Genetic characterization and authentication of Dimocarpus longan Lour. using an improved RAPD technique

Abstract

ABSTRACT. Dimocarpus longan Lour. is an edible and traditional herb in China, commonly referred to as longon. An improved randomly amplified polymorphic DNA (RAPD) protocol was here developed in order to determine the geographical origins of D. longan samples collected from 5 provinces in the southern and southwestern areas of China, including Sichuan, Hainan, Fujian, Guangdong, and Guangxi. Generally, the improved RAPD method generated good fingerprinting of the 5 samples using the selected 17 primers. In particular, primers SBS-A5, SBS-A13, SBS-I9, SBS-I20, SBS-M1, and SBS-Q12 produced distinguishable bands that clearly separated all 5 cultivars, suggesting that there are variations in RAPD genetic sites among the samples. The similarity index ranged from 0.69 to 0.76. The Sichuan and Hainan clades clustered together with a 0.73 similarity index. The Guangxi and Fujian clades clustered together with a 0.76 similarity index, and they formed the sister clade to the Sichuan/Hainan clade with a 0.71 similarity index. The Guangdong clade was in a basal polytomy with a 0.70 similarity index. Based on the abundant DNA polymorphisms, these longan accessions are distinguishable using our improved RAPD technique. Therefore, RAPD analysis is an effective technique in distinguishing the geographical origins of D. longan. Moreover, the improved method could also be employed for a variety of applications including genetic diversity and fingerprinting analyses.

Development and significance of RAPD-SCAR markers for the identification of Litchi chinensis Sonn. by improved RAPD amplification and molecular cloning

“…These technologies can help systematic biologists identify cultivars, species and populations [19]. RAPD is one of the frontline techniques, and in recent years, a number of plants or other organisms have been characterized by standard and improved RAPD analysis [3,13,21,22,23]. The technology has also been found to help study genetic diversity in newly found or modified species [24,25,26,27,28].…”

“…SCAR markers usually have a high level of polymorphism owing to higher annealing temperatures, and longer primers with sequence specificity [17]. When RAPD is combined with SCAR markers, the procedure becomes a simple PCR analysis using PCR primers designed from the sequence of RAPD amplicons [13,16,17], as indicated in our earlier research [18,19,20,21]. In this study, we used DNA samples of L. chinensis collected from Fujian, Hainan, Guangdong, Guangxi and Sichuan, and a DNA sample of Dimocarpus confinis from Guangxi to improve RAPD amplification from our previous study [13].…”

Development of novel SCAR markers for genetic characterization of Lonicera japonica from high GC-RAMP-PCR and DNA cloning

“…One of the limitations of this technique is the lower level of repeatability of banding patterns if the amplification reactions are not optimized (Williams et al, 1990;Agarwal et al, 2008). In our previous studies we used an improved RAPD technique with a prolonged RAMP time, which increased the band numbers, repeatability, and DNA production (Fu et al, 2000;Mei et al, 2014;Fu et al, 2015), as confirmed by ISSR . We successfully used high GC-content primers with a GC content of 8-10 nucleotides over a length of 10 oligonucleotides (80-100% GC content of nucleotides) and improved RAPD (high GC-RAMP-PCR), to further increase the RAPD specific bands and the amplifying efficiency.…”

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning

“…A sequence-related amplified polymorphism analysis by Sun et al (2006) revealed significant genetic variation between G. lucidum and G. sinense. Zhao et al (2003) showed 80-100% polymorphism in genetic materials in different Ganoderma species, and Mei et al (2014b) showed high levels of genetic distance between G. gibbosum, G. tropicum, G. sinense, and G. lucidum. This high genetic variability enabled the generation of species-specific SCAR markers.…”