# The Influence of Parent Pairs with Different Genetic Distances on the Genetic Diversity of Offspring in Strongylocentrotus intermedius

## TL;DR

Breeding sea urchins with genetically distant parents helps maintain offspring diversity, preventing inbreeding issues in aquaculture.

## Contribution

This study demonstrates that using distantly related or mixed parent pairs preserves higher genetic diversity in sea urchin offspring.

## Key findings

- Offspring from distantly related or mixed parents retained higher genetic diversity compared to closely related pairs.
- Closely related parent pairs led to significant genetic diversity loss in offspring.
- Mixed mating strategies are recommended to sustain genetic diversity in breeding programs.

## Abstract

Maintaining genetic diversity in farmed sea urchins is essential to prevent health and productivity declines caused by inbreeding. This study tested whether breeding parents with distinct genetic backgrounds preserves diversity in offspring. We compared three strategies: pairing distantly related, closely related, or mixed parents. Offspring from distantly related or mixed parents retained higher genetic diversity, while closely related pairs led to significant losses. Although all offspring showed reduced diversity compared to wild populations, the findings highlight that avoiding close genetic matches and diversifying parent selection can mitigate declines. This approach offers practical solutions for sustainable aquaculture, ensuring healthier populations and long-term industry resilience.

To identify effective strategies for preserving the genetic diversity of Strongylocentrotus intermedius populations, this study employed 15 SSR loci and SSR-seq technology to construct three parental mating groups based on different genetic distances: relatively distant (0.33640), relatively close (0.13051), and mixed (0.29916). These mating groups were used to produce three corresponding offspring populations: the distant group (D), the close group (C), and the mixed group (M). A total of 150 offspring from these populations were genotyped to analyze the effects of parental genetic distance on the genetic diversity of their offspring. The results showed that the observed allele number (Na) in the D and M groups was 4.200 and 4.733, respectively, both lower than the parental family population (FP) group (5.000) but higher than the C group (3.571). The effective allele number (Ne) in the D and M groups was 2.782 and 2.728, respectively, slightly below that of the parental FP group (2.816) but greater than the C group (2.211). Similarly, the observed heterozygosity (Ho) in the D and M groups was 0.496 and 0.488, respectively, both below that of the parental FP group (0.522) but above the C group (0.447). The expected heterozygosity (He) in the D and M groups was 0.586 and 0.579, respectively, slightly lower than the parental FP group (0.595) but higher than the C group (0.487). Additionally, the polymorphism information content (PIC) in the D and M groups was 0.530 and 0.531, respectively, indicating high polymorphism, although slightly lower than the parental FP group (0.546) and significantly higher than the C group (0.438). These findings indicate that the genetic diversity of all the three offspring populations declined to varying degrees compared to the parental population, with the C group experiencing the most severe reduction. In contrast, the D and M groups maintained comparably higher levels of genetic diversity, which were comparable to each other. This study underscores the importance of increasing the genetic distance between parents or adopting mixed mating strategies to sustain genetic diversity in breeding populations. These approaches are recommended for future breeding programs to ensure the long-term conservation and sustainability of genetic resources.