Development of InDel markers and establishment of a specific molecular marker of the new strain (SW-81) in Pyropia haitanensis

With the increase in the number of new strains (varieties) of Pyropia , the morphological markers are more and more difficult to meet the requirement of germplasm management. However, it is a new approach and trend to develop molecular markers based on genome re-sequencing. In the present study, we developed insertion/deletion (InDel) markers based on the re-sequencing of Pyropia haitanensis , and a specific molecular marker was screened out using polymorphic InDel markers for the germplasm identification of the new strain ( SW-81 ) of P. haitanensis . A total of 8616 InDel sites were detected from the re-sequencing data, of which the short fragments (1–3 bp) were the absolute dominant type, accounting for 81.13%, with an average of one InDel site per 5.92 kb. Moreover, 200 InDel primers were randomly synthesized to analyze the effectiveness, and the 65 pairs of effective primers were finally obtained, of which 40 pairs were polymorphic InDel markers, with the polymorphism amplification rate of 20.00%. A specific molecular marker (InDel-2) was screened out for the germplasm identification of SW-81 strain, and this marker had the same identification effect on the conchocelis , and the blades cultivated at indoor and sea areas. The above-mentioned results showed that there were abundant InDel loci in the genome of P. haitanensis , and the gene sequence of the same loci varied among different strains, showing the polymorphism of amplification products. The polymorphism analysis based on the InDel marker could provide an effective approach for the management and identification of germplasm resources. • There are abundant InDel loci in Pyropia haitanensis genome, and the polymorphism amplification rate is about 20%. • A large number of high-quality InDel markers of Pyropia were developed for the first time. • A specific molecular marker (InDel-2) of the new strain ( SW-81 ) of P . haitanensis was successfully identified.