Parentage identification and population genetic analysis of Lateolabrax maculatus families based on 40K SNP liquid-phase array

【Objective】 To evaluate the feasibility of parentage identification in spotted seabass （Lateolabrax maculatus） using a gene array in terms of accuracy and success rate， and to establish a precise molecular traceability system， which could provide theoretical basis for germplasm resource conservation， inbreeding control， and the development of a molecular breeding system for Lateolabrax maculatus.【Method】 Eighty-three Lateolabrax maculatus individuals from five families （F1， F5， F6， F7， and F8） cultured in the same pond were collected. Parentage identification and population genetic analysis were performed using a self-developed 40K liquid-phase SNP array for Lateolabrax maculatus to systema-tically evaluating the genetic characteristics of different Lateolabrax maculatus families and the applicability of gene array technology in parentage identification.【Result】 The observed heterozygosity （Ho） of 5 Lateolabrax maculatus families ranged from 0.2423 to 0.3725， with average of 0.3273； expected heterozygosity （He） from ranged 0.2476 to 0.3238， with average of 0.2913； and PIC ranged from 0.2045 to 0.2575， with average of 0.2349， indicating generally low polymorphism for the families except F7. Genetic differentiation was high between F6 and F1 and between F6 and F7 genetic differentiation coefficient （F_st） > 0.15， genetic differentiation was low between F7 and F8 （F_st < 0.05）， and genetic differentiation was moderate between other family pairs （0.05 < F_st < 0.15）. Population genetic structure analysis based on raw pedigree data revealed that the five families of Lateolabrax maculatus could be divided into six genetic clusters， with F6 showing higher admixture and greater genetic diversity within the group. Under known-parent conditions， the cumulative identification rate of the five families of Lateolabrax maculatus for both parents reached 88.00%， with an actual identification rate of 65.33%； the cumulative single-parent identification rate was 88.00%， with an actual rate of 66.67%. The Mendelian error rate ranged from 0.44% to 0.73% （< 0.90%）. The population genetic analysis based on pedigree correction showed that the five families of Lateolabrax maculatus were ultimately clustered into six genetic groups， consistent with the results obtained from the analysis based on raw pedigree data. Kinship analysis indicated that individuals within the same family were more closely related， whereas those from different families exhibited relatively distant relationships.【Conclusion】 Using a 40K SNP liquid-phase array， parentage identification and population genetic analysis have been conducted. The results reveal moderate to low levels of genetic polymorphism for the five Lateolabrax maculatus families reared in a common pond， significant genetic differentiation and relatively distant kinship among families， and the the five families are ultimately divided into six genetic clusters. These findings demonstrate that gene array technology is a reliable approach for evaluating population genetic structure and kinship among Lateolabrax maculatus families， which can accurately elucidate their genetic relationships and pedigree structure， and provide technical support for Lateolabrax maculatus germplasm resource management and family purity control.