Population genetics analysis of the black rockfish Sebastes schlegelii in Northern China based on 2b-RAD simplified genome sequencing

Abstract

The black rockfish Sebastes schlegelii is an important fishery species in Japan, South Korea, and China. Overfishing has severely depleted the natural resources of S. schlegelii in recent years, leading to the initiation of programs aimed at enhancing fish stock. However, the genetic structure of northern populations remains elusive, posing challenges in collecting and preserving germplasm resources. In this study, a total of 191 S. schlegelii individuals from seven populations, including one cultured population (Changdao: CDYZ) and six wild populations (Lianyungang: LYG; Qingdao: QD; Weihai: WH; Changdao: CDYS; Beidaihe: BDH) sequenced by 2b-RAD method and their population genetics was analyzed using 27,064 SNPs obtained. The results indicated low genetic diversity in both wild and cultured populations (PIC < 0.25, Ho: 0.174-0.273, He: 0.173-0.234), with the cultured population exhibiting higher diversity than the wild ones. Moderate genetic differentiation existed between the cultured population and six wild populations (0.05 < Fst < 0.25). However, the genetic differentiation was lower among the other wild populations (Fst < 0.05). The analyses of population genetic structure indicated that the wild populations clustered together first and finally with the cultured population CDYZ, which clustered separately except for one individual. Therefore, scientific breeding programs and germplasm conservation can be important in stabilizing genetic structure. In addition, gene flow among the seven populations was high (Nm > 1). This study provides a theoretical basis for conserving and rationalizing germplasm resources for S. schlegelii.

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

“…This result was also in accordance with the results of Peng et al, who used comparative mtDNA loop analysis to study the population structure and genetic diversity of the S. schlegelii populations in the Bohai Sea (Qingdao, Jinzhou, and Dalian), where there was no significant population genetic structural differences and low population genetic differentiation (F ST = −0.0113-0.0061) within the geographical range of the S. schlegelii population [36]. In addition, the pairwise F ST values obtained were also similar to those obtained by Cao et al (wild populations: F ST < 0.05) with a similar sampling design and 2b-RAD sequencing method [37]. In addition, the pairwise F ST level of S. schlegelii populations (F ST = 0.01356, 0.01360, and 0.01678) was less than many other marine organisms, such as Clupea pallasii (F ST = 0.064-0.106) [38], Acanthopagrus latus (the highest F ST was 0.4288) [39], and Brachionichthys hirsutus (overall F ST = 0.043) [40].…”