Sequence-related Amplified Polymorphism Research Articles

Genetic polymorphism between and within Mediterranean and Red Sea populations of the green turtle (Chelonia mydas) as revealed by sequence-related amplified polymorphism (SRAP)

Genetic polymorphism between and within Mediterranean and Red Sea populations of the green turtle (Chelonia mydas) as revealed by sequence-related amplified polymorphism (SRAP)

Development of SCAR Markers to Identify Medicinal Cultivars of Paeonia lactiflora.

Paeoniae Radix, the dried root of Paeonia lactiflora, is one of the most important ingredients in Kampo medicine. It is known that Paeoniae Radix is derived from various P. lactiflora cultivars, including medicinal and horticultural cultivars, and that cultivar identification by DNA analysis has been unsuccessful. We attempted to develop sequence characterized amplified region (SCAR) markers as useful DNA markers for the identification and herbal medicine authentication of two cultivars developed in Japan, 'Bonten' and 'Kitasaisho,' which are two superior medicinal strains of P. lactiflora. Sequence-related amplified polymorphism (SRAP) analysis was conducted on fourteen P. lactiflora cultivars, and polymorphic fragments specific to 'Bonten' or 'Kitasaisho' were detected. Then, SCAR markers for 'Bonten' and 'Kitasaisho' were developed from the sequence information of these polymorphic fragments. Thirty cultivars of P. lactiflora and five herbal medicine samples were used to validate the specificity of the developed SCAR markers. As a result, we confirmed that our SCAR markers can identify 'Bonten' or 'Kitasaisho' from the plant samples and the herbal medicine samples. Thus, we have successfully designed two highly specific DNA markers and established an easy, rapid, and cost-efficient method to identify specific cultivars of P. lactiflora. Our SCAR markers are expected to contribute to the maintenance of P. lactiflora cultivars such as 'Bonten' as superior medicinal strains, the development of more elite cultivars in the future, and the deterrence of outflow of original cultivars to foreign countries.

Genetic diversity and population structure of Moroccan Botrytis spp. strains, causing chocolate spot disease in faba bean

Chocolate spot (Botrytis spp.) is one of the most important foliar diseases limiting the yield and seed quality of faba bean (Vicia faba L.) worldwide. Knowledge of the population structure of the pathogen is key to developing appropriate breeding strategies for disease management. This study aims to assess the genetic diversity and population structure of 75 Botrytis spp. isolates collected from seven major faba bean growing regions in Morocco. Genetic diversity was assessed using 30 Sequence Related Amplified Polymorphism (SRAP) primer combinations. Eight primer-combinations generated 118 polymorphic alleles and had discriminated between different isolates with an average PIC value of 0.28. The Moroccan Botrytis spp. populations presented a high genetic diversity that was more distributed within populations (99%) than among populations. Population structure analysis revealed that the genetic diversity was not linked to geographic locations, indicating limited geographic delimitation and significant gene flow. The data will be useful to improve the faba bean breeding program to develop effective resistant cultivars. To our knowledge, this is the first study carried out on the genetic variability of Botrytis spp. Isolates from faba bean In Morocco.

Analysis of Hypericum accessions by DNA fingerprinting and flow cytometry

Hypericum perforatum, H. umbellatum, H. maculatum, and H. hircinum accessions originating from botanical gardens across Europe were examined by flow cytometry and molecular markers. 2C DNA content of 17 Hypericum perforatum accessions (Hp) and the H. perforatum cultivar Topaz amounted to between 1.56 pg and 1.62 pg. In four Hp accessions some individual plants were found with a DNA content corresponding to 6Cx (2.34 - 2.39 pg). All plants of accession Hp8 showed a DNA content of 6Cx (2.41 pg). In root tips of Hp plants with an average DNA amount of 1.58 pg, 32 chromosomes were detected, corresponding to 2n = 4x. This is the first ploidy and/or DNA content report for H. umbellatum, H. maculatum and H. hircinum. H. umbellatum and H. maculatum, each contained 0.76 pg DNA and 16 chromosomes were counted. The 2C DNA content of H. hircinum was 1.00 pg with the best metaphase plate revealing 32 chromosomes. Additionally, a combined marker analysis, based on inter-simple sequence repeats (ISSR) and sequence related amplified polymorphism (SRAP), was conducted to gain a better understanding of diversity especially within the accessions of H. perforatum. A total of 27 (11 ISSR and 16 SRAP) primer combinations were screened, showing 699 bands, of which 661 were polymorphic. UPGMA clustering revealed that accessions from the same geographic area tended to be more closely related, while H. maculatum was grouped separately from all H. perforatum accessions. Both methods have shown similar sensitivities in detecting the genetic diversity of the analyzed genotypes. Our results may be useful for Hypericum breeding programs and the development of effective conservation strategies.

