Introduction
Luciobarbus brachycephalus, commonly known as the Aral barbel, is a fish species of significant commercial value in China, playing a crucial role in regional aquaculture economies. The use of high-density genetic linkage mapping combined with quantitative trait locus (QTL) analysis has become an effective method for understanding the genetic mechanisms behind complex traits in aquatic species.
Methodology
This study aimed to construct a high-density linkage map based on single nucleotide polymorphisms (SNPs) using whole-genome resequencing. The research involved male and female parent fish and 165 F1 full-sib progenies. The goal was to perform comprehensive QTL mapping of six economically important growth-related traits to identify candidate genes involved in growth regulation in L. brachycephalus.
Results
Pearson correlation analysis revealed strong associations among all six growth-related traits (r > 0.8, P < 0.001), suggesting pleiotropic regulation through shared genetic factors. The high-density linkage map for L. brachycephalus included 164,435 high-quality SNPs across 50 linkage groups, covering the entire genome with a total length of 6,425.95 cM. The marker density was exceptional, with an average inter-marker distance of 0.10 cM, making it the most precise genetic map for this species to date. This precision facilitates accurate candidate gene localization and improved marker-assisted selection. Through QTL mapping analysis, several genomic regions significantly associated with growth-related traits were identified. Notably, a major QTL for body height was located on linkage group LG27, while two distinct QTLs for body weight were found on LG20 and LG26. Four longitudinal growth traits (total length, body length, fork length, and preanal body length) co-localized within the same significant QTL interval on LG27. These QTL intervals explained 6.27-39.36% of the phenotypic variance for the respective traits. Additionally, putative candidate genes potentially regulating each target trait were identified through comprehensive analysis of these significant QTL intervals.
Discussion
This integrated approach lays the groundwork for marker-assisted selection and enhances the understanding of growth-related genetic mechanisms in this important species. The Aral barbel, native to the Aral Basin and other regions, was introduced to China in 2003 and has since become a significant aquaculture resource due to its rapid growth rate and adaptability. However, the species faces a bottleneck in genetic diversity due to intensive inbreeding within small breeding populations. To support sustainable development, there is an urgent need to develop improved varieties with enhanced growth performance and disease resistance through systematic breeding programs.
Growth traits are critical economic characteristics in aquaculture, and genetic improvement programs have focused on these traits. Traditional breeding methods, such as mass selection and hybridization, are labor-intensive and have long breeding cycles. In contrast, marker-assisted selection (MAS) offers a more precise and efficient alternative for genetic improvement. MAS can significantly accelerate breeding progress by enabling early-life selection with greater accuracy when validated molecular markers linked to target traits are available.
The implementation of MAS in breeding programs requires prior identification of genomic regions and candidate genes associated with economically important traits. This foundational work enables precise selection of offspring carrying desirable genetic variants, thereby accelerating genetic improvement. QTL mapping has emerged as a powerful tool for elucidating the genetic architecture of complex traits in aquatic species.
Technological Advancements
Early genetic mapping studies used low-throughput molecular markers, resulting in limited marker density and reduced QTL mapping resolution. The development of next-generation sequencing (NGS) technologies has dramatically reduced genome sequencing costs and enabled comprehensive detection of genetic variants. Whole-genome resequencing (WGRS) has emerged as a particularly powerful tool for population-scale variant discovery, offering advantages such as genome-wide characterization of genetic diversity, construction of ultra-high-density linkage maps, and precise genome-wide association studies.
Current Study
Prior to this study, only one genetic linkage map existed for L. brachycephalus, developed using SLAF-seq strategy. This map comprised 4,304 unique loci across 50 linkage groups. In the present study, an F1 full-sib family of L. brachycephalus was established, and WGRS was employed to characterize genomic variations. This approach enabled the construction of a high-density SNP-based linkage map and precise genome-wide QTL analysis to identify genomic regions and candidate genes associated with growth performance.
Conclusion
The study constructed a high-density SNP-based genetic linkage map for L. brachycephalus using WGRS data. Analysis revealed strong correlations among six economically important growth-related traits, suggesting pleiotropic regulation by shared genetic factors. A total of 146 million high-quality SNPs were identified, of which 164,435 were successfully mapped. The final linkage map comprises 50 linkage groups spanning 6,425.95 cM, with an average genetic distance of 0.10 cM between markers. Genome-wide QTL analysis identified multiple significant loci associated with growth-related traits, with peak LOD scores explaining 6.27%–39.36% of the phenotypic variance. This refined map enables precise localization of growth-related candidate genes, significantly advancing marker-assisted breeding for L. brachycephalus.
🔗 **Fuente:** https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2025.1644874/full