Gene-centromere mapping in meiotic gynogenetic European seabass

Abstract

BackgroundFully isogenic lines in fish can be developed using “mitotic” gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in this process has seldom been applied. We used ddRADseq to generate SNP markers in a meiotic gynogenetic family of European seabass (Dicentrarchus labrax): (i) to verify the lack of paternal contribution in a meiotic gynogenetic family; (ii) to generate a gene-centromere map from this family; (iii) to identify telomeric markers that could distinguish mitotic gynogenetics from meiotic gynogenetics, which sometimes arise spontaneously in mitotic gynogenetic families.ResultsFrom a single meiotic gynogenetic family consisting of 79 progeny, 42 million sequencing reads (Illumina, trimmed to 148 bases) resolved 6866 unique RAD-tags. The 340 male-informative SNP markers that were identified confirmed the lack of paternal contribution. A gene-centromere map was constructed based on 804 female-informative SNPs in 24 linkage groups (2n = 48) with a total length of 1251.02 cM (initial LG assignment was based on the seabass genome assembly, dicLab v1). Chromosome arm structure could be clearly discerned from the pattern of heterozygosity in each linkage group in 18 out of 24 LGs: the other six showed anomalies that appeared to be related to issues in the genome assembly.ConclusionGenome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study. The large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynogenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gynogenetics.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3826-z) contains supplementary material, which is available to authorized users.

Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing

“…Both RAD and ddRAD-seq have been widely applied in aquaculture breeding and genetics studies (Robledo et al 2018). In particular, ddRAD-seq has been applied for genotyping large multiplexed datasets (e.g., Maroso et al 2018), construction of genetic linkage maps (e.g., Recknagel et al 2013;Oral et al 2017), analyzing life history traits (e.g., Pukk 2016), mapping sex determining loci (e.g., Palaiokostas et al 2015;Brown et al 2016), genomic predictions and genome-wide association studies (e.g., Barria et al 2018), assessing genetic diversity (e.g., Hosoya et al 2018;Tony et al 2015;Siccha-Ramirez et al 2018;Torati et al 2019), phylogeography (e.g., Stobie et al 2018, and species identification in tilapias (Syaifudin et al 2019).…”

A cost effective alternative method to ddRADseq library construction during size selection

“…PCR enrichment of the final library is essential step so as to ensure amplification of desired size range in the final library (Peterson et al, 2012). In standard ddRADseq libraries 12 to 18 PCR cycles are routinely used (Peterson et al, 2012;Capblancq et al, 2015;Palaiokostas et al 2015;Yang et al, 2016;Burns et al, 2017;Oral et al, 2017;Cumer et al, 2021). The higher the PCR cycles increases the risk of PCR duplicates, while the lower PCR cycles camouflage the existing diversity.…”

“…The ddRADseq library was generated originally by following Peterson et al (2012) protocol with minor modifications detailed elsewhere (Palaiokostas et al, 2015;Leitwein et al, 2016;Oral et al, 2017). Each sample (200 ng DNA) was digested with two restriction enzymes, EcoRI-HF (G^AATTC) and MspI (C^CGG) for 120 minutes at 37 °C in 25 µL reaction volume.…”

Genome‐wide analysis facilitates estimation of the amount of male contribution in meiotic gynogenetic three‐spined stickleback (Gasterosteus aculeatus)

“…Nevertheless, most of these studies, with the exception of Oral et al . (2017), have used measures of heterozygosity and/or homozygosity but have not taken an approach that tracks paternal‐specific alleles within experimentally produced meiotic gynogenetic crosses.…”