Accuracy of short sequence repeats on single‑parent parentage identification in Chinese shrimp Fenneropenaeus chinensis

Abstract

Based on the parentage identification results using 4 polymorphic short sequence repeats (SSRs) with both parents known, we assessed the accuracy of parentage identification for a single known parent using the same 4 SSRs and 4 other additional SSRs for 2507 Chinese shrimp Fenneropenaeus chinensis recaptured from Jiaozhou Bay in a ‘molecular marker recapture’ program. We detected a high variability in the 4 SSR loci EN0033, RS0622, FCKR002, and FCKR013. The 4 polymorphic loci produced a ≥99.99% cumulative exclusion probability for both known parents. We identified 8 parentage relationships with a logarithm (base 10) of odds (LOD) score of ≥3.0. Similar results were obtained when the 4 additional SSR loci were included. The cumulative exclusion probability decreased to 99.42% for a single known parent using the old 4 SSR loci, which enabled detection of 30 and 44 parentage relationships with a ≥3.0 LOD score for known paternity and maternity, respectively. Inclusion of the additional 4 SSR loci raised, the cumulative exclusion probability to ≥99.99%. However, the number of parentage relationships detected with an LOD score of ≥3.0 was reduced to 8 for the groups with known paternity or maternity, similar to the result obtained with both parents known. In this study, the accuracy of single-parent parentage identification using SSR loci was confirmed. Authentic parentage identification with a single known parent should incorporate both the cumulative exclusion probability and LOD score. Our research provides an alternative method for parentage identification in Chinese shrimp.