# Genome-Wide Development and Validation of KASP-Based SNP Markers in Neophocaena asiaeorientalis asiaeorientalis

## TL;DR

This study develops and validates 19 SNP markers for the Yangtze finless porpoise to help conserve this critically endangered species by analyzing genetic diversity.

## Contribution

The study introduces 19 highly polymorphic SNP markers for population genetics and conservation of the Yangtze finless porpoise.

## Key findings

- 19 highly polymorphic SNP markers were successfully developed and validated using KASP technology.
- The Poyang Lake population showed higher genetic diversity when analyzed with these markers.
- The markers are effective for detecting genetic variation and can support conservation management.

## Abstract

The critically endangered Yangtze finless porpoise urgently requires effective conservation strategies, for which understanding its genetic diversity is essential. This study developed a suite of reliable molecular markers to support such efforts. By integrating chromosome-level genome data with whole-genome resequencing, candidate genetic variants were identified and subsequently validated using high-throughput Kompetitive Allele-Specific PCR (KASP) technology. A total of 19 highly polymorphic single nucleotide polymorphism (SNP) markers were successfully established. Population analysis employing these markers revealed higher genetic diversity in the Poyang Lake population, demonstrating their potential efficiency in detecting genetic variation. These newly developed SNP markers provide a practical and robust tool for future population genetics research and informed conservation management of the Yangtze finless porpoise.

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is the only extant freshwater cetacean species inhabiting the Yangtze River in China. Facing significant threats from habitat degradation and human activities, this critically endangered species requires urgent conservation efforts. A thorough understanding of its genetic diversity is fundamental for informing effective conservation strategies. To address the need for stable and reliable molecular markers, this study aimed to develop and validate a set of highly polymorphic single nucleotide polymorphism (SNP) markers. Candidate SNPs were initially identified based on chromosome-level genome and whole-genome resequencing data, yielding a total of 1070 candidate loci. Following the principle of even distribution across chromosomes, 50 SNPs were randomly selected for Sanger sequencing validation, from which 35 polymorphic SNPs were preliminarily confirmed. These 35 SNPs were subsequently genotyped using the Kompetitive allele-specific PCR (KASP) assay, which successfully validated 19 highly polymorphic markers. Genetic diversity analysis using these SNPs successfully captured moderate-to-high polymorphism in the Poyang Lake population, demonstrating the capability of these markers in detecting genetic variation. The SNP markers developed in this study show promising applicability for genetic diversity assessment in the Yangtze finless porpoise. Further validation across broader geographic and demographic samples will be essential to confirm their potential efficiency for detecting spatial heterogeneity and informing region-wide management strategies.