HIGH-RESOLUTION LINKAGE MAPPING AIDED BY GENOME SURVEY AND TRANSCRIPTOME SEQUENCING IN PORTUNUS TRITUBERCULATUS: APPLICATIONS IN GROWTH-RELATED QTL AND GENE IDENTIFICATION

Jianjian Lv a,b,*  Baoquan Gao a,b  Ping Liu a,b  Jian Li a,b
a Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, P.R.China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao,China.
b Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, China.
* E-mail: lijian@ysfri.ac.cn

A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, linkage mapping was constructed for Portunus trituberculatus using specific-length amplified fragment sequencing (SLAF-seq). A high-resolution genetic linkage map with 10,963 markers was obtained, as far as we know, this has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM.

A genome survey and transcriptome sequencing enabled 2,378 explicit annotated markers to be anchored to the map. Quantitative trait locus (QTL) mapping revealed 12 growth-related QTLs with a high mean PVE value of 23.7. Nine genes identified from the growth-related QTL region were considered important growth-related candidate genes. In particular, RE1-silencing transcription factor and RNA-directed DNA polymerase genes encoded nonsynonymous amino acids, which suggests a potential influence in growth regulation.

We have demonstrated that high-resolution linkage mapping aided by genome survey and transcriptome sequencing could serve as an important platform for QTL mapping and the identification of trait-related genes.