We published new whole-genome restriction mapping technology using "Subhaploid"-Based RAD Sequencing

On July 01, 2017, our group have developed a sequencing-based HAPPY mapping approach called RadMap, which provides an efficient and flexible tool for high resolution physical mapping and genome scaffolding. The new method, published in the journal Genetics, and also selected as the recommended paper.

Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit at tainable map resolution. The HAPPY mapping method, which was invented by Dear and Cook, represents an appealing way to generate high-resolution physical maps in a rapid and cost-effective manner. HAPPY mapping is a genome mapping method that is analogous to classical linkage mapping except that the chromosome breakage and segregation are replaced by in-vitro analogs. It does not require any polymorphic markers and can also be easily adapted to any desired level of resolution. However, because each aliquot in a HAPPY panel contains very little genomic DNA (e.g.3 pg for human DNA; Dear 2005), the lack of faithful amplification of each aliquot DNA to provide enough material for genotyping a large number of markers has been the bottleneck of this method, and this has prevented such a simple and powerful method from coming into general use since it was invented 20 years ago. Here, we develop a new approach by incorporating two major technical improvements to the original HAPPY mapping method: (i) use of fosmid/BAC clone pools as a HAPPY mapping panel to bypass the requirement of PCR-based amplification of each aliquot of DNA, and (ii) use of the 2brestriction site-associated DNA sequencing (2bRAD-seq) (Wang et al. 2012) for high-throughput marker profiling and whole-genome restriction mapping. The new approach, which we called RadMap, provides an efficient and flexible method for high-resolution physical mapping and genome scaffolding.

Professor Zhenmin Bao and Professor Shi Wang are co-corresponding authors of this study. This research was granted by the National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, AoShan Talents Program supported by Qingdao National Laboratory for Marine Science and Technology and Chang Jiang Scholars Program of Ministry of Education.