Morphological and molecular characterization of banana clones growing in Turkey

This study was conducted to estimate genetic relationships among banana clones growing in Turkey via some morphological parameters and two molecular marker systems. In terms of yield parameters such as bunch weight, hand number, fruit weight, and total fruit number, Grand Nain (GN) clone came to the forefront with the highest values. It was followed by Azman (AZ), Dwarf Cavendish (DC), and Erdemli Yerli (EY) clones, respectively. To see the variation between clones more clearly, 24 RAPD (Random Amplified Polymorphic DNA) primers and 48 SRAP (Sequence Related Amplified Polymorphism) primer combinations were used in molecular analysis. The total number of amplified bands was 194, and 142 of them were polymorphic for RAPD analysis. The total and polymorphic bands per primer ranged from 0 to 14. A total of 272 bands were obtained from SRAP analysis, of which 154 were polymorphic. The total number of bands per primer varied between 0 and 11, and the number of polymorphic bands varied between 0 and 10. According to the dendrogram formed by unweighted pair group method with arithmetic averages (UPGMA) analysis, clones were collected in two main groups. In all evaluation methods, EY was completely separated from the other clones. GN, DC, and AZ were gathered on a single branch in the dendrogram. As a result of the SRAP assessment, DC and GN were the closest related clones. Contrary to the SRAP results, GN and AZ were identified as the most genetically related clones in morphological and RAPD assessments. This study showed that morphological and molecular characterization could be useful to assess the relationship among banana clones.

Molecular characterization of wild carob (Ceratonia siliqua L.) genotypes by sequence-related amplified polymorphism (SRAP) techniques in turkey

Carob (Ceratonia siliqua L.) with limited widespread in Turkey is considered as secondary forest tree. In this study, molecular characterizations were made for 508 genotypes of seven different carob populations colelcted from Eagean, Western and Eastern Mediterranean regions of Turkey with the aid of sequence-related amplified polymorphism (SRAP) technique. Identification of wild carob genotypes, relativity levels and genetic variations among them were performed. Genetic similarities among 508 wild carob genotypes collected from Eagean, Western and Eastern Mediterranean regions of Turkey varied between 0.20-1.00 and there was a large variation among the genotypes. The genetic similarities among 250 wild carob genotypes collected from Aegean region varied between 0.36-1.00. The genetic similarities among 154 wild carob genotypes collected from Western Mediterranean region varied between 0.23-1.00. The genetic similarities among 102 wild carob genotypes collected from Eastern Mediterranean region varied between 0.21-1.00. Through the molecular analyses conducted with SRAP primers, besides the large variations among the entire genotypes, large variations were also observed between the genotypes of different regions. With this study, genetic variations were put forth among the wild carob genotypes naturally growing in different regions of Turkey. It was concluded based on present findings that marker system could reliably be used to put forth genetic variations among wild carob genotypes.

Analysis of leaf morphology variation and genetic diversity via SRAP markers for near-threatened plant Acer truncatum

