Considerations for Maintaining Family Diversity in Commercially Mass-Spawned Penaeid Shrimp: A Case Study on Penaeus monodon

Abstract

Skewed family distributions are common in aquaculture species that are highly fecund, communally (mass) spawned, and/or communally reared. The magnitude of skews pose challenges for maintaining family-specific genetic diversity, as increased resources are required to detect individuals from underrepresented families, or reliably determine relative survival as a measure of family performance. There is limited understanding of family skews or changes in family proportion of communally reared shrimp under commercial rearing conditions and particularly how this may affect genotyping strategies to recover family performance data in breeding programs. In this study, three separate batches of shrimp, Penaeus monodon, were communally spawned and reared, and then sampled as larvae when ponds were stocked at 30 days of culture (DOC) and as juveniles from commercial ponds during harvest at 150 DOC. A total of 199 broodstock contributed to the 5,734 progeny that were genotyped with a custom multiplex single nucleotide polymorphism (SNP) panel, and family assignments were cross-referenced using two parentage assignment methods, CERVUS and COLONY. A total of 121 families were detected, with some families contributing up to 11% of progeny at 30 DOC and up to 18% of progeny at harvest. Significant changes were detected for 20% of families from 30 to 150 DOC, with up to a 9% change in relative contribution. Family skew data was applied in several models to determine the optimal sample size to detect families, along with the ability to detect changes in relative family contribution over time. Results showed that an order of magnitude increase in sampling was required to capture the lowest represented 25% of families, as well as significantly improve the accuracy to determine changes in family proportion from 30 to 150 DOC. Practical measures may be implemented at the hatchery to reduce family skews; a cost-effective measure may be to address the initial magnitude differences in viable progeny produced among families, by pooling equal quantities of hatched larvae from each family. This study demonstrates the relationships between skews in families under commercial conditions, the ability to accurately detect families, and the balance of sampling effort and genotyping cost in highly fecund species such as shrimp.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

“…The similar condition was described in Premachandra et al [ 3 ], where they found the SNP pedigrees tended to split part of the full-sib families determined by microsatellites into smaller groups or produced single individuals unrelated to any other members. Moreover, the default low genotyping error rate of 0.01% to 1% seemed too low even for a relatively low-density SNP panel [ 80 ], allowing only for ≤ 2 genotyping errors for a whole panel of 208 SNPs, which might cause interference to a certain extent and lead to the erroneous assignment of parents. Hall et al [ 40 ] detected a genotyping error rate of 5% in GBS data, which suggested a finer selection of SNP loci would be needed to alleviate the consequence brought by such kind of error.…”

Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation

“…This was to keep the population size per generation as close as possible to number of individuals per generation in S1 (5000). In addition, the allocation of the number of progeny and their respective distribution was based on the study of maintaining the genetic diversity in P. monodon carried out by Foote, et al 50 . They found that the highest contribution of a single family for P. monodon bred in captivity was 18%.…”

“…genomic selection (GS), has been widely adopted for enhancing commercial traits in animal breeding 6 . In aquaculture for example, GS has been shown to predict breeding values (BV) more accurately for growth traits in Atlantic salmon 7 , common carp 8 , Nile tilapia 9 , channel catfish 10 , large yellow croaker 11 , yellowtail kingfish 12 , yellow drum 13 , Pacific oyster 14 , scallop 15 , 16 , whiteleg shrimp 17 and banana shrimp 18 compared to pedigree-based BV predictions and has recently been reviewed for applications in aquaculture by Zenger et al 19 . GS uses the information obtained from genotypic markers to improve the accuracy of BVs.…”

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

“…Quite often it is not possible to manually tag or separate family lines. As a result, genotyping progeny and broodstock, and assigning parentage through molecular means is essential as it enables the recovery of pedigree information and ensures breeding programs are managed effectively [27,58].…”

“…Since the progeny were the first generation of wild broodstock pairings, inbreeding was not included. Prior sib-ship assumptions were excluded allowing for highly skewed family sizes commonly observed in mass-spawning aquaculture systems [58]. Likewise maternal and paternal polygamy were allowed to account for potential of half-sib breeding designs that utilise artificial insemination.…”