UPGMA Dendrogram Research Articles

Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

High-throughput phenotyping to detect anthocyanins, chlorophylls, and carotenoids in red lettuce germplasm

Some plant pigments are strong antioxidants and benefit human health. Given their low cost and popularity, biofortified lettuce cultivars can promote consumption of these compounds. In this study, we assessed anthocyanin, chlorophyll, and carotenoid content in 30 red lettuce genotypes, as well as the Soil Plant Analysis Development index (SPAD) and vegetation indices (CIG, CVI, GNDVI, and NDVI), using high-throughput phenotyping. We calculated vegetation indices by using images of the plant canopy obtained from a remotely piloted aircraft (RPA) together with a red, green, and near-infrared band camera. The SPAD index and leaf pigments were measured through traditional laboratory methods, which are costly and time-consuming. Genetic variability among the genotypes for leaf pigments was confirmed by the Scott-Knott test and UPGMA dendrogram. Anthocyanin was the pigment that most contributed to genetic diversity and highly correlated with CIG, CVI, and GNDVI. These indices also moderately correlated with chlorophylls and carotenoids. Genotypes with higher pigment content, especially anthocyanin, had higher indices. Therefore, the image-based plant phenotyping technique correlated with the traditional methodology and can provide an alternative for indirect selection of plants with high leaf pigment content, especially anthocyanin, in red lettuce.

The existence of Anoplotrupes stercorosus (Scriba, 1791) (Coleoptera: Geotrupidae) for Turkiye is validated from Gölcük Natural Park in Isparta Province

Recent trip in the forest lands of Gölcük Natural Park revealed a new earth-boring dung beetle record for Isparta province: Anoplotrupes stercorosus. Comparative analysis of partial cytochrome oxidase subunit 1 (CO1) displayed with UPGMA dendrogram confirmed genus Anoplotrupes.

English

An adequate knowledge regarding the genetic issues of natural populations is imperative for developing conservation and stock improvement plans. The present research work was aimed to assess the genetic variability and structuring patterns in six natural populations of Cirrhinus mrigala from Punjab province, Pakistan. The PCR based amplification of targeted loci was carried out by employing a total of 12 microsatellite markers. Based on the study inferences, moderate level of genetic diversity was observed in all the populations. The average number of alleles (Na) varied from 3.750 to 4.416 and those of effective number of alleles ranged between 3.112 to 3.856 in all the examined populations. The mean values of observed and expected heterozygosity were measured as 0.563 to 0.685 and 0.669 to 0.739, respectively. The average values of inbreeding coefficient (FIS) ranged from 0.019 to 0.184. Significant deviation from HWE was detected in 9 out of 72 tests. Among all the population pairs, low to moderate level of genetic differentiation was found. After applying AMOVA, it was revealed that most of the variations (81.15%) lied within individuals. The UPGMA dendrogram resulted in two distinct clusters. The present study inferences would be helpful for setting up effective strategies to avoid the loss of genetic variability in C. mrigala populations.

Genetic Analysis and Selection Criteria in Bambara Groundnut Accessions Based Yield Performance

The knowledge of genetic variability and breeding techniques is crucial in crop improvement programs. This information is especially important in underutilized crops such as Bambara groundnut, which have limited breeding systems and genetic diversity information. Hence, this study evaluated the genetic variability and established the relationship between the yield and its components in Bambara groundnut based on seed weight using multivariate analysis. A field trial was conducted in a randomized complete block design with three replications on 28 lines. Data were collected on 12 agro-morphological traits, and a statistical analysis was conducted using SAS version 9.4 software, while the variance component, genotypic and phenotypic coefficient variation, heritability, and genetic advance values were estimated. A cluster analysis was performed using NT-SYS software to estimate the genetic relations among the accessions. The results showed significant variability among the accessions based on the yield and yield component characteristics. The evaluated lines were grouped into seven primary clusters based on the assessed traits using the UPGMA dendrogram. Based on the overall results, G5LR1P3, G1LR1P3, G4LR1P1, G2SR1P1 and G3SR1P4 performed the best for the yield and yield components. These improved lines are recommended for large-scale evaluation and utilization in future breeding programs to develop high-yield Bambara groundnut varieties.

