A SNP MAP OF THE EUROPEAN SEA BASS GENOME BASED ON A MEIOTIC GYNOGENETIC FAMILY
Introduction
One of the objectives of the AQUAEXCEL project(EU FP7)is to develop isogenic clonal lines for commercially important species in Europe, including the European sea bass (Dicentrarchus labrax), as a resource for aquaculture-related research.The challenges in developing such lines include low survival of doubled haploid clone founders (produced through androgenesis or mitotic gynogenesis)and discriminating between such doubled haploids, fish with biparental inheritance (arising through failure of gamete irradiation) and meiotic gynogenetics (arising through spontaneous retention of the second polar body in gynogenetics). Reliable marker techniques are needed for screening putative clone founders. The present study aimed to generate a genetic linkage map from a meiotic gynogenetic family of European sea bass to be able to define telomeric markers, which are able to differentiate between meiotic and mitotic gynogenesisto aid the reliableproduction of isogenic lines.The approach of genotyping-by-sequencing,using double digest Restriction-site Associated DNA (ddRAD) sequencing on a MiSeq (Illumina) platform, enabled the rapid discovery of genome-wide Single Nucleotide Polymorphism (SNP) markers for dense linkage maps (Peterson et al., 2012).
Materials-Methods
A meiotic gynogenetic familywas generated by UV irradiation of sperm and pressure shocking of fertilized eggs (following Peruzzi and Chatain, 2000).DNA from eighty offspring and parents was used as template for ddRAD sequencing. Following SNP filtering,male informative markers allowed screening of any male contribution, while female heterozygous markers were assigned/integrated intothe sea bass draft reference genome contigs (Reinhardt R, personal communication)across 25 available linkage groups (2n = 48).Crossover hot-spots were identified per individual for chromosome arms in each linkage groupby scoring homozygote/heterozygote distribution along the chromosome on the physical map. A genetic linkage map was constructed based on 804 SNP markers and 11 microsatellites (Chistiakov et al., 2005; García De León et al., 1995) from previous studies.
Results
A total of 54 million raw reads were produced and assembled into 6 866 unique RAD-tags. No paternal contribution was detected from 340 informative SNPs. 804 female heterozygous markers were used to produce the map.An average of 0.86 ±0.38 crossovers were identified per chromosome arm along 25 LGs (see example in Figure 1).
Discussion and Conclusion
By using ddRAD sequencing of a meiotic gynogenetic family of sea bass, we confirmed cytogenetic studies showing that the sea bass has mostly acrocentric chromosome pairs (Cataudella et al., 1973), and we successfully localised the centromere of each chromosome inthe genomic maps for this species, based on 804 informative SNP markers and 11 microsatellites.The large number of telomeric markers identified in this study is of interest to discriminate between meiotic and mitotic gynogenetics with greater accuracy than the previous set of microsatellite markers, a step in the development of isogenic clonal lines from outbred founders, for the reliable production of isogenic clonal lines for aquaculture related research. The present results add to the genomic resources available for the sea bass.
References
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