| Heterosis, as a very important genetic phenomenon, is widespread in the nature, and has been widely applied in agriculture, which has gained great achievements. The genetic mechanism of heterosis has been debated for nearly a century, but no consistent conclusion has been got. The prevalence of next-generation sequencing technologies provides new insights into the study of the genetic basis of heterosis. Scallops are important aquaculture species in our country. The success of the hybridization between Argopecten irradians and Argopecten purpuratus not only promotes the development of the breeding work of scallops, but also provides new materials for the study of heterosis in scallops.1.The genome survey analysis of A. irradians, A. purpuratus and their hybridsThe genome survey sequencing is performed for A. irradians, A. purpuratus and their hybrids. A total of 108.8 Gb data is obtained with the sequencing depth of 29,29, 20 separately. Genome survey analysis is carried out for the three scallops to study their genome essential characteristics, including the genome size, heterozygosity, repeats and GC content. The genome size of the hybrid scallop is approximately equal to the sum of A. irradians and A. purpuratus, and the heterozygosity of the hybrid scallop is extremely low, indicating that the hybrid receives one haploid genome from each parent and the phenomenon of large chromosomes deletion or doubling does not occur. The characteristics of repeat sequence and GC content of the hybrid scallop are similar with their parents. The genomes of the three scallops are assembled by the software SOAPdenovo, and comparative genome analysis is performed with the assembled sequences. It turns out that there is greatly difference between the genome of A. irradians and A. purpuratus, which is possibly related to the generation of heterosis of the hybrid scallop. And the genome of the hybrid is more similar to the A. purpuratus, showing some preference.2.Segregation distortion analysis for a A. irradians*A. purpuratus family and A. irradians self-fertiling familyAn A. irradians×A. purpuratus hybrid family and a half-sib A. irradians self-fertiling family are constructed.2b-RAD libraries are constructed and sequenced for the two families. SNP markers are genotyped by the software RADtyping, and segregation distortion analysis is performed. There are 1696 SNP genotyped in hybrid family with 54.5% deviated from the mendelian ratio (P<0.05). And for the type of Aa X Aa,81.1% distorted markers are caused by zygotic selection and 9.4% by germinal selection. In inbred family, there are totally 4058 SNP markers genotyped with 59.8% deviated from mendelian ratio (P<0.05). And 67.9% distorted markers are affected by by zygotic selection and 25.6% by germinal selection. The distorted markers caused by zygotic selection of both hybrid and inbred families can be categorized into dominance effect and overdominance effect, and dominance effect occupies a greater ratio. There are 1149 SNP shared by the two families. Segregation distortion analysis for these markers finds that some markers are distorted in the same direction in the two families with the distortion degree same or not, and some markers are distorted in the opposite direction, which provides important candidate markers for the study of heterosis.3.High density linkage maps construction and QTL mapping for economic important traitsHigh-resolution genetic linkage maps are separately constructed for A. irradians and A. purpuratus of the hybrid family. For the map of A. irradians, there are 2994 markers on the map spanning 16 linage groups. The marker density varies from 100 to 293 with an average of 187. The length of the map is 945.95 cM with an average marker interval of 0.32 cM, and the coverage of the map reaches as high as 98.9%. The resolution of the map is the highest for A. irradians at now. For the map of A. purpuratus,1583 markers are grouped into 16 groups. The marker density varied from 25 to 176 with an average of 99. The length of the map is 800.5 cM with an average marker interval of 0.51 cM, and the coverage of the map reaches 98.0%. This the first linkage map for A. purpuratus, the density of which has reached high resolution. With the two maps, three QTLs controlling growth-related traits are identified, with two controlling adductor muscle weight separately locating on LG11 of A. irradians and LG2 of A. purpuratus, and another one controlling body weight locating on LG2 of A. purpuratus. Besides, one QTL that controls shell color is identified, which locates on LG2 of A. irradians. Deduced from the segregation and QTL mapping results of the shell color, it is probably controlled by one single gene simply. For the map of A. irradians of the inbred family, there are 1437 markers spanning 16 linkage maps. The marker density varied from 251 to 189 with an average of 90. The length of the map is 831.9 cM with an average marker interval of 0.59 cM, and the coverage of the map reaches 97.5%. There are 14 segregation distortion regions found on the map, which are mainly caused by germinal selection.4.Expression profile differential analysis of hybrid scallops with their parentsRNA-seq libraries are constructed and sequenced for adductor muscle of 4 A. irradians,4 A. purpuratus and 10 hybrids with the sequencing data of 13.9 Gb, 12.9Gb and 36.7 Gb. Transcriptomes of A. irradians and A. purpuratus are first assembled and annotated as the reference sequence for further analysis. Comparative transcriptome analysis of A. irradians and A. purpuratus finds that the GO annotation and classification of the two scallops are highly similar, but the difference of the sequence is great. Expression profile differential analysis of hybrid scallops with their parents find that the difference between hybrids and A. irradians is much greater than that between hybrids and A. purpuratus, and the expression profiles between hybrids and A. purpuratus are also more similar. So, the gene expression of the hybrids shows some extent preference. GO enrichment of the different expression genes between hybrids and A. irradians suggests that the up-regulate genes mainly participate the process of mitochondria formation and energy metabolism, and the down-regulate genes mainly participate the process related to the immune. |
PDF Full Text Request