Morphological and molecular characterization of recombinant inbred lines for dormancy related traits in rice (Oryza sativa L.)

The study was carried out to assess the genetic relatedness of 119 recombinant inbred lines along with their parents BPT 2231and MTU 1001 based on morphological and molecular characterization. Data recorded for 10 morphological characters was used for grouping genotypes into different clusters by using Tocher’s and UPGMA dendrogram methods. Under D2analysis, the genotypes were grouped into 6 clusters and out of 10 characters studied, free amino acids contributed maximum divergence followed by days to 50% flowering and test weight. The genotypes grouped in cluster III recorded strong dormancy both at 5 days and 10 days after harvesting whereas the genotypes of cluster IV recorded maximum grain yield/plant. Four polymorphic markers were used for genotyping of the RIL population and the lines viz.,SD 3, SD 12, SD 15, SD 68, SD 72, SD 87 and SD 113 which were categorized as strongly dormant upto 10 days after harvesting also exhibited similar banding pattern with the dormant parent MTU 1001 when amplified with more than two markers. Among the 119 RIL population studied, SD 12 manifested banding pattern as that of the dormant parent MTU 1001 with all the four polymorphic markers viz., RM346, RM22565, RM7051 and RM10793 under study and also exhibited <10% germination at 10 days after harvesting. The number of alleles detected for each of the 4 polymorphic markers ranged from 2 to 4 per loci with mean value of 2.75 alleles per locus. The dendrogram analysis divided the entire population into two distinct clusters at the distance of 2.25. The RILs viz., SD11, SD12, SD15, SD27, SD30, SD63, SD65, SD68, SD74, SD75, SD80 along with the dormant parent MTU 1001(SD 121) which recorded less than 50% germination and categorized as strongly dormant under phenotyping were grouped in cluster IB2 in molecular analysis thus revealing the similarity between the two methods.

ISSR-Based Genetic Diversity Assessment of Genus Jasminum L. (Oleaceae) from Pakistan.

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon’s information index, polymorphism percentage, effective allele number, Nei’s genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei’s unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.

Genetic variability of cultivated plum (Prunus domestica L. & Prunus salicina Lindl.) in Morocco assessed by ISSR markers

Moroccan plum cultivars were genetically characterized for assessing diversity and relatedness. In this study, a total of 23 plum cultivars were analyzed using 14 Inter-Simple Sequence Repeat (ISSR) primers. A total of 100 bands were obtained, of which 84 were polymorphic (84%). The mean values of PIC, Rp, I and Ht were 0.45; 3.03; 0.42 and 0.27, respectively, implying the important genetic variability between the plum cultivars. Furthermore, the coefficient of genetic differentiation (GST) between all groups was 0.21 indicating that 21 % of total genetic variability was between groups and 79 % was within groups. The UPGMA dendrogram and Bayesian model-based clustering approach identified four gene pools of cultivars independently of their geographic origin and denomination. These results showed that the ISSRs markers can be a useful tool for detecting molecular polymorphism and to survey the genetic diversity in this fruit crop.

Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD

BackgroundLeishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. More analytic methods and data are still needed. Random amplified polymorphic DNA (RAPD) technology can sensitively identify slight intraspecific differences, and it is a powerful tool to seek species-specific markers. This work attempted to identify Chinese Leishmania isolates from diverse geographic regions at the genomic level. Meanwhile, specific markers of the L. donovani complex were also developed by RAPD.MethodsRAPD was applied to 14 Chinese Leishmania isolates from diverse geographic regions and 3 WHO reference strains. The polymorphic sites of amplification were transformed into a data matrix, based on which genetic similarity was calculated, and a UPGMA dendrogram was constructed to analyse the genetic diversity of these Leishmania isolates. Meanwhile, the specific amplification loci of the L. donovani complex were TA-cloned, sequenced and converted into sequence characterized amplified region (SCAR) markers, which were validated preliminarily in 17 available Leishmania strains in this study and analysed by bioinformatics.ResultsThe cluster analyses showed that the three Leishmania sp. isolates SC10H2, SD and GL clustered together and apart from others, the strains of the L. donovani complex clearly divided into two clades, and the three isolates Cy, WenChuan and 801 formed a subclade. Three specific SCAR markers of the L. donovani complex, i.e., 1-AD17, 2-A816 and 3-O13, were successfully obtained and validated on 17 available Leishmania strains in this study. Through bioinformatic analyses, Marker 1-AD17 may have more specificity for PCR detection of VL, and Marker 3-O13 has the potential to encode a protein.ConclusionsThe RAPD results verified that the undescribed Leishmania species causing visceral leishmaniasis (VL) in China was a unique clade distinguished from L. donovani and revealed that there was genetic differentiation among Chinese L. donovani. The identification of L. donovani-specific markers may help to provide a foundation for future research attempting to develop new specific diagnostic markers of VL and identify specific gene functions.

Analysis of genetic divergence in safflower genotypes through morphological characters

The increase in energy consumption in Brazil and in the world generates an increasing need to seek renewable and non-polluting energy, such as biofuels. Safflower (Carthamus tinctorius L.) is a plant with a great oil production capacity and potential for biodiesel production that presents high productivity and easy edaphoclimatic adaptation. It can be an economic culture option in crop rotation practiced by farmers, however it is still necessary to obtain more technical information about its cultivation and about the adapted and improved cultivars. Thus, the estimate of genetic divergence from morphological characters using multivariate techniques has become a common alternative among breeders. In this sense, the objective of this research was to carry out an analysis of the genetic divergence among the 49 safflower genotypes from the germplasm bank of the Instituto Mato Grossense do Algodão (IMA-MT), based on 13 morphological descriptors recommended by the International Board for Plant Genetic Resources - IBPGR (1983) and Ministério da Agricultura, Pecuária e Abastecimento - MAPA (2013). The divergence analysis was performed by means of the dissimilarity matrix based on multi-categorical variables and to identify the most similar genotypes, Tocher's optimization grouping methods and the hierarchical average grouping method between groups were used. The estimates of the dissimilarity coefficients ranged from 0.00 to 0.46, indicating the presence of genetic diversity among the evaluated genotypes. The highest dissimilarity value was between genotypes 29 and 9, 42 and 1, 42 and 32, 47 and 9, which are the most genetically divergent and thus promising materials for future genetic crosses. The UPGMA dendrogram and tocher grouping were partially consistent and effective in grouping safflower genotypes.

Diversity and genetic structure of Spondias tuberosa (Anacardiaceae) accessions based on microsatellite loci

Introduction: Spondias tuberosa is a tree endemic to the semiarid region of Brazil with fruticulture potential. Objective: To estimate the diversity and genetic structure of S. tuberosa accessions from four areas of the semiarid region of Brazil, in order to facilitate conservation genetic resources studies in this species. Methods: DNA was extracted, using the CTAB 2x method, from leaf samples of 24 accessions of S. tuberosa available in the germplasm bank at Embrapa Semiárido, Brazil. Ten microsatellite loci were used in this study. Results: The UPGMA dendrogram, generated with a Jaccard coefficient similarity matrix, contains four groups at a 0.44 cutoff point. The similarity coefficient ranged from 0.30 to 0.84, indicating great divergence among the accessions. A Bayesian analysis conducted with the software Structure suggests there are two subpopulations, one formed by accessions from the Januária region and another by accessions from the Juazeiro, Uauá and Petrolina regions. The ΦST value of 0.12 for the analysis of molecular variance indicates moderate genetic differentiation among the four populations, suggesting that the genetic variability is moderately structured in function of region. Conclusions: Together, the analyses indicate that the genetic diversity of S. tuberosa is not uniformly distributed in the studied regions. Thus, germplasm from a greater number of populations should be collected to increase the germplasm bank genetic diversity of the species.

