Genetic Profiling of Sida rhombifolia Originated from Several Indonesian Ethnicities Based on Sequence-Related Amplified Polymorphism Markers

Sida rhombifolia is one of wild flowering plants that grows easily in many habitats with moderate humidity, with some usefulness in traditional medicine. Genetic characterization of Sida rhombifolia accessions originated from 12 ethnicities of Indonesia was analyzed based on Sequence-Related Amplified Polymorphism (SRAP) Markers. The genomic DNA were extracted from leaf samples and then were characterized by using the SRAP marker system according to Li and Quiros (2001). Nine pairs of SRAP primer resulted high polymorphic bands and were used in the genetic profiling. The data analysis was performed using GenAlEx to calculate genetic distance, Principal coordinate analysis, and Analysis of Molecular Variance (AMOVA), also using POPGENE to assess genetic diversity (Hs and Ht) and Nm to predict gene flow among populations. The coordinate analysis showed that the accessions originated from ethnicities along Wallacean line tend to differ genetically from most other locations. However, the results of analysis of molecular variance suggested that there were only slight differences (0.1%) found between ethnicities, while most genetic variances (99.9%) were found mostly among accessions within populations. The results suggested that there was an extensive genetic flow and plant spreading among Sida rhombifolia plant populations, resulting more homogenous genetic characters among most populations, while high diversity within population. The calculation of the number of migration (Nm = 1.7341) confirmed that the high rate of gene flow had occurred between populations.

Genetic Diversity and Molecular Characterization of Worldwide Prairie Grass (Bromus catharticus Vahl) Accessions Using SRAP Markers

Prairie grass (Bromus catharticus Vahl) is an important grass species that could be used in the production systems of certified seed and high-quality forage for grazing ruminants. In the present research, a sequence-related amplified polymorphism (SRAP) marker was employed to detect the genetic variability and structure of 80 prairie grass accessions from all over the world. Altogether, 460 reliable bands were amplified from 47 SRAP primer pairs with 345 (75%) polymorphic bands. The average values of discrimination power (DP) and polymorphic information content (PIC) were 0.753 and 0.317, respectively. Both the UPGMA clustering and PCoA analyses grouped the 80 accessions into five clusters, whereas the STRUCTURE analysis showed that 80 prairie grass accessions possessed three genetic memberships (K = 3). The results of the Mantel test showed that the distance matrix has a moderately positive correlation between the morphological and molecular data sets (r = 0.524). A poor genetic differentiation (Fst = 0.045) was discovered among the six geo-groups of accessions. Besides, the highest intragroup genetic diversity was found in the North America group (He = 0.335). This study provides a genetic structure and diversity case for prairie grass, and supplies new clues for the study and utilization of prairie grass.

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.

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.

Seleksiyonla Elde Edilmiş Bazı Ceviz Genotiplerinde SRAP Tekniği Kullanılarak Genetik Çeşitliliğin Belirlenmesi

Turkey is among the few countries in terms of plant diversity. An example of this situation is the variation in walnut seedlings grown from seed throughout the country. The genetic material to be used in fruit breeding should be original and the genetic relations among the genotypes should be well elucidated. In this research, genetic diversity was investigated among the walnut genotypes selected from Uşak province of Turkey with the use of molecular markers. In this study, molecular results showed that the 19 SRAP primer combinations produced, on average, 171 bands in the accessions examined, of which 77.2% were polymorphic. Base lengths of the bands obtained from markers varied between 100-1500 bp. The similarity ratio of walnut genotypes varied between 0.21 – 0.85. According to the results of the study, it was determined that SRAP marker system can be used to determine genetic diversity among walnut genotypes.

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

China is one of the native places of yams with abundant representative local varieties. However, the genetic differences between these local varieties remains unclear, thus considerably inhibiting their utilization and development. In this study, 26 phenotypic traits of 112 accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. A total of 56 variations of 20 quality traits were detected in 112 accessions, and the most diverse phenotypic trait was stem color. Meanwhile, seven principal components were obtained from 26 phenotypic traits, with a cumulative contribution rate of 69.39%, and all the accessions were divided into six groups by clustering the phenotypic traits. Unweighted pair-group method with arithmetic means and principal coordinate analysis based on SSR-SRAP marker data showed that 112 accessions were also divided into six groups, similar to the result of phenotypic traits but with a slight difference among few accessions. Results of genetic structure analysis showed that 112 accessions could be divided into two groups; one group composed of the accessions of D. opposita, the most abundant resource in China, and the other group was a collection of the other accessions. In addition, the analysis of the origin and genetic relationship of yam also indicated that the specie of D. opposita may have originated in China. These results clarified the genetic differences in yam in China, thereby providing a basis for the identification, evaluation, and conservation of yam resource.

Morphologic and molecular assessments of cucumber (Cucumis sativus L.) landraces

In this study, 90 locally grown cucumber (Cucumis sativus L.) landraces were collected and morphologically characterized using 20 descriptors derived from UPOV (International Union for the Protection of New Varieties of Plants). Genetic diversity and relationships of the genotypes were revealed using 20 sequence-related amplified polymorphism (SRAP) marker combinations. The discrimination power of each polymorphic marker (estimated by the polymorphism information content) ranged from 0.15 to 0.99 with an average of 0.73. Dice's similarity coefficient ranged between 0.00-1.00. The cluster analysis that was conducted using the unweighted pair group method of arithmetic averages (UPGMA) for both molecular and morphologic data showed that all of the genotypes fell into two main groups and many subdivisions. According to morphological data, fruit length, diameter and weight of the genotypes were determined between 6.5 - 32.5 cm, 25 - 52 mm and, 28 - 625 g respectively. It is clear from the results, a moderate level of genetic diversity, which has the potential for broadening the genetic base, was observed among the Turkish cucumber landraces.

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.