FN Archimer Export Format
PT J
TI Methods for identifying and interpreting sex‐linked SNP markers and carrying out sex assignment: application to thornback ray (   Raja clavata   )
BT 
AF Trenkel, Verena
   Boudry, Pierre
   VERREZ-BAGNIS, Veronique
   Lorance, Pascal
AS 1:1;2:2;3:3;4:1;
FF 1:PDG-RBE-EMH;2:PDG-RBE-PFOM;3:PDG-RBE-BRM-LEMMMB;4:PDG-RBE-EMH;
C1 Ifremer, EMH Nantes, France
   Univ Brest, Ifremer, CNRS, IRD, LEMAR Plouzané ,France
   Ifremer, LEMMMB Nantes ,France
C2 IFREMER, FRANCE
   IFREMER, FRANCE
   IFREMER, FRANCE
SI NANTES
   BREST
SE PDG-RBE-EMH
   PDG-RBE-PFOM
   PDG-RBE-BRM-LEMMMB
UM LEMAR
IN WOS Ifremer UPR
   WOS Ifremer UMR
IF 1.251
TC 9
UR https://archimer.ifremer.fr/doc/00640/75231/75376.pdf
LA English
DT Article
CR EVHOE EVALUATION HALIEUTIQUE OUEST DE L'EUROPE
   RAIE-JUVES
BO Thalia
DE ;association-based approach;F(ST)outlier analysis;neural net;sex assignment error;sex-determination system;sex-linked SNP;thornback ray
AB Sex determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, non‐invasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: i) identification of heterozygote excess in one sex, ii) F ST outlier analysis between the two sexes and iii) neuronal net modelling. These methods were applied to a large SNP dataset (4604 SNPs) for 1680 thornback rays (Raja clavata ). Using method i), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata ) indicated that all 19 SNPs are likely located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method ii) identified eight SNPs probably located on different chromosomes. Method i) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males). 
PY 2020
PD NOV
SO Molecular Ecology Resources
SN 1755-098X
PU Wiley
VL 20
IS 6
UT 000553501400001
BP 1610
EP 1619
DI 10.1111/1755-0998.13225
ID 75231
ER

EF