Whole-genome sequencing of leopard coral grouper(Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution

Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7%(784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 proteincoding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper.Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes(DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

Marker-assisted selection of YY supermales from a genetically improved farmed tilapia-derived strain

DEAR EDITOR, Genetically improved farmed tilapia (GIFT)and GIFT-derived strains account for the majority of farmed tilapia worldwide.As male tilapias grow much faster than females,they are often considered more desirable in the aquacultural industry.Sex reversal of females to males using the male sex hormone 17-α-methyltestosterone (MT)is generally used to induce phenotypic males during large-scale production of all male fingerlings.However,the widespread use of large quantities of sex reversal hormone in hatcheries may pose a health risk to workers and ecological threats to surrounding environments. Breeding procedures to produce genetically all-male tilapia with limited or no use of sex hormones are therefore urgently needed.

First identification of two co-existing genome-wide significant sex quantitative trait loci(QTL) in red tilapia using integrative QTL mapping

Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.