International Journal of Marine Science, 2025, Vol.15, No.4, 186-198 http://www.aquapublisher.com/index.php/ijms 189 inheritance and high variability rate. One of the earliest related work was the analysis of the sequence of the Japanese mackerel mtDNA control region. The study found that the Japanese mackerel population in the Yellow Sea and East China Sea in China share a majority haplotype, with low nucleotide diversity and no significant geographical differentiation (Widayanti et al., 2024). Nuclear DNA microsatellite (SSR) markers are also used in early population research of mackerels due to their high polymorphism. Radhakrishnan et al. (2018) developed 12 microsatellite sites and analyzed narrowband mackerel samples from five locations in the northern Indian Ocean (Arabic Sea and Bay of Bengal). The results showed that the alleles of each population were very similar, with the overall F_ST value only 0.0023~0.027, and AMOVA showed that most of the variations came from within the population. Bayesian clustering analysis failed to distinguish the geographical origin of the samples, supporting the conclusion that narrow-band mackerels in this area belonged to a single group. This is consistent with mtDNA research, indicating that the genetic connectivity of narrowband mackerel populations is very high along the coast of India. Experts used microsatellites to detect the differences between broadband mackerels in the northern and central South China Sea, and found that there were statistical differences in the frequency of alleles in the two groups, and speculated that it may have a certain degree of isolation due to coastal water mass barriers (Zeng et al., 2012). 3.2 Advances in the application of nuclear genome and SNP markers With the advancement of molecular biology technology, researchers have begun to use single nucleotide polymorphism (SNP) markers in the nuclear genome to analyze the mackerel population structure. Nuclear DNA can reflect bi-line information of parents and has more advantages in exploring recent population dynamics. Shui et al. (2009) used AFLP (amplified fragment length polymorphism) for the first time to analyze the Yellow Sea and East China Sea Japanese mackerel. The results showed that the genetic differentiation index between the populations in the two sea areas was about 0.04, reaching a significant level. This is very different from the mitochondrial results, suggesting that the nuclear gene may have detected weak structures not reflected by the maternal marker (Li et al., 2024). Although AFLP is not as accurate as SNP, this study provides clues for the existence of hidden differentiation of mackerels. In the past decade, high-throughput sequencing has allowed people to develop thousands of SNP markers for population genetic analysis. Many recent achievements have taken advantage of this advantage (Siccha-Ramirez et al., 2018). 3.3 New perspectives brought by multigenomic technology (such as RAD-seq, WGS, ddRAD, etc.) In recent years, high-throughput sequencing technology has developed rapidly, with a variety of simplified genome sequencing methods such as whole genome resequencing, RAD-seq (restriction enzyme fragment association sequencing), ddRAD, DArTseq, etc., which can obtain massive genetic markers at one time. These multigenomic technologies have revolutionized the genetics of marine fish populations. Compared with traditional research that relies on several gene fragments or dozens of microsatellite sites, the new technology can generate thousands of SNP markers, greatly improving statistical power, and is particularly suitable for detecting subtle population differentiation and gene flow patterns. For fish with high mobility such as mackerel, previous studies have often made it difficult to distinguish the population structure due to the low genetic differences, and the application of multigenomic data overcomes this problem. Widayanti et al. (2024) used environmental DNA technology combined with high-throughput sequencing to evaluate fish diversity in Taiwan Straits, and also detected the frequency difference in the occurrence of Japanese mackerels in different seasons, suggesting that population dynamics are related to seasonal changes in ocean currents (Widayanti et al., 2024). Although this study is not aimed at the genome of mackerel, it demonstrates new technologies that can provide information on group changes in mackerels on the ecological time scale. In terms of whole genome sequencing, Li et al. (2024) have constructed a high-quality chromosomal-level reference genome of broadband mackerel. This provides a basis for future group comparisons of mackerels in the whole genome-wide range. With the reference genome, gene variants associated with population differentiation and local adaptation can be more accurately located, identifying potential adaptive genetic markers (Siccha-Ramirez et al., 2018).
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