To fully protect and utilize Acer truncatum resources, the phenotypic variation and genetic diversity of A. truncatum in different regions should be understood. In this study, leaves of A. truncatum trees from 15 provenances were used as experimental materials to analyze leaf morphological variation and genetic diversity at the molecular level. The results showed that the sizes of leaves of A. truncatum trees from different provenances were significantly different, and there was a certain correlation with the geographical environment: leaf size gradually decreased with increasing longitude, latitude and elevation. According to principal component analysis (PCA), the variation in leaf morphology among provenances concerned mainly the petioles, leaf width, and leaf length; there was no correlation between leaf morphological variation and geographic distance. From 240 pairs of sequence-related amplified polymorphism (SRAP) primer combinations, 12 pairs that met the conditions were identified, and a total of 267 bands were amplified; 252 of the bands were polymorphic, with a polymorphism percentage of 94.38%, and an average of 22.25 bands and 21 polymorphic bands were amplified from each pair of primers. Ne, H and I indicated that A. truncatum has relatively high genetic variation and a rich genetic diversity at the species level. Among the provenances, H and I were 0.1754 and 0.2707 respectively, indicating that the genetic diversity among the provenances of A. truncatum was low. There were differences in genetic diversity parameters among the various sources. Yongji, Shanxi (6) had the highest genetic diversity, and Huixian, Gansu (15) had the lowest genetic diversity. The genetic similarity coefficients among the various sources ranged from 0.8404 to 0.9558, the range of variation was 0.1154, and the average coefficient was 0.9006. The provenance of Taian, Shandong (4) and Yongji, Shanxi (6) had the closest genetic relationship, with a genetic similarity coefficient of 0.9558 and a D of 0.0824; Pingquan, Hebei (2) and Huixian, Gansu (15) were the most distantly related, with the largest D , and a genetic similarity coefficient of 0.8404. Cluster analysis based on the genetic similarity coefficient also showed that the D s and geographic distances of A. truncatum from different provenances were not correlated. These results provide a reference for research on A. truncatum germplasm management and ecological adaptability. • The leaf size gradually decreased with increasing longitude, latitude, and elevation. • The leaf morphology variation was mainly in the petioles, leaf width, and leaf length. • Among the provenances, H and I were 0.1754 and 0.2707, respectively. • The D s and geographic distances from different provenances were not correlated.

Morphometric analysis and genetic diversity in Hedera L. (Araliaceae) species populations using sequence related amplified polymorphism

In temperate latitudes across Europe, North Africa, and Asia, the genus Hedera L. colonizes forest understory and riparian vegetation. The goal of this research was to investigate SRAP (Sequence-related enhanced polymorphism) markers in overall 70 successions of Hedera types, that is comprised of three species Hedera helix L.; Hedera colchica (K.Koch) K.Koch and Hedera pastuchovii Woronow. Overall, 76 (Number of total loci) (NTL) DNA bands were created via polymerase chain reaction amplifications (PCR) amplification of three Hedera types. These bands were obtained by combining five distinct selective primers. The overall amount of amplified varied from 10 to 18. The projected impartial gene diversity (UHe) ranged from 0.013 (Hedera colchica) to 0.34 (Hedera colchica) (Hedera helix). The genetic similarity of three varieties is considered to be between 0.63 to 0.90. The clustering findings revealed two main groups. Hedera helix and Hedera colchica have the least affinity in the SRAP (Sequence-related amplified polymorphism) indicators study. Our findings revealed excellent molecular recognition of every genotypes tested, indicating that the Hedera accessions exhibit a lot of genetic variation. This discovery might be useful in breeding control techniques for genetic preservation and cultivar growth.

Gene flow and genetic diversity in Consolida (Ranunculaceae) using sequence related amplified polymorphism

The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. Iraq is one of the richest countries for the genus in South-West Asia. The genetic diversity was assessed through Sequence-related amplified polymorphism. To uncover genetic diversity and species characteristics in Consolida species, were studied through a molecular data. Seventy individuals related to five Consolida were collected in 5 provinces. A total of 75 (Number of total loci) (NTL) DNA bands were produced through polymerase chain reaction amplifications (PCR) amplification of five Consolida species. These bands were produced with the combinations of 5 selective primers. Present results showed that sequence-related amplified polymorphism have the potential to identify and decipher genetic affinity in Consolida species. Current results have implications in biodiversity and conservation programs. Besides this, present results could pave the way for selecting suitable ecotypes for forage and pasture purposes in Iraq.

Assessment of Genetic Diversity and Population Structure of the Endangered Astragalus exscapus subsp. transsilvanicus through DNA-Based Molecular Markers.