Genetic diversity of the wild Asian lotus (Nelumbo nucifera) from Northern China

Asian lotus (Nelumbo nucifera Gaertn.) is an aquatic plant with ornamental, cultural, economic, and ecological values. China has abundant germplasm resources of Asian lotus. However, in many areas, the wild Asian lotuses have been destroyed and the germplasms is now facing extinction. In addition, the knowledge of the genetic diversity of the wild Asian lotus in China is poor. To identify and protect the germplasms of Chinese wild Asian lotus, eleven genomic-SSR primers, three EST-SSR primers, and three chloroplast DNA primers were used to investigate the genetic diversity among 69 samples of wild Asian lotus from 25 locations in northern China. The genetic diversity of 27 samples of wild Asian lotus from southern China and other countries, the ancient Asian lotus, Asian lotus cultivars from China, and Asian-American hybrids was also compared. The genetic diversity of the wild Asian lotus from northern China was characterized as medium, and the mean values of observed heterozygosity (Ho) and expected heterozygosity (He) were 0.087 and 0.552, respectively. Based on a UPGMA dendrogram and STRUCTURE analysis, the wild Asian lotus samples in northern China were divided into three groups. The wild Asian lotus samples from northern China contained 16 haplotypes. The Nei's genetic distance between the wild Asian lotus samples from the Songhua River basin and the Liao River basin in northeastern China was relatively small, and these germplasms might be relatively primitive compared to those from other regions. This study provides essential information regarding the genetic diversity of the wild Asian lotus resources in northern China, and provides a basis for further analysis of population-level genetic evolution through high-throughput sequencing.

Cysteiniphilum marinum sp. nov., isolated from coastal seawater.

Six aerobic Gram-negative bacteria were isolated from seawater in Guangdong Province, P.R. China. Cells were observed to be Gram-negative, aerobic, non-motile and non-spore forming. Growth of the designated type strain 19X3-30T occurred at a temperature range of 14-37°C (optimum, 28°C), a pH range of 6.0-8.0 (optimum, pH 7) and up to 7.5% NaCl (optimum, 1.5%; w/v), and was enhanced by CO2 and L-cysteine supplementation. The major polar lipids identified in strain 19X3-30T were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The principal cellular fatty acids profile showed the presence of anteiso-C15:0, anteiso-C17:0 and C18:0 (> 8% of total fatty acids), and the respiratory quinone was ubiquinone 8 (UQ-8). According to the analysis of 16S rRNA gene sequences, these strains represented a novel species within the family Fastidiosibacteraceae, sharing maximum similarities with Cysteiniphilum litorale DSM 101832T (96.6%) and Cysteiniphilum halobium DSM 103992T (95.3%). Phylogenetic dendrograms based on 16S rRNA gene and protein marker genes from the genomic sequences both indicated that the strains formed a monophyletic lineage closely linked to the genus Cysteiniphilum, which was also supported by the UPGMA dendrogram based on the MALDI-TOF MS profile. The genomic DNA G + C contents of six strains ranged from 38.0% to 38.1%. Based on different taxonomic genomic metrics, phylogeny and phenotypic features, we propose that the strains warrant the assignment to a novel species, for which the name Cysteiniphilum marinum sp. nov. is proposed. The type strain is 19X3-30T (= KCTC 82154T = CGMCC 1.18585T).

Comparative palynology and taxonomic implication of Jasminum L. (Oleaceae) species from Pakistan on the bases of scanning electron microscopy.

