Current status of research on aquaculture genetics and genomicsinformation from ISGA 2018

The ISGA(International Symposium on Genetics in Aquaculture)is an important conference in the field of aquaculture genetics,which is held every three years.This year,the meeting was hosted by James Cook University,in Cairns.The conference sessions included biotechnology and functional genomics,sex control,genomic prediction,selective breeding and quantitative genetics,industrial use of genetics,genome technology,genetics of diseases and stress,genetics of nutrition,epigenetics,genomics and metabolomes,population genetics and ethics,food safety,as well as environmental risks.Many new and interesting unpublished data,including those for new aquaculture species,marker-assisted selection,genomic selection and genome editing using Crispr/Cas9 technologies,were reported at the conference.In this brief review,we highlight the novel and interesting researches on aquaculture genetics and genomics to give readers an overview of the current status and trends of aquaculture genetics and genomics research.

Heritability of growth traits in the Asian seabass (Lates calcarifer)

Growth is an economically important trait in aquaculture.To improve growth trait of the Asian seabass(Lates calcarifer)we have been carrying out,since 2004,a selective breeding program.This study focuses on growth traits in the F2 fish generation,comprised of offspring from 23 mass crosses from 383 F_(1) brooders.Using genotyping analysis for 10 microsatellites from both brood stock and progeny we have reconstructed the pedigree of each mass-cross.For F_(2) generation at 90 days post hatch(dph),we have recorded body weight(BW)for 12,117 individuals and total length(TL),standard length(SL)and condition factor(K_(tl) and K_(sl))for 3530 individuals;and all five traits for 2136 individuals at 270 dph.At 90 dph the average BW was 46.88±20.95 g.Combining pedigree information,recorded growth traits and Restricted Maximum Likelihood method,we have estimated that the narrow sense heritability(h^(2))in F_(1) fish for BW,TL,SL,K_(tl) and K_(sl) was at,90 dph,0.12±0.03,0.11±0.03,0.10±0.03,0.20±0.04 and 0.11±0.03,respectively and,at 270 dph,0.34±0.07,0.32±0.07,0.30±0.06,0.13±0.04 and 0.11±0.04,respectively.At 90 dph the realised heritability for BW was 0.13.Comparing with F_(1) generation,the growth performance of F_(2) fish was increased by 14.4%.Heritability of growth traits will be useful for future genetic improvement programmes of the Asian seabass.

Who eats whom,when and why?Juvenile cannibalism in fish Asian seabass

While juvenile cannibalism plays an important role in the evolution of organisms in natural populations,it is a serious problem in aquaculture.A number of genetic and environmental factors result in different rates of cannibalism.Whether there is kin recognition in juvenile cannibalism in fish is poorly understood.We studied cannibalism and kinship recognition in juveniles of Asian seabass using molecular parentage analysis with polymorphic microsatellites.In the three mass crosses,under an ordinary feeding scheme without size grading,the rate of juvenile loss due to cannibalism was 1.08% per day.In the group without feeding for 24 h,2.30%±0.43% of offspring per day were lost within 24 h due to cannibalism.We detected that juveniles avoided cannibalizing their siblings when they were not hungry,whereas cannibalism among siblings increased when they were hungry.These data suggest that there is kin discrimination in fish cannibalism.Raising genetically closely related offspring in the same tanks and appropriate levels of feeding may reduce the rate of cannibalism.We hypothesized that the chemical cues for kin discrimination might be secreted by fish skins.To test this hypothesis,we analyzed gene expression profiles in the skins of juveniles under slightly and very hungry conditions using RNA sequencing and bioinformatics analysis.Genes differently expressed under slightly and very hungry conditions were identified.Among them,genes from the trypsin family were significantly downregulated under starved conditions,suggesting that they may play a role in kin discrimination.

Pluripotent stem cells secrete Activin A to improve their epiblast competency after injection into recipient embryos

It is not fully clear why there is a higher contribution of pluripotent stem cells （PSCs） to the chimera produced by injection of PSCs into 4-cell or 8-cell stage embryos compared with blastocyst injection. Here, we show that not only embryonic stem cells （ESCs） but also induced pluripotent stem cells （iPSCs） can generate F0 nearly 100% donor cell-derived mice by 4-cell stage embryo injection, and the approach has a ＂dose effect＂. Through an analysis of the PSC-secreted proteins, Activin A was found to impede epiblast （EPI） lineage development while promoting trophectoderm （TE） differentiation, resulting in replacement of the EPI lineage of host embryos with PSCs. Interestingly, the injection of ESCs into blastocysts cultured with Activin A （cultured from 4-cell stage to early blastocyst at E3.5） could increase the contribution of ESCs to the chimera. The results indicated that PSCs secrete protein Activin A to improvetheir EPI competency after injection into recipient embryos through influencing the development of mouse early embryos. This result is useful for optimizing the chimera production system and for a deep understand- ing of PSCs effects on early embryo development.

Genes for sexual body size dimorphism in hybrid tilapia(Oreochromis sp.x Oreochromis mossambicus)

Tilapias are important aquaculture species.Male-biased sexual size dimorphism is very common and males are preferred for aquaculture in tilapia.However,the mechanisms underlying sexual dimorphism remain to be elucidated.One hundred and thirty-six sex-biased genes,of which 23 were male-biased and 113 were femalebiased,were identified via reanalysis of a muscle transcriptome data using the latest reference genome assembly.These genes were mapped to KEGG pathways that are related to somatic cell metabolism,growth and differentiations,such as MAPK,FoxO4 and metabolism pathways as well as developmental processes responsible for skeletal muscle development.Pathways related to cell growth and proliferations such as MAPK signaling pathways are upregulated in males while pathways regulating cell division such as FoxO4 are upregulated in females.Sex-biased genes in tilapia skeletal muscle have higher evolution rates(dN/dS)compared to unbiased genes.Female-biased and male-biased genes showed 17.4%and 13.5%higher dN/dS,respectively,compared to unbiased genes.Our results suggest that some of the male and female sex-biased genes were under selection pressures.Three SNPs located in the promoter region of one sex-biased gene RASGRF1 on LG1 were associated with bodyweight differences in the hybrid tilapia.These sex-biased genes identified in this study may serve as candidate genes for future functional analysis on sexual size dimorphism and for developing DNA markers for selecting fast-growing saline tilapia in aquaculture.