Hereditary linkage maps are indispensable tools in genetic and genomic studies. a large number of expressed sequence tags.7,22 The direction of the present study was also shaped by our immediate need for building up an integrative genomic platform that unifies a variety of genomic resources, such as genome map, linkage map and physical map, and facilitates future genetic, genomic and breeding studies on individual was chosen for genome survey sequencing. Genomic DNA was extracted from its adductor muscle using the standard phenol/chloroform extraction method.23 Three paired-end DNA libraries with insert sizes of 175, 500 and 800 bp were constructed by following the Illumina’s standard DNA library preparation protocol and were then sequenced using the Illumina HiSeq2000 platform. Raw reads were first filtered to remove low-quality reads resulting from base-calling duplications or adapter contamination. Clean reads were assembled using the SOAPdenovo software, which applies the graph structure to construct contigs. Subsequently, all reads were realigned to the contigs and the paired-end information was used to join unique contigs into scaffolds. Finally, intra-scaffold gaps were filled using paired-end extracted reads that had one read uniquely aligned on a contig and another read located in a gap region. Genomic sequences were archived in the Sequence Read Archive (SRA) database (accession no. SRP018107). Our group has recently reported the most comprehensive transcriptome resource for by 454 sequencing of cDNA libraries generated from PDGFRA diverse developmental stages and adult tissues,7 which offer an superb basis for gene annotation from the acquired scaffolds. Genomic scaffolds had been 1st annotated by aligning the 20 056 transcriptomic isogroup sequences (i.e. the longest isotig in each isogroup) onto these scaffolds using the GMAP system.24 To improve the annotation rate, the unannotated scaffolds were compared against the Swiss-Prot and nonredundant (NR) protein directories using BlastX, with an strain produced by our group with top features of red shell, fast growth and disease resistance. Growth-related qualities including shell size, shell width, shell elevation and bodyweight had been measured for many grouped family members in age 15 weeks. Among these grouped family members exhibiting large within-family variant of development qualities was particular for linkage and QTL evaluation. 2.3. 2b-RAD sequencing 2b-RAD libraries had been prepared for just two parents and 96 progenies by following a protocol produced by Wang genome. A distinctive barcode was integrated into each collection during library planning, and all libraries had been pooled for single-end sequencing (1 50 bp) using an Illumina GA-II sequencer. MK-0518 All of the 2b-RAD sequences had been archived in the SRA data source (accession no. SRA065207). 2.4. Series data preprocessing and genotyping Natural reads were trimmed to eliminate adaptor sequences initial. The terminal 3-bp positions had been excluded from each read to remove artefacts that may possess arisen at ligation sites. Reads without limitation sites or including ambiguous base calls (N), long homopolymer regions (>10 bp), excessive numbers of low-quality positions (>5 positions with quality of <10) MK-0518 or mitochondrial origins were MK-0518 removed. The remaining trimmed, high-quality reads formed the basis for subsequent analysis. 2b-RAD genotyping was performed using the RADtyping program v1.0 (http://www2.ouc.edu.cn/mollusk/detailen.asp?Id=727) under default parameters. The RADtyping program has recently been developed by our group, and it is an integrated pipeline that enables both accurate codominant and dominant genotyping in mapping populations. 2.5. Linkage map construction Segregating markers that could be genotyped in at least 80% of the individuals were considered as high-quality markers and were retained for further analysis. For each segregating marker, goodness of fit of the observed with the expected Mendelian ratio was assessed using the 0.05) were included in map construction. Linkage analysis was performed using the JoinMap 4.0 software.25 Sex-specific maps were first constructed for each parent. Maternal and paternal datasets were created using the function Create Maternal and Paternal Population Nodes in the JoinMap program, which was.