High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

Abstract

The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex-and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general.

A first generation microsatellite-based linkage map of the Chinese mitten crab Eriocheir sinensis and its application in quantitative trait loci (QTL) detection

“…Our study shows that the estimated genome lengths (G oa ) of the female (2430.9 cM) were close to the male (2658.4 cM), indicating that the recombination rate (0.91:1) does not differ between sexes (i.e., no heterochiasmy) in the mitten crab. When we made a revision of our manuscript, a most recently published SNP linkage map for this species also showed no difference in the recombination rates between sexes (Cui et al, 2015). These results are consistent with those of the swimming crab P. trituberculatus (1.01:1) .…”

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

“…All the effective SLAF marker sequences were presented in Supplementary Table S1. In comparison with 10,358 markers previously identified within a northern population32, the resultant effective primer numbers in our present study increased largely when genotyped in the intercross family between northern and southern populations. The abundance of polymorphic markers implied the high heterozygosity and complexity of the crab genome.…”

“…Thus, the genome coverage of the male, female, and sex-average linkage map was 98.30%, 98.30% and 98.64%, respectively. Considering that the present map lengths are much longer than the map created by Cui et al 32. using only SNP markers32, we tried to use only SLAF markers for reconstruction of the map (Supplementary Figure S2).…”

“…As for shrimps and crabs such as Penaeus monodon 27, Fenneropenaeus chinensis 28, Litopenaeus vannamei 29 and Portunus trituberculatus 30, previous linkage maps were constructed mainly relying on dominant markers AFLP or RAPD. Only several SNP and/or SSR-based high dense linkage maps have been recently reported31323334. The Chinese mitten crab is the most economically important cultivated crab species in China.…”

“…In recent year, transcriptomic analysis using RNA-Seq technology was conducted on the immunity, molt, metamorphosis and reproduction38404142. A high-density linkage map of the mitten crab including 10,358 markers was developed on a northern population with 2b-RAD method32, but the markers identity is obscure because their sequences of the nucleotide have neither been described nor deposited in the data bank. The crab whole genome sequencing work has just been finished in our lab.…”