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Comparison of microsatellites and SNPs for pedigree analysis in the Pacific oyster Crassostrea gigas

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Abstract

Knowledge of the pedigree relationships between individuals is a prerequisite ‬in genetics research, and the application of molecular markers for pedigree analysis has been a booming science for over a decade. Owing to the high variability, microsatellites are considered as the marker of choice for studies on pedigree analysis. Nevertheless, single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose in recent years due to the low mutation rate and genotyping error rate. To compare the utility of microsatellites and SNPs in assigning parentage in the Pacific oyster (Crassostrea gigas), we genotyped 384 parental and offspring individuals using 12 multiplexed microsatellites and 50 SNPs. In this study, all microsatellite loci showed high informative (PIC >0.5), while most SNPs were middle informative (0.25 <PIC <0.5). CERVUS simulations revealed that using nine microsatellites or 38 SNPs, the power of parental assignment could reach 100%. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously assigned to a pair of parents when nine microsatellites or 50 SNPs were used. For microsatellites, the combined exclusion power with one parent known (EXCL2) could reach one when three microsatellites multiplex PCRs or more were used, whereas EXCL2 was 0.9999 for the 50 SNPs. In general, six SNPs were needed to obtain an equivalent exclusion power for pedigree analysis with a microsatellite locus in C. gigas. The information obtained in this study will be useful for assigning parentage in C. gigas using both marker systems.

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Acknowledgements

This study was supported by the grants from the National Natural Science Foundation of China (31372524), Shandong Seed Project, Shandong Province (2014GHY115002, 2016ZDJS06A06), and Qingdao National Laboratory for Marine Science and Technology (2015ASKJ02).

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Authors and Affiliations

  1. Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, China

    Ting Liu, Qi Li, Lingfeng Kong & Hong Yu

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China

    Qi Li

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  1. Ting Liu
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Correspondence to Qi Li.

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Liu, T., Li, Q., Kong, L. et al. Comparison of microsatellites and SNPs for pedigree analysis in the Pacific oyster Crassostrea gigas . Aquacult Int 25, 1507–1519 (2017). https://doi.org/10.1007/s10499-017-0127-0

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  • DOI: https://doi.org/10.1007/s10499-017-0127-0

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