Jasminum L. is the largest genus containing ~200 species found wild mostly in the tropical regions of the world. The comparative palynological study of nine Pakistani Jasminum species with SEM showed zonocolpus, trilobate, and tricolpus pollen types with simple endocolpus apertures which are plesiomorphic and conserved in the Jasminum species. The equatorial pollen view was prolate, subprolate, and perprolate with elliptic, lobate, subcircular whereas polar view was subtriangular in all species. Few characters were specific to some species like heteropolarity in Jasminum grandiflorum and foveolate exine ornamentation with rounded heterobrochate in Jasminum angulare whereas reticulate and angular homobrochate character was common in other species. The UPGMA dendrogram based on qualitative characters did not support the phylogenetic classification of the genus Jasminum as these are highly conserved. The quantitative data showed more variation in some characters whereas few characters showed little or no variation. A greater variation in pollen size was observed among the variants of same species, for example, Jasminum humile showed highly variable polar length and equatorial diameter as compared to other species. Minimum variation was observed in colpus length which divided all species in to two groups. The large lumina were specific to Jasminum nitidum and broader muri was the prominent characteristic of Jasminum angulare. Some species like Jasminum sambac and Jasminum azoricum were unable to develop true pollen due to structural or functional disabilities. So, the quantitative characters of pollen are only suitable for palynological based grouping of Jasminum species but less suitable to infer their evolutionary relationship.

Molecular Diversity Analysis of Somaclonal Variants of Potato (Solanum tuberosum L.) by Random Amplified Polymorphic DNA Markers

Aims: An experiment was conducted to analyze the DNA fingerprinting and genetic diversity of nine potato (Solanum tuberosum L.) somaclonal variants and three check varieties.
 Place and Duration of Study: The experiment was carried out at the Biotechnology laboratory of the Department of Biotechnology, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh during November, 2013 to December, 2014.
 Methodology: The somaclonal variants investigated were SIP-3, SIP-5, SVP-6, SVP-18, SVP-19, SVP-25, SVP-55, SVP-56 and SVP-68, while the check varieties were Cardinal, Diamant and Asterix. Six RAPD primers were used to perform PCR reaction after genomic DNA was extracted from young leaves.
 Results: The selected 6 primers produced total 54 distinct and differential amplified DNA bands of size range 88 bp to 3265 bp, where 47 bands (~87%) were polymorphic and 7 bands (~13%) were monomorphic. The pair-wise inter-genotype similarity indices were ranged from 61.59% to 93.55% with an average of 74.31%. The Nei’s genetic distance among 12 potato genotypes was estimated from 0.0972 to 0.6217 whereas, genetic identity was between 0.5370 and 0.9074. Here, the distantly linked accessions among the somaclonal variations with check varieties were SVP-6 (to Cardinal and Diamant) and SVP-25 (to Asterix). In addition, the UPGMA dendrogram segregated the 12 potato genotypes into two broad clusters containing 8 and 4 genotypes, respectively. Furthermore, the dendrogram also displayed the highest genetic distance between SVP-6 vs SVP-68 genotype pair.
 Conclusion: Significant relationship and diversity were found among the studied 12 genotypes. This genetic diversity among the potato genotypes would be utilized for further potato improvement.

Morphological and genetic polymorphism of the introduced population of Prunus pumilaL. in Chelyabinsk Province

Background.Studying genetic polymorphism of the Prunus pumilaL. representatives with a wide range of variability in morphological characters will make it possible to identify promising genotypes with high combining ability for hybridization.Material and methods.The study covered 39 genotypes from the Chelyabinsk cultivated population and 6 genotypes from Khakassia, with extreme or intermediate expressions of such characters as fruit size, color and shape; stone shape and surface structure; leaf blade serration and shape; plant habitus, and some others. Genetic distances were calculated using the data matrix for binary states of presence (1) or absence (0) of amplified fragments with the Past Program (Gower). The UPGMA dendrograms were obtained in TREECON (version 1.3b).Results and discussion. The selected 5 ISSR and 2 RAPD primers demonstrated their effectiveness in detecting genetic polymorphism in the studied accessions. In individual cases, a weak connection of separate markers with leaf blade edge serration, stone surface structure, plant habitus, and geographic origin of the genotype was detected. Concurrent inclusion of all primers and genotypes in the cluster analysis failed to group the studied P. pumilasamples into clades according to the presence/absence of any traits, which may attest to their close genetic affinity. An independent clade with reliable bootstrap support (100%) was formed only for the genotypes of the taxonomically close sp. P. tomentosaThunb., analyzed as an external group. Moreover, this clade manifested (with the 86% reliability of bootstrap support) differences between the hybrid genotypes of P. pumila× P. tomentosa(F3) and the genotype of P. tomentosa. Parent pairs promising for fruit quality and shrub shape improvement through breeding were identified using the produced indices of genetic distinction.

