Sex locus and sex markers identification using whole genome pool-sequencing approach in the largemouth bass (Micropterus Salmoides L.)

The mechanism of sex determination in teleost evolves in an amazing speed contrary to mammals and birds. Different populations of the same species may use different sex determination systems. Largemouth bass is an aquaculture importance and recreational fish, which belongs to the family of Centrarchidae, genus Micropterus . However, molecular basis of genetic sex determination currently remains unclear. We applied a whole genome pool-sequencing approach to better characterize sex determination in this fish. Our results confirmed that sex determination system in largemouth bass is male heterogametic (XX/XY). In this study, males and females genomic DNA pools were sequenced using a whole genomic sequencing approach. Using genome comparative analysis, we identified a large sex differentiated region (~ 1.7 Mb) at the beginning of chromosome 7 on largemouth bass. This non-recombination region contained enriched male-biased fragments and high-density of male-biased genetic polymorphisms. Meanwhile, sequence synteny analysis between/within sex chromosomes showed that many chromosomal rearrangement events have taken place in this region. Based on this genetic information, we successfully developed male specific genetic markers. Additionally, 96 genes were located on that sex differentiated region, whereas “usual suspects” sex determining gene didn't exist in this region. It is implied, in largemouth bass, a new gene has evolved as the master sex determining gene. Our results exhibited that largemouth bass has a large sex locus on Chromosome 7, which is likely the largemouth bass sex chromosome. The presence of numerous chromosomal rearrangements and the absence of “usual suspects” sex determining gene in this sex differentiated region indicate recombination is suppressed on that region and a new master sex determining gene may be co-opted in largemouth bass. Besides, we also developed sex-linked genetic markers. Our study will facilitate future researches on sex determination and aquaculture applications in largemouth bass. • A pool-sequencing strategy was conducted to explore sex genetic differences between males and females. • A large sex differentiated region (~1.7 Mb) was identified on chromosome 7 of assembly HNU_Msal_1.0. • Male-specific fragments were enriched within/around sex differentiated region, which help us establishing sex-specific markers. • Largemouth bass was confirmed to use a male heterogametic system (XX-XY).