Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Abstract

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r=0.78) was better than that of the RAPD marker system (r=0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.

Short Communication: Assessment of genetic diversity in Lai (Durio kutejensis) local cultivars of Batuah (Indonesia) using ISSR marker

“…25 specific bands were formed by 10 ISSR primers consisted of different number of bands as follows; four bands in Lai Bara, one band in Lai Apel, two bands in Lai Kuning, four bands in Lai Belimbing, six bands in Lai Merah, three bands in Lai Besar, four bands in Lai Durian, and one band in Lai Mahakam. According to Cui et al (2016), specific bands can be used to develop the SCAR marker for a molecular identity of different varieties or lines in a further study.…”

“…ISSR markers provided basic genetic knowledge among durian cultivars, and the detailed group of cultivars slightly differed from RAPD markers and the taxonomic characters (Vanijajiva 2012). Furthermore, It does not require the knowledge of the whole DNA sequence for designing DNA primers because it amplifies the specific region of two microsatellite motifs (Cui et al 2016). ISSR have been used to investigate many plants such as sorghum (Basahi 2015), Magnolia wufengensis (Chen et al 2014), genus of Cymbopogon (Baruah et al 2017), Rhododendron trifolium (Xu et al 2017), genus of Lilium (Zhao et al 2014), Andrographis paniculata (Tiwari et al 2016), and Aethionema (Sunar et al 2016).…”

Intra Specific Analysis of Gloriosa Superba (L) Through Issr Finger Printing and Dna Sequencing of Ecotypes Collected From Different Accessions of Tamil Nadu State, India

“…DNA based molecular markers such as ISSR to assess the genetic diversity and phylogentic relationships [21].…”

Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers

“…ISSR markers could amplify and result in many loci for one primer since the inter-SSR regions are spread over and distributed throughout the genome of organisms (Reddy et al 2002). Due to the many advantages of the ISSR markers compared to the other PCR-based DNA markers, the genetic study using this marker is extending throughout the plant species (Gebrehiwet et al 2019;Ghimire et al 2019;Ismail et al 2019;Mohammadi and Bahramikia 2019), macroalgae (Cui et al 2017), fungi (Kandan et al 2016;Mitina et al 2017;Anand and Kapoor 2018), and animal (Perez de Rosas et al 2017;Jasso-Martinez et al 2018;Gu et al 2019).…”