Genetic diversity of local durian from Tidore Island based on morphological and moleculer data for tropical fruit conservation in North Maluku

Durian is a tropical fruit that has substantial economic value. One of the durian production centers in North Maluku is Tidore Island. This study’s objective was to identify genetic diversity, taxonomic status, and local durian conservation models in North Maluku. Data collection method with purposive sampling technique. Morphological data, including 142 characters (stems, leaves, flowers, and fruit), were analyzed descriptively and arranged by UPGMA dendrogram with the outgroup (D. kutezensis). Molecular data were obtained by using the PCR RAPD technic. Genetic diversity of local durian Tidore based on morphological characters produced 7 clusters with the closest genetic distance to local durian (R4-R10) with a similarity value of 0.887. Genetic diversity of local durian Tidore based on PCR RAPD technic produced 5 clusters with the closest genetic distance to local durian (R10-R12) with a similarity value of 0.977. The value of Tidore’s local durian dissimilarity is close to 10%; it can be assumed that the genetic diversity of Tidore’s local durian is at the level of intraspecies diversity. Gap analysis recommends that Tidore’s local durian conservation model is appropriate with the durian breeding program through an in-situ selection of superior traits and conservation..

English

DNA fingerprinting is rapid, easy, and efficient method for discrimination, identification and characterization of various genotypes for protection of plant breeder’s rights (PBRs). Present study was designed for DNA fingerprinting and genetic diversity assessment of 25 GM cotton genotypes (possessing Cry1Ac gene) using 297 SSR markers through conventional PCR and Polyacrylamide gel electrophoresis. Out of 297 SSR markers, 25 markers were not amplified, 28 were monomorphic and 244 were polymorphic. A total of 1537 alleles were amplified among which 1294 (84.18%) were polymorphic. PIC value in our study ranged from 0.08 to 0.93 with an average of 0.73. Unique allelic pattern was observed for nineteen genotypes whereas six genotypes were identified using two-step identification methods. The UPGMA dendrogram divided the genotypes into two distinct clusters. Cluster I was comprised of 20 genotypes whereas cluster II was comprised of four genotypes. MNH-1020 did not obey any clustering and remained separated. The results of the structure analysis were complementary to cluster analysis and the population was divided into two subgroups. Our results evidenced narrow genetic base of the cotton genotypes cultivated in Punjab Pakistan due to use of common parents in the pedigree/parentage. Further, we proposed a core set of markers for future DNA fingerprinting and genetic diversity studies. The information generated in this study will be helpful in variety registration and subsequent protection under PBRs. Further our findings will be useful in selection of SSR markers for future studies which are focused on DNA fingerprinting and genetic diversity assessment. © 2021 Friends Science Publishers

Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits.

The online version contains supplementary material available at 10.1007/s12298-021-00978-4.

Assessment of genetic diversity in sea buckthorn (Hippophae rhamnoides L.) accessions from Mongolia based on RAPD markers

Hippophae rhamnoides L., which belongs to the Elaegnaceae family, is one of the medically and environmentally valuable berry crops with its high nutritious and bioactive compounds. Despite its high demand in the food, medicinal and agricultural industries, this species has been less studied molecularly. In view of this, an effort has been made in the present study to characterize 24 accessions of H. rhamnoides collected from different geographical regions of Mongoliaa through random amplified polymorphic DNA (RAPD) markers. A total of 10 RAPD primers were used in the present study for their ability to produce clear, scorable amplicons. The RAPD analysis totally generated 87 bands, of which 84 (96.34%) were polymorphic, pointing to a high degree of genetic variation. The similarity coefficient ranged from 0.4-1 with the mean of 0.78. The UPGMA dendrogram was generated using these data grouped accessions into two main clusters. Cluster analysis reflected a relatively close relationship between accessions grown at the same or neighbouring areas. Thus, our data could be informative for further selection and management of germplasm collections and crossing strategies for sea buckthorn.