Astragalus exscapus L. subsp. transsilvanicus (Schur) Nyár. (Fabaceae) is a rare plant endemic to the Transylvanian Plateau, represented by 24 identified populations. Limited information on the genetic variation and population structure is available, which obstructs efficient measures for conservation strategy. The present study aimed to analyze the genetic diversity and population structure of eight populations of A. exscapus subsp. transsilvanicus revealed by sequence-related amplified polymorphism (SRAP) markers. A total of 164 bands were amplified, 96.7% of which (159) were polymorphic. Nei’s gene diversity index (He) was estimated to be 0.228 at the population level and 0.272 at the subspecies level. The genetic differentiation among populations (Gst) was 0.165, which indicated a low proportion of total genetic diversity. The analysis of molecular variance (AMOVA) indicated that 17% of the total variation of A. exscapus subsp. transsilvanicus is found among the populations, while 83% was found within the populations. A UPGMA dendrogram, principal coordinate analysis, and the STRUCTURE software grouped the populations into two clusters uncorrelated with the provenience of the 125 individuals, which might be attributed to fragmentation processes, insect pollination, population size, and specific environmental conditions of the habitats.

Study on morphological and genetic diversity of Rehmannia glutinosa cultivated in Japan.

It is said that Rehmannia glutinosa is grouped into two types, Akaya and Kaikei, in Japan. However, previous reports of genetic analysis of R. glutinosa in commercial products suggest the existence of varieties other than these two, and therefore, it is inappropriate to simply classify them into these two varieties. In this study, we clarified the diversity of R. glutinosa cultivated in Japan on the basis of morphological observation and genetic analysis. We conducted principal component analysis (PCA) of R. glutinosa morphology, including leaf surface color, leaf undersurface anthocyanin coloration, root shape, and the ratio of string root. We also performed (1) sequence-related amplified polymorphism (SRAP) analysis and (2) polymorphism analysis of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) gene region. We were able to separate Akaya type from Kaikei type, and to divide Kaikei type into three small groups. These two gene analysis methods were also useful in estimating the patrilineal and matrilineal strains of a hybrid origin. Our findings revealed that Akaya type and Kaikei type can be distinguished on the basis of morphological and genetic analyses, and that Kaikei type cultivated in Japan exhibited morphological and genetic diversity.

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 Population Structure of Moroccan Isolates Belong to Alternaria spp. Causing Black Rot and Brown Spot in Citrus.

Alternaria alternata is one of the most important fungi causing various diseases on citrus worldwide. In Morocco, Alternaria black rot (ABR) and Alternaria brown spot (ABS) are two major diseases causing serious losses in commercial cultivars of citrus. The aim of the present work was to study the genetic diversity and the population structure of isolates belonging to sect. Alternaria obtained from infected citrus fruits, collected from seven provinces at different locations in Morocco (markets, packinghouses, and orchards). Forty-five isolates were analyzed by sequence-related amplified polymorphism (SRAP) markers, and cluster analysis of DNA fragments was performed using UPGMA method and Jaccard coefficient. Cluster analysis revealed that isolates were classified in four distinct groups. AMOVA revealed also a large extent of variation within sect. Alternaria isolates (99%). The results demonstrate that no correlation was found among SRAP pattern, host, and geographical origin of these isolates. Population structure analyses showed that the Alternaria isolates from the same collection origin had almost a similar level of admixture.

Genetic diversity and relationships among populations of jackfruit, an underutilized nutrient-rich climate-smart fruit tree crop in Kenya and Uganda

ABSTRACT Jackfruit (Artocarpus heterophyllus Lam.) is an underutilized fruit tree crop in East Africa. Despite its importance for food and nutritional security, only limited information exists on the extent of genetic variability among Ugandan and Kenyan jackfruit populations. This study was aimed at analyzing the extent of genetic diversity in jackfruit germplasm from selected regions of Kenya and Uganda. A total of 30 mature fruit samples were collected randomly from three districts (Kampala, Wakiso and Mbale) in Uganda and five counties (Siaya, Kwale, Mombasa, Busia, and Murang’a) in Kenya. Genetic characterization was using six simple sequence repeat (SSR) and nine sequence-related amplified polymorphism (SRAP) markers. The results revealed that 62.50% of the loci for SSR and 82.14% for SRAP markers were polymorphic. The average polymorphism information contentwas 0.48 for SSR and 0.56 for SRAP markers. The Jaccard’s similarity coefficient ranged from 0.55 to 1.0 for SSR and from 0.33 to 0.93 for SRAP markers, indicating considerable genetic diversity among jackfruit germplasm. Based on combined SSR and SRAP data, analysis of molecular variance revealed greater genetic diversity within the populations (76%) than among the eight populations (24%). Dendrogram and principal coordinate analysis separated the germplasm into two clusters, with several intermediates. The germplasm distribution among the clusters and sub-clusters was not associated with the geographical region. The significant genetic variability existing in Ugandan and Kenyan jackfruit germplasm can be used to improve jackfruit through breeding. The substantial genetic diversity should enable jackfruit breeders to develop high-yielding varieties with improved quality traits.

