Identification of a Sex-Linked SNP Marker in the Salmon Louse (Lepeophtheirus salmonis) Using RAD Sequencing

Abstract

The salmon louse (Lepeophtheirus salmonis (Krøyer, 1837)) is a parasitic copepod that can, if untreated, cause considerable damage to Atlantic salmon (Salmo salar Linnaeus, 1758) and incurs significant costs to the Atlantic salmon mariculture industry. Salmon lice are gonochoristic and normally show sex ratios close to 1:1. While this observation suggests that sex determination in salmon lice is genetic, with only minor environmental influences, the mechanism of sex determination in the salmon louse is unknown. This paper describes the identification of a sex-linked Single Nucleotide Polymorphism (SNP) marker, providing the first evidence for a genetic mechanism of sex determination in the salmon louse. Restriction site-associated DNA sequencing (RAD-seq) was used to isolate SNP markers in a laboratory-maintained salmon louse strain. A total of 85 million raw Illumina 100 base paired-end reads produced 281,838 unique RAD-tags across 24 unrelated individuals. RAD marker Lsa101901 showed complete association with phenotypic sex for all individuals analysed, being heterozygous in females and homozygous in males. Using an allele-specific PCR assay for genotyping, this SNP association pattern was further confirmed for three unrelated salmon louse strains, displaying complete association with phenotypic sex in a total of 96 genotyped individuals. The marker Lsa101901 was located in the coding region of the prohibitin-2 gene, which showed a sex-dependent differential expression, with mRNA levels determined by RT-qPCR about 1.8-fold higher in adult female than adult male salmon lice. This study’s observations of a novel sex-linked SNP marker are consistent with sex determination in the salmon louse being genetic and following a female heterozygous system. Marker Lsa101901 provides a tool to determine the genetic sex of salmon lice, and could be useful in the development of control strategies.

Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae)

“…tified as A. decepta, however, had a mitochondrial and nuclear genotype matching that of male A. arapahoe and was considered a female representative of this taxon (see below). This led to identification of sex chromosome-linked SNPs, the allelic patterns of which differed from those in autosomal loci(Carmichael et al, 2012) but were consistent with the interpretation of the origin of A. arapahoe.…”

Identification of sex‐specific markers and heterogametic XX/XY sex determination system by 2b‐RAD sequencing in redtail catfish (Mystus wyckioides)

“…The mechanisms of sex determination in animals are remarkably diverse, that is, they show genetic and/or environmental sex determining mechanisms Palaiokostas et al, 2013). During the past decades, traditional technologies have been successfully applied to the development of sex-specific molecular markers in fish such as AFLP and RAPD, but they failed in some species (Gao, Wang, Yao, Tiu, & Wang, 2010;Sriphairoj, Na-Nakorn, Brunelli, & Thorgaard, 2007;Yarmohammadi, Pourkazemi, Ghasemi, Saber, & Chakmehdouz, 2011 TA B L E 3 Primers used to amplify the X-specific allele sequence necessary, has successfully applied to identify sex-specific markers in several fish species (Anderson et al, 2012;Carmichael et al, 2013;Wilson et al, 2014). During the past decades, traditional technologies have been successfully applied to the development of sex-specific molecular markers in fish such as AFLP and RAPD, but they failed in some species (Gao, Wang, Yao, Tiu, & Wang, 2010;Sriphairoj, Na-Nakorn, Brunelli, & Thorgaard, 2007;Yarmohammadi, Pourkazemi, Ghasemi, Saber, & Chakmehdouz, 2011 TA B L E 3 Primers used to amplify the X-specific allele sequence necessary, has successfully applied to identify sex-specific markers in several fish species (Anderson et al, 2012;Carmichael et al, 2013;Wilson et al, 2014).…”

Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

“…However, sex chromosomes are difficult to identify in crustaceans because of the large number of chromosomes (e.g., on average 110 chromosomes for American lobster; Hughes, ) and the small chromosome size (Legrand et al., ). Although markers associated with sex determination can be identified by approaches such as that used here, or as conducted in salmon lice ( Lepeophtheirus salmonis, Carmichael et al., , but see also Gamble & Zarkower, ), most of the crustacean sex‐determining systems are poorly understood and understudied (Legrand et al., ). Taking advantage of RAD‐sequencing, we provide the first evidence of a male heterogametic system in the American lobster (XX/XY).…”