# Uniqueness of Heilongjiang Mandarin Fish (Siniperca chuatsi): Identifying Growth-Related Functional Loci Through Whole-Genome Analysis Across Four Geographic Populations

## TL;DR

This study identifies unique genetic markers in Mandarin fish from different regions that are linked to growth, with six beneficial markers found only in the Heilongjiang population.

## Contribution

The study is the first to identify population-specific growth-related genetic loci in Siniperca chuatsi using whole-genome analysis.

## Key findings

- Four geographic populations of Siniperca chuatsi were found to be genetically distinct.
- 26 significant SNPs associated with growth were identified, linked to 158 potential functional genes.
- The Heilongjiang population uniquely possessed six beneficial genotypes linked to superior growth.

## Abstract

This study aimed to analyze growth differences and genetic characteristics in Mandarin fish (Siniperca chuatsi) from different regions. We performed genome sequencing on 90 fish from four geographic populations. For the first time, we identified unique genetic markers linked to growth that were specific to these populations. Our analysis confirmed that the four populations are genetically distinct. We initially discovered 26 key genetic variations significantly associated with growth, potentially influencing it through metabolic pathways and other biological processes. Further analysis pinpointed 13 significant genetic markers and identified their beneficial types associated with superior growth. Notably, the Heilongjiang population uniquely possessed six of these beneficial genetic types, which may represent population-restricted candidate markers relevant to growth-related breeding potential. These findings provide new candidate molecular markers and supporting data that may inform future breeding strategies and require further validation under controlled conditions.

To analyze growth trait differences and genetic characteristics of Siniperca chuatsi from distinct geographic populations, whole-genome resequencing was performed on 90 samples from Heilongjiang (HLJ), Hubei (HB), Hunan (HN), and Anhui (AH), and for the first time, population-unique growth-related loci were detected. Population structure analysis indicated that the four populations were genetically distinct (K = 4). A preliminary Genome-Wide Association Study (GWAS) revealed 26 significant growth-related SNPs linked to 158 potential functional genes, which were primarily enriched in Metabolic pathways, the NOD-like receptor signaling pathway, and Necroptosis, suggesting their possible roles in growth regulation. Non-tag SNP capture within functional genes yielded 24 known significant loci and 118 potentially linked loci. On this basis, one-way ANOVA ultimately identified 13 SNPs significantly associated with growth, and their advantageous genotypes were characterized. Notably, this study revealed, for the first time, that the HLJ population possesses six population-unique genotypes significantly linked to superior growth traits, which may represent population-restricted candidate markers associated with growth-related variation. The results of this study provide new candidate molecular markers and supporting data that may inform future breeding strategies pending further validation.