Biological Effects And Genetic Mechanism Of Inbreeding Depression In Japanese Scallop(Patinopecten Yessoensis)

Inbreeding has long been recognized as having deleterious effects on fitnesscomponents, and it is pervasive among species. Owing to the possible mechanism andselectivepressure of inbreeding depression, it has been a hot area of research in thefield of evolution and breeding. The enormous fecundity and various mating systemsof bivalves make them favorable species for the study of inbreeding. Japanese scallopis one of the most important species in northern China. In recent years, some amountof inbreeding appears in cultured stocks. The objective of this research is toinvestigate the manifestation of inbreeding from the phenotypic level as well as thepossible genetic and regulatory mechanism from both the genomic and thetranscriptomic level.1. Biological effects of inbreeding depression in Japanese scallopSome hermaphrodite individuals were found in breeding populations of Japanesescallop, using which we established selfed families with inbreeding coefficient0.5, F2families and controlled families respectively. To investigate inbreeding effects,fertility rate, hatching success, survival and growth in different life periods werecompared. We found most traits were significantly affected by different levels ofinbreeding except fertility rate. The depression of hatching success was6.2timesworse in selfed group than that in F2group, while larval survival and growth was3.7~7.8and1.5~3.1times worse respectively. On the other hand, inbreedingdepression had different impact on different traits. Fitness components suffers morefrom inbreeding than growth traits. The depression was7.84%~15.85%in survivalwith the increasing of F of10%, whereas it was only0.93%~5.13%in growth traits.Inferred from the changing trend of depression, it seems that fitness traits and growthtraits have their own regulatory mechanism, and inbreeding depression is due to deleterious alleles of both large and small effect, a mixed model system. From theperspective of purging the genetic load, inbreeding depression is likely to be a majordriving force in maintenance of high heterozygosity of marine bivalves.2. Construction of linkage map and analysis of segregationdistortionUsing the2b-RAD technique, we established a linkage map using aself-fertilizing line derived from a hermaphrodite Japanese scallop. A total of1289SNPs were mapped with average intervals of1.29cM, total length of1633.87cM,and coverage of98.3%. Further analysis of all genotyped markers indicated that58.8%of markers deviated from the mendelian ratio (P<0.05).The distorted markers wereequallyaffected by zygotic selection (49.04%) and germinal selection (50.96%),zygotic selection can be furthur categorized into homozygote deficiency (45.10%) orhetero-excess (43.79%), however, some overdominance locus maybe caused bylinkage of several deleterious alleles.17segregation distortion regions (SDRs),possibly linked with important genes or regions, were clustered on11of19linkagegroups. Gene annotation results and enrichment analysis shows that most of thesedistorted markers are closely related to signaltransduction and enzyme activityregulation and mainly act in extracellular domain possibly as a response toenvironmental stress. These results demonstrated that for the first time, distortedmarkers tends to be clustered in genome. The dominance and co-dominance theory ofinbreeding depression may both play a part in organism,however, some amount of“pseudo-overdominance” do exist. This genome-wide linkage and deviation analysisfacilitated our research on the mechanism of inbreeding depression and thedeveloping of important genes that linked with inbreeding depression.3. Expression profile differental analysis of selfed families and control groupRNA-Seq sequencing library was constructed using5individuals of two selfedfamilies and control group, respectively. Using the reference genome of Japanesescallop and data of annotation,17087genes were detected in all sequencing library.After comparison with control group,2055shows significant differental expressed inselfed families, among which1629(79.3%) can be annotated，828(50.8%) showesup-regulation and776(47.6%) down-regulation. Overall, selfed families displayed a down-regulated in gene expression, mainly in much more serious down-regulated ofsome genes.493genes co-exist in two selfed groups and showed almost the samechanging trends, only24(4.8%) showed different trend. Most of these Differentialexpression gene are related to protein synthesis, metabolism of nucleic acid, lipid metabolism, oxidative phosphorylation, immunologic defence and cytoskeletonicsystem. Furthur analysis showed that down-regulated genes mainly focus in EGF-likefamilis, with the function of regulating growth and differentiation, which may causedepression of growth traits. All up-regulated genes, however, shows no significantenrichment, which may be an response to the down-regulation of EGF. This researchoffer us a series candidategene for reveal of possibly key regulation genes andregulation and control mechanism.