Genetic diversity analysis of lactic acid bacteria isolated from regional yogurt samples

Probiotics are live, non-pathogenic microorganisms which have enormous health benefits. Yogurt is a potential source of probiotic bacteria. Lactic acid bacteria are the most common and major group of probiotic bacteria that can be found easily in different dairy products. The aim of study was the genetic diversity analysis using random amplified polymorphic DNA (RAPD) marker from regional yogurt samples of Bangladesh. Ten probiotic isolates from yogurt samples of different sweet meat shops of Sylhet and Mymensingh Divisions of Bangladesh were used. Morphological and biochemical tests were performed to ensure the presumptive probiotic characteristics of isolated bacteria. All isolates were cultured in De Man, Rogosa, and Sharpe (MRS) medium to exhort the growth of lactic acid bacteria. Genomic DNA was extracted by Ampicillin Lysozyme Tandem method. Four random RAPD primers were used in this study for detecting genetic diversity of these isolated bacteria. Among them, OPA 18 showed the maximum number of reproducible bands. Nei’s genetic distance was performed for determining Pair-wise Genetic Distance. UPGMA and NJ dendrogram were performed based on molecular data showing that all the isolates could be divided into two major clusters. Data analysis revealed that isolates from the same location were closely related and showed less genetic variation whereas, isolates from geographically different regions exhibited more genetic diversity. Bang. J. Livs. Res. Vol. 27 (1&2), 2020: P. 55-63

Geographical Survey and Genetic Variation Studies of Few Chilly Varieties Collected from Different Regions of Karnataka, India

Chillies are widely used throughout the world in the form of spice and are also used in making beverages and medicines. They are rich in vitamins, especially in vitamin A and C. Chillies contain lots of minerals like potassium, magnesium, and iron. They have been employed for pain relief as they are known to inhibit pain messengers and hence their extracts are used to alleviate the pain of arthritis, headaches, burns, and neuralgia. It is also claimed that they have the power to boost the immune system and lower cholesterol. They are also helpful in getting rid of gut parasites. In this regard we attempted to do a geographical survey about the chilly varieties and chilly growing states in India. We collected the local varieties of chillies available in Karnataka and performed genetic variation studies to understand their relationship at the genetic level. PCR analysis was done using the selected random amplified polymorphic DNA (RAPD) marker to identify the polymorphic loci between the genotypes taken. DNA Barcoding was done to validate the species using basic local alignment search tool (BLAST) and Clustal Omega, further dendrogram was constructed which guide the joining linkage rule of unweighted pair group average (UPGMA) and the genetic distance to compute from matrix table. The results obtained highlight the relationship between species of Capsicum annum, Capsicum frutescens which are closely related followed by Capsicum pubescens and Capsicum baccatum providing knowledge about its application in genetics and plant breeding in developing efficient hybrid variety.

Evaluation of Genetic Diversity in Ocimum spp. using Agro-morphological Traits and RAPD Marker

In the present study, morphological and genetic diversity is revealed among the four species of Ocimum. Among the morphological characters plant height, the number of leaves, leaf area, leaf width, leaf length, stem circumference and mitotic index studied and contributed a greater proportion of variations. RAPD markers revealed a high degree of polymorphism (88.89%) among the species of Ocimum. Dendrogram study revealed that the species O. gratissimum and O. basilicum are very closely related whereas O. kilimandscharicum and O. sanctum are distantly related in the phylogenetic history.

A Study on the Genetic Variation in Licorice (Glycyrrhiza glabra) Iran by Molecular DNA Markers (RAPD)

Thirty ecotypes of licorice (a medicinal plant) from all of Iran were collected and genetically evaluated. To assess the genetic diversity of licorice, genomic DNA was extracted using Winnepenninckx method (CTAB method). 12 random primers were used to perform PCR. All 12 primers showed obvious and repeatable bands. Totally, 1343 bands were produced. Bands size varied from 250 to 5000 bp. Percentage of polymorphism and polymorphic loci was 88.83% and 95.5%, respectively. The highest number of band was related to primer OPN-08 (band 188). The highest similarity between Esfaraien and Bojnourd ecotypes is equal to 0.647. Kermanshah and Orumieh ecotypes had the lowest similarity that was 0.3. Dendrogram divided 30 ecotypes into 5 groups in terms of genetic distance. Generally, surveying the variation in genotypes of licorice using RAPD marker showed that this marker can be useful in identifying the polymorphism, estimating the genetic distance, and managing germplasm.

Sex identification in Nepenthes adrianii from Baturraden Botanical Garden: Genetic analysis using RAPD Markers

Nepenthes adrianii is one of pitcher plant species that grows endemically in Mount Slamet, Central Java. At present, it is one of pitcher plant collections of Baturraden Botanical Garden. Since N. adrianii is dioecious and both sexes are difficult to distinguish morphologically, early sex determination supporting its conservation at Baturraden Botanical Garden is needed. One approach can be performed with the use of RAPD molecular markers. Hence, this study aims to know whether differences in RAPD pattern between male and female N. adrianii exist or not and also to find out what the differences are. Genomic DNAs were extracted from leaves of 4 males, 2 females, and 2 sexually unidentified individuals. The extracted DNAs were then used to analyze DNA variation between male and female N. adrianii employing RAPD technique. As many as five oligonucleotide primers (OPA-15, OPK-16, OPP-15, OPP-08, and OPO-08) were used to amplify N. adrianii DNA. The results showed that one primer, i.e. OