Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers

Abstract

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10−3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called “clones”, “varieties”, or “cultivars”. Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

“…Additionally, the genetic diversity of olive accessions could be assessed based on newly developed SSR markers, and thus it is possible to select certain cultivars for hybridization to achieve new olive cultivars with potential usefulness. In recent years, DNA fingerprints have been successively established in many plants, such as chrysanthemum, oil camellia, durian, and pistachio (Zhang et al, 2014;Chen et al, 2016;Siew et al, 2018;Mannino, Gentile & Maffei, 2019). In the olive, DNA fingerprinting is considered very important because both the productivity and quality of olive products are intrinsic characteristics of the original cultivars (Muzzalupo et al, 2018).…”

Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

“…The results showed that when the sample size was enlarged, the specific fragments of the single marker would lose their specificity. The application of single marker analysis to identify specific accessions from large samples would be thus restricted [34].…”

Dual Use of a Biopolymer From Durian (Durio zibethinus) Seed as a Nutrient Source and Stabilizer for Spray Dried Lactobacillus Plantarum

“…Fiber and minerals in fruit wastes, have been shown to be able to immobilize L. acidophilus cells during fermentation, which resulted in increased growth (Teh et al, 2009). In addition, many durian types are known to exist, which can be classified based on morphologic characteristics such as seed size and shape (Siew et al, 2018). We therefore extracted DSG from four durian types, with different seed shapes.…”