Transcriptome Analysis Of Related Phenotypes To Muscovy Duck Breeding

Muscovy duck is an excellent species,because of high broodiness and low fecundity, affect its breeding efficiency. RNA-Sequencing (RNA-Seq) is one of the next-generation sequencing (NGS) techniques with the characteristics of high-throughput and low cost, providing a powerful technology platform for identifying genes related to poultry reproductive performance development.In this study, nesting and laying moscovy duck as material. Using the Illumina HiSeqTM 2500 platform on the hypothalamus, pituitary, ovary tissue RNA-seq sequencing. The main results were as follows:1.Through the two cDNA library were sequenced, we obtained more than 2 millions high quality reads in each library, approximately 10.87 Gb transcriptome data. The total length of unigene was about 8752.11 Mb, and the average length of unigene was 202 bp. For each of the two samples,>50% of all reads were aligned on Anas platyrhynchos reference genome.2. Through the analysis of gene expression we can find that:when muscovy duck was in the condition of state and the nest egg, the numenber of different expression genes was 1459, which upregulating the expression was 635 and downregulating the expression was 824. Unigene sequences were aligned to public databases such as NR (Non-redundant Protein Sequence Database in GenBank), Swiss-Prot (Swiss-Prot Protein Sequence Database), KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Cluster of Orthologous Groups of proteins) and GO (Gene Ontology), then 1382 unigenes,94.72% of total, got functional annotations.1382 unigenes were matched to NR protein database,439 unigenes were matched to 25 functional category of COG database,1308 unigenes were matched to GO database.1325 unigenes were matched to Swiss-Prot database.3. We refined the genes tructure, found 1427 new gene and got functional annotations. This study analyzed six types of alternative splicing, include Exon Skipping, Alternative 5’splice sites, Alternative 3’splice sites, Intron retention, Alternative First Exon and Alternative Last Exon.The result show that, Exon Skipping is the most, with 48.56% in alternative splicing event and 41.31% in alternative splicing gene.4. SNP analysis will help to study the variation of single nucleotide caused by the change of the protein function. By comparison with the reference genome sequence, the laying period of 310389 SNP,298560 SNP in broodiness period.These SNP provide a basic To search for broodiness and production traits genetic markers in Muscovy Duck.In this study, we got a large number of the muscovy duck transcriptome informations acquired by transcriptome sequencing. Through the analysis of the data, we enriched the muscovy duck transcriptome, lay a good foundation for the research of muscovy duck molecular mechanism.