Genetic Relationship among Three Populations of Pearl Oyster Pinctada fucata ssp. martensii in Guangxi, China
ZOU Jie1,2, PENG Huijing1,2, ZHENG Debin3, ZHANG Shoudu4
1. Guangxi Academy of Sciences, Nanning 530000, China; 2. Guangxi Institute of Oceanology Co., Ltd, Beihai 536000, China; 3. Tianjin Bohai Sea Fisheries Research Institute, Tianjin 300457, China; 4. Marine Science Research Institute of Shandong Province, Qingdao 266000, China
Abstract：In order to explore the cross population hybridization of pearl oyster Pinctada fucata ssp. martensii in Guangxi, 15 samples of 2-year-old pearl oyster were randomly selected from the wild population (F1), the breeding population (“Haixuan No. 1” F4) and the cultured population in the Beihai were used for double-enzyme digestion by Sea15 1-end EcoRⅠ (G^AATTC) and 2-end NlaⅢ (Hin1Ⅱ, CATG^), and then 500 ng of qualified DNA samples were constructed using ddRAD library construction method. The pair-end sequencing library was used in the length of 300—500 bp to analyze the genetic relationship among the three populations through single nucleotide polymorphism (SNP) markers. More than 585 000 SNPs of the 3 populations were statistically obtained, with the observed heterozygosity of 0.1975, 0.1679 and 0.1783, the expected heterozygosity of 0.2545, 0.2469 and 0.2732, average inbreeding coefficient of 0.2075, 0.3449 and 0.3465, and the polymorphism information content of 0.2032, 0.2089 and 0.2241. The inbreeding coefficient of breeding population was close to cultured population, and there was higher genetic polymorphism in wild population and cultured population than that in the breeding population. The phylogenetic tree and PCA analysis revealed that some samples of breeding population and cultured population had close genetic relationship. Fst analysis showed that the minimal genetic differentiation index was observed between breeding population and cultured population, indicating that some parents were likely to be homologous. The wild population, breeding population and cultured population had average number of runs of homozygosity (ROH) of 59.1, 49.5 and 56.6, the average length of ROH 0.312 Mb, 0.313 Mb and 0.311 Mb, and the average SNPs content 59, 50 and 73, the range of FROH 0.0149—0.0240, 0.0159—0.0201 and 0.017—0.0246, respectively, indicating that the real inbreeding phenomenon of each population was not obvious. The average linkage disequilibrium(LD) decay distances were 0.4 kb in wild population, 0.4 kb in breeding population and 0.2 kb in cultured population(r2=0.2), and the attenuation rate of cultured population>wild population>breeding population, which was related to artificial breeding. The findings indicate that wild population × breeding population or wild population ×cultured population could be used in cross breeding project, and the results may serve as an alternative way to learn about the maintenance and utilization of genetic resources of pearl oyster population in Guangxi.
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2023, Vol. 42 
