SRAP analysis of brown planthopper (Nilaparvata lugens) populations maintained on differential rice host varieties

Chaerani, Dadang A, Fatimah, Husin BA, Sutrisno, Yunus M. 2021. SRAP analysis of brown planthopper (Nilaparvata lugens) populations maintained on differential rice host varieties. Biodiversitas 22: 4266-4272. Brown planthopper (Nilaparvata lugens Stål) biotypes differ in virulence to rice varieties carrying different Bph resistance genes. These biotypes are reported can be genetically discriminated against using DNA markers. Four brown planthoppers (BPH) populations, which displayed two virulence phenotypes, have been produced by selection and adaptation on four differential host varieties. Sequence-related amplified polymorphism (SRAP) marker preferentially amplifies the coding regions in the genome and, thus, can discriminate the observed virulence variations among those populations. This study aimed to analyze the genetic variation of four developed BPH populations using SRAP markers. Genetic analysis of a total of 40 BPH females with 18 polymorphic primers revealed equal genetic diversity parameter values among populations (Na: 1.1 to 1.4, Ne: 1.2 to 1.3, I: 0.22 to 0.29, He: 0.14 to 0.18, and UHe: 0.15 to 0.19). Analysis of population structure by AMOVA indicated low genetic variation among populations (9%). Still, pairwise PhiPT population values between all pairs of the population revealed the presence of moderate genetic differentiations (PhiPT ranged from 0.57 to 0.133, P<0.01). Two partial clusters in plots of PCoA were corresponded to two virulence groups, indicating the ability of SRAP markers to discriminate virulence phenotype. Further selection and adaptation are expected can form four desired virulence patterns with complete genetic separation among the population before its application as resistance screening agents of rice lines.

Study of Genetic Diversity of the Aphid Predator Hippodamia variegata (Goeze) in Different Areas of Syria Using SRAP markers

This study was conducted in 2020 at the Laboratory of Biotechnology, Agronomy Department and Research Center for Biological Control Studies, Faculty of Agriculture, Damascus University. This study aimed to determine the genetic diversity of the variegated ladybug aphid predator Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae) collected from different regions in Syria using the SRAP technique (Sequence-related Amplified polymorphism). The number of amplified fragments was 101 bands, 99 of which were polymorphic with a polymorphism rate of 97.99%. The number of polymorphic fragments ranged between two bands by using the primers pair SRAP-12 and 13 bands by using the primers pair SRAP-1, with an average of 6.6 bands for each primers pair. The lowest polymorphism rate was 83.33% for primers pairs SRAP-4 and SRAP-9, whereas the highest polymorphism rate was 100% for the rest of the primers pairs. The results obtained on the degree of genetic diversity of the predator's individuals H. variegata showed that the highest value for percent disagreement values was 0.904 between samples from Damascus and Latakia (Fedio) and Homs and Latakia (Fedio), whereas the lowest value for percent disagreement values was 0.271 between samples from Damascus and Sweida. The phylogenetic tree showed that the studied populations were divided according to their geographical distribution into two main groups; the first group included samples collected from the regions of Damascus, Sweida, and Homs with a genetic distance of 15.51, whereas the second group included samples collected from the regions of Tartous, Jabla (Beit Yashout), and Lattakia (Fedio) with a genetic distance of 11.08. This is the first study to determine genetic diversity of H. variegata in Syria. Keywords: Genetic diversity, predator, Hippodamia variegata, SRAP, Syria

Genetic diversity analysis of Piper betle from eight accessions of Indonesia based on SRAP markers

Nabilla S, Safira UM, Puspita PJ, Subositi D, Maruzy A, Artika IM. 2021. Genetic diversity analysis of Piper betle from eight accessions of Indonesia based on SRAP markers. Biodiversitas 22: 3401-3408. Leaves of betel vine (Piper betle Linn.) have been used as a traditional medicine in various regions in Indonesia. However, the genetic diversity of this plant has not been well recorded. Considering its diverse usage in traditional and folk medicine, it is essential to analyze and document the genetic diversity of Piper betle L. with the aim to collect the scientific data of betel vine genetics in Indonesia. This study aims at analyzing the population structure and genetic diversity of betel vine from the Singkil, Gayo Serbajadi, Baduy, Bandung, Hutan, Kalisusu, Kaledupa, and Mekongga accession groups of Indonesia using the sequence-related-amplified polymorphism (SRAP) marker technique. Genomic DNA was isolated from each accession and then used as a template for DNA amplification using PCR. As many as 16 SRAP primer combinations were screened for the genetic diversity analysis. Optimization of primer combinations resulted in 7 selected combinations based on their ability to generate clear amplification patterns and polymorphic bands. These were then employed for genetic diversity analysis. The genetic distance dendrogram showed the lowest similarity coefficient was 0.62 and that the betel vine grouping pattern was not based on genotype. The Singkil population had the highest genetic diversity and the Hutan population had the lowest. The mean value of Nei's genetic diversity index was 0.0985, while Shannon's information index was 0.01459 and the percentage of polymorphic loci was 25.81. This study concluded that the level of betel vine diversity is low.

Genetic and Flower Volatile Diversity in Natural Populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria: Toward the Development of a Core Collection

We studied the genetic and flower volatile diversity in natural populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers and gas chromatography/mass spectrometry (GC/MS) analysis of flower volatiles from individual plants. Two regions, including the Kresna Gorge and Eastern Rhodopes, typical for the species comprising eight populations and 239 individual plants were included in this study. An analysis with 11 SSR markers and eight SRAP primer combinations showed that SRAP markers were substantially more informative than the SSR markers and were further used for genetic diversity analysis. The results showed low-range to mid-range genetic differentiation between the populations with pairwise fixation index (Fst) values ranging between 0.0047 and 0.11. A total of 10 genetic clusters were identified. An analysis of the flower volatile diversity identified a total of 63 compounds with the vast majority of plants belonging to the carvacrol chemotype and just a single plant to the thymol chemotype. Large deviations were observed for individual compounds within each region as well as within the populations. Hierarchical clustering showed a clear sample grouping based on the two different regions. In addition, an in-depth analysis identified six major and 23 minor metabolite clusters. The overall data set and cluster analysis were further used for the development and testing of a simple and straightforward strategy for the selection of individual plants for the development of a core collection representing the sampled natural populations for this species in Bulgaria. The proposed strategy involves precise genetic clustering of the tested plants followed by the selection of a minimal set from each genetic cluster representing the different metabolite clusters. The selected core set was further compared with a core set extracted by the PowerCore software. A comparison of the genetic and metabolic affiliation of the members of both sets showed that the reported approach selected representatives from each genetic cluster and minor metabolic cluster, whereas some metabolic clusters were unrepresented in the PowerCore set. The feasibility and efficiency of applying the pointed strategy for the development of a core collection representing both the genetic and metabolite diversity of natural populations in aromatic and medicinal plants toward subsequent steps of selection and breeding are discussed.