchronous ovarian development in the future.
刀鲚（ Coilia nasus）是自然栖息于长江中下游和中国近海的洄游鱼类，具有较高养殖潜力和经济价值。然而，雌性个体间性腺发育速度的显著差异导致群体卵巢成熟时间不一致，从而延长了群体繁殖周期。另外，刀鲚卵巢早熟也可能限制该物种的的早期生长。该研究结合全基因组关联分析（GWAS）和比较转录组分析（RNA-seq），挖掘与刀鲚群体卵巢异步发育相关的潜在SNP和候选基因。通过全基因组重测序对刀鲚雌性群体进行基因分型，获得了2 120 695个高质量SNP，其中39个SNP与卵巢发育具有暗示相关性。在LG21上发现了一个包含30个暗示性相关SNP的显著信号峰， cpne5a被确定为该峰的主效基因，基于 cpne5a进行了单标记关联分析和单倍型关联分析，得到了与表型显著相关的4个遗传标记（ P<0.05）和7个单倍型（r 2>0.9）。通过对卵巢早熟（PM）和卵巢正常成熟（NM）个体的转录组分析，分别在刀鲚的大脑和卵巢组织中筛选出29和426个在大小群体之间重叠的差异表达基因（DEGs）。综合GWAS和转录组分析结果，我们确定了HPG轴激素分泌、细胞外基质、血管生成和间隙连接相关的基因和生物途径参与了刀鲚群体卵巢异步发育。本研究结果为深入了解鱼类卵巢发育的分子机制提供了理论基础，并为后续刀鲚卵巢同步发育品系的遗传育种提供参考。.
Keywords: Coilia nasus; GWAS; Ovarian development; SNP; Transcriptome.