Genetic mechanism of body size variation in groupers:Insights from phylotranscriptomics

Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size,providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates.Herein,we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea.Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size,respectively.A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups.Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups.These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks.Based on our results,we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection,leading to genetic variations in metabolic patterns,organ development,and lifespan,resulting in body size divergence between the two locally adapted populations.These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

A New Problem with Cross-Species Amplification of Microsatellites: Generation of Non-Homologous Products

Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology. However, microsatellites are not always available for the species to be studied and their isolation could be time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of electromorphs from seven catfish species belonging to three different families （Clariidae, Heteropneustidae and Pimelodidae）. A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4 microsatellite loci isolated from the species Clarias batrachus. Two hundred and forty PCR-products representing all 50 electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all species tested, whereas primers for the other two loci produced specific and polymorphic bands from some non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance of size homoplasy will lead to obvious complications in phylogenetie interference, population genetic and evolutionary studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to application of cross-species amplification of microsatellites.

Isolation and characterization of polymorphic microsatellite loci in large yellow croaker, Larimichthys crocea

An （AC）n-microsatellite-enriched library for Larimichthys crocea was constructed in this study. Primers for fifty simple sequence repeat （SSR） loci were synthesized and genotyped on 30 L. crocea individuals from Guanjingyang wild population （WP） in Fujian Province and 38 individuals from Ningbo cultured population （CP） in Zhejiang Province. Only 21 loci were successfully amplified and polymorphic in two populations. In WP, the observed heterozygosity （Ho） ranged from 0.233 to 0.900 and the expected heterozygosity （HE） ranged from 0.326 to 0.893, with an average of 7.8 alleles/locus, the polymorphism information content （PIC） ranged from 0.283 to 0.866 （mean 0.731）. In CP, the Ho ranged from 0.189 to 0.892 and the HE ranged from 0.333 to 0.800, with an average of 4.4 alleles/locus. The probability test showed significant departures from HWE in 9 and 2 of the 21 loci in WP and in CP, respectively. Deficiency of heterozygotes at four loci showed the presence of null alleles （P 〈0.01）. The PIC of 20 microsatellite loci in WP were greater than 0.50. Overall, these novel markers are potentially useful for the study of population genetics, construction of genetic linkage and quantitative trait loci maps in large yellow croaker.

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.