Development of molecular markers lınked to QTL/genes controllıng Zn effıcıency.

Zinc (Zn) deficiency is a widespread problem in reducing the yield and quality of crop plants worldwide. It is important to utilize molecular markers linked to Zn efficiency to develop high Zn efficient cultivars in pepper (Capsicum annuum L.). In present study, genetic map was constructed using a F2 populations derived from C. annuum L. (Alata 21A) × C. frutescens L. (PI 281420) cross. The quantitative trait locus (QTLs) for Zn efficiency were mapped using F2:3 population. A genetic map with 929.6cM in length and 12 linkage groups were obtained using 62 markers (31 sequence-related amplified polymorphism (SRAP), 19 simple sequence repeat (SSR) and 11 random amplified polymorphic DNA (RAPD) markers). The 41 linked QTLs related with nine (9) Zn efficiency characters were mapped on linkage groups. Results suggest that selecting plants for tolerance to Zn deficiency are expected to be rather responsive among segregating populations for breeding and developing Zn efficient genotypes in pepper. The molecular markers are expected to aid selection and expedite breeding peppers resistant to Zn deficiency in soils low for available Zn contents.

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

Abstract. 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.

Local Rice Genetic Relationship Kuantan Singingi District Using Sequence-Related Amplified Polymorphism (SRAP)

Rice (Oryza sativa L.) is an important food crop that is the staple food of more than half of the world's population because it contains nutrients that the body needs. Information on the genetic diversity of local rice scattered in the Kuantan Singingi Regency is still not available. Due to this fact, the genetic diversity of local rice can be identified by DNA analysis. A DNA-based molecular marker that can be applied as a plant genetic marker is SRAP. The SRAP (Sequence Related Amplified Polymorphism) marker system is one of the powerful molecular tools for the clarification of individual sex and estimating the genetic diversity of plant species. This study aims to determine the genetic relationship of rice plants in the Kuantan Singingi Regency through SRAP markers. Twenty-four (24) local genotype samples were used in this study. Observational data were processed using Ms. software. Excel and (NTSYS-pc) version 2.02. The results obtained 17 fragments in Primer M, which resulted in a similarity analysis between 71% to 100%. There are two (2) groups at 75% similarity, then there are five (5) groups at 81% similarity and there are four (4) groups that have 100% similarity. The results of this study are expected to be taken into consideration in developing rice breeding strategies in the future.

SRAP Molecular Markers Linked to Three Morphological Traits in Egyptian Bread Wheat (Triticum aestivum L.)

Sequence Related Amplified Polymorphism (SRAP) molecular technique was used for assessing the genetic diversity of eight Egyptian bread wheat (Triticum aestivum L.) genotypes. Five SRAP primers combinations were able to expose the polymorphism between the studied genotypes. The percentage of polymorphism (P %) ranged from 40 to 79.90 %. Furthermore, the Polymorphic Information Content (PIC) values for SRAP primers combination varied from 0.11 to 0.31 with an average of 0.19. The ME5F-EM2R and ME1F-EM2R primer combination cleared higher levels of polymorphism of 66.67 and 76.90%, respectively. The results of Single Marker Analysis (SMA) showed that the SRAP marker ME1-EM21320bp could be considered probably as candidate marker linked to spike length in the tested genotypes. Moreover, ME1-EM2900bp and ME1-EM2575bp could be considered as markers linked to plant height and tillers number /plant traits, respectively. Results of Single Marker Analysis (SMA) showed significant marker-trait associations for spike length (P= 0.04), plant height (P= 0.02) and number of tillers/plant (P= 0.03). Me1F-Em6R850bp marker could be also considered as candidate markers probably linked to plant height, with a specific fragment of 850bp for the tolerant genotype (P1). UPGMA cluster analysis based on SRAP markers separated the studied wheat genotypes into three significantly different clusters. The dendrogram based on morphological traits divided the studied wheat genotypes into two different clusters. The Mantel test revealed that there was a positive but non-significant correlation between the genetic similarities based on phenotypic data and SRAP marker (r = 0.36, P> 0.05).

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

Abstract. 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.