Full-length transcriptome sequence and SSR marker development for genetic diversity research in yellowfin seabream Acanthopagrus latus

Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China.

Aquaculture species diversification in China

China has been the top aquaculture producer in the world since 2002.Over 800 species and 240 improved varieties have been used in China’s aquaculture,which is the most diverse collection of species on this planet.Species diversification,along with other aquaculture technologies,contributes significantly to the increase of China’s aquaculture production,whereas the use of too many species in aquaculture has resulted in some issues related to the environment and sustainability.We provide an updated overview of the species currently used in Chinese aquaculture in this paper.We examine critically the main drivers of species diversification in China with examples.We also introduce Chinese approaches to improve and certify new species and varieties for commercial production.We believe that further species diversification is not a priority in China’s aquaculture,while further improvement of aquaculture technologies for major and native species is essential for green,profitable,and sustainable(GPS)aquaculture.The implications of China’s experiences with species diversification for global aquaculture species diversification are discussed.

The integrated analyses of metabolomics and transcriptomics in gill of GIFT tilapia in response to long term salinity challenge

The Nile tilapia,Oreochromis niloticus,GIFT strain is suggested to be a good candidate for culture in brackish water.Gill is regarded as the dominate site of osmo-regulation.Recently,the mechanisms underlying salinity challenge in gill of tilapia are getting increasing attention.In this study,an integrated analysis of metabolomics and transcriptomics on gill of GIFT tilapia under salinity 17 and 27 challenge for three and a half months are conducted.1164 DEGs in the comparison 0 vs 17 and 910 DEGs in the comparison 0 vs 27 are identified.Many typical genes involved in osmo-regulation are found,including calcium/calmodulin-dependent protein kinase II beta 1,Aquaporin 3,Potassium channel subfamily K member,chloride channel 2,Solute Carrier Family 12 Member 8,Solute Carrier Family 12 Member 2,Na^(+)/K^(+)ATPase.Some biosynthesis,metabolism,energy or transport related pathways are over-represented,such as Synthesis of UDP-N-acetyl-glucosamine,Synthesis of substrates in N-glycan biosynthesis,Biosynthesis of DPAn-3 SPMs,Metabolism of lipids,Gluconeogenesis and SLC-mediated transmembrane transport.In addition,totally 23 metabolites are significantly responded in gill under salinity challenge.Of which,11 metabolites including 12-Hydroxyeicosatetraenoic acid and choline are significantly down-regulated and 8 metabolites including adenine,Lys-Pro,inosine are significantly up-regulated under salinity challenge.Our study provides an important database for further functional analysis of osmo-regulation in gill of Nile tilapia.

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.

Editorial special issue: Emerging and disruptive technologies for aquaculture

In the past few decades,aquaculture has been one of fastest growing sectors in agriculture.Since 2014,aquaculture has produced more fish for human consumption than wild-caught fish(FAO,2016).The rapid development of aquaculture has been enhanced by the application of science and the introduction of new technologies.It is anticipated that the global population size will be 9.7 billion by 2050.Further increase in aquaculture production may be the only way to meet the human requirement for high-quality protein and omega-3 fatty acids.Novel emerging and disruptive technologies,including genomic selection,genome editing,information/digital technology,solar energy,and novel marketing strategies with blockchain are being applied in many sectors of agriculture.The applications of these technologies in aquaculture lag far behind the agriculture sector.We expect that in the coming years,many emerging and disruptive technologies will be applied in the aquaculture industry,which will lead the industry to be considered more green,sustainable and profitable.