**1. Introduction**

Single nucleotide polymorphisms (SNPs) are DNA sequence polymorphisms caused by the transformation or transposition of a single nucleotide at the genomic level [1]. SNP markers are a tool for studying the genetic structure of species [2]. Since any base of genomic DNA can be mutated, SNP molecular markers are ubiquitous in animals and plants [3]. SNPs have the advantages of a large number, a wide distribution, strong representativeness [4], good genetic stability, and convenience for high-throughput and highly automated detection and analysis [5]. The distribution of SNPs in the genome can comprehensively reflect a population's genetic variation [4].

*L. kasmira* is a typical reef-dwelling fish found throughout the Indo-Pacific region, from Australia in the east to Japan in the north [6]. Individuals of this species are mainly distributed around the South China Sea islands, Taiwan waters, and in the southern portion of the East China Sea [7]. *L. kasmira* has a bright yellow surface and a reddish underside; the side of the body bears four blue longitudinal bands, with an indistinct black spot between

**Citation:** Zhao, F.; Guo, L.; Zhang, N.; Yang, J.; Zhu, K.; Guo, H.; Liu, B.; Liu, B.; Zhang, D.; Jiang, S. Genetic Diversity Analysis of Different Populations of *Lutjanus kasmira* Based on SNP Markers. *J. Mar. Sci. Eng.* **2022**, *10*, 1547. https://doi.org/ 10.3390/jmse10101547

Academic Editor: Nguyen Hong Nguyen

Received: 26 September 2022 Accepted: 14 October 2022 Published: 20 October 2022

**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

the third and fourth blue bands [8]. In recent years, the habitat of this species, i.e., coral reefs and mangroves, has been reduced and degraded due to anthropogenic destruction and environmental pollution [9]. Moreover, *L. kasmira* suffers from overfishing due to its delicious meat, high economic value, and spawning clusters [7]. At present, studies on *L. kasmira* mainly focus on its physiological ecology and molecular systematics [7–9]; there are no reports on the development of SNP markers and the genetic diversity level of *L. kasmira*. In this study, the whole-genome SNPs of *L. kasmira* were first discovered by restriction site-associated DNA sequencing (RAD-seq) technology [10] and then used to analyze the genetic diversity and structure of this fish species, providing a theoretical basis for the rational development and conservation of its germplasm resources.
