Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata

Abstract

Highlights ► This is the first SNP panel developed for parentage assignment in an abalone species. ► SNPs discovery was carried out using an existing transcriptomic data set, and yielded a panel of 298 SNPs with >90% call success across >1000 genotyped individuals. ► A subset of 123 SNPs was used to successfully assign parentage in 98.9% of 945 offspring from 40 parents representing 189 mixed families. ► Parentage assignment revealed that broodstock reproductive success was highly variable, and suggests that careful management of genetic variability would be needed if implementing individual selection in hatchery produced progenies.

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

“…As expected for mostly non-model species, the present study highlights a general paucity of published mitochondrial and nuclear genome assemblies, population-scale data, as well as geographical metadata submitted to barcode databases (BOLD, GenBank), with some mollusk populations better described at the population genomic level, i.e., Crassostrea sp., Mytilus sp., Haliotis sp., and Pecten sp. (Zbawicka et al, 2014a(Zbawicka et al, , 2018Fraïsse et al, 2016;Mathiesen et al, 2016;Wenne et al, 2016;Gutierrez et al, 2017;Harney et al, 2018;Wilson et al, 2018;El Ayari et al, 2019;Masonbrink et al, 2019;Paterno et al, 2019;Vendrami et al, 2019a,b). It is worth noting that the phylogenetically robust data reported here significantly increases the number of released complete mitochondrial genome sequences by 6-fold for R. decussatus, five-fold for R. philippinarum, three-fold for A. islandica, and D. polymorpha, and finally two-fold for H. rufescens, H. tuberculata, and P. maximus.…”

Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self‐fertilization: Effect of null alleles

“…The use of alternative methods to statistical analysis for estimating null alleles frequency in those populations is highly recommended, as well as increasing the number of studied loci and eliminating those that present significantly high frequencies of null alleles (Bürkli, Sieber, Seppälä, & Jokela, ; De Sousa, Finkeldey, & Gailing, ; Estoup, Jarne, & Cornuet, ; Oddou‐Muratorio et al, ; Stadhouders et al, ); redesigning primers to avoid the presence of mutations affecting the primer pairing with flanking zones (Holm et al, ; Reece et al, ); and, whenever possible, performing a segregation analysis to infer the parental genotypes. Another option is the use of SNPs markers, since they are easier to identify, show Mendelian segregation, and exhibit few null alleles at controlled crosses, compared to microsatellites (Harney et al, ).…”

Potential for Genetic Improvement of Resistance to Perkinsus olseni in the Manila Clam, Ruditapes philippinarum, Using DNA Parentage Assignment and Mass Spawning

“…This means a high risk of inbreeding and loss of genetic diversity. Estimated N e can give an indication of the risk of inbreeding, and in order to increase the accuracy of inbreeding estimations, the variability of family representation can be considered when calculating Ne, according to Harney et al (29) and Chevassus (61), expressed as:…”

“…Thus, distinguishing between families would evidently require raising large numbers of them separately, a method that comes with major disadvantages including high costs, extensive infrastructure, and the risk of confounding factors such as "tank effect" and "family effect, " which can significantly decrease the accuracy of estimated breeding values (25). Despite the difficulties associated with obtaining parentage information for shellfish, several recent studies have successfully applied SNP panels for parentage assignment in order to estimate genetic parameters of traits of commercial interest in mollusks (26)(27)(28)(29). That said, most of the studies carried out so far seeking to evaluate the potential for genetic gain in bivalves have focused on traits such as disease resistance, growth rate, meat yield, and visual aspects such as shape and shell color, and relatively few have tackled the estimation of genetic parameters across all traits simultaneously (30).…”