Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)—10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
Highlights
The sea louse (Lepeophtheirus salmonis) is an ectoparasitic copepod that infests many marine fish species and is of particular concern to the Atlantic salmon (Salmo salar) aquaculture industry
The current study has shown that the largest male:female recombination rate differences occur with the sex chromosome SL15 making it tempting to speculate that the Z-chromosome or even the undifferentiated W-chromosome may preferentially house such “mate choice specific” genes
Large differences in recombination rates were detected between the sexes, with the largest male:female recombination difference present within the sex linkage group SL15
Summary
The sea louse (Lepeophtheirus salmonis) is an ectoparasitic copepod that infests many marine fish species and is of particular concern to the Atlantic salmon (Salmo salar) aquaculture industry. Because of the economic importance of this parasite, there is considerable interest in developing genomic resources to better understand the biology of this species. This includes understanding the physiological processes and genes involved in conferring adaptive resistance to therapeutics used to kill the species and span to understanding the genes involved in regulating behaviours such as mate choice and host selection. A fundamental step in this process is the construction of a high-density genetic marker map that can be used to track allelic variants of genes which may be involved in sea louse adaptation and selection. Multiple sea louse families were used, which facilitated an investigation into the nature of differences in recombination rates between the sexes in this species, as well as examining differences in recombination rates among individuals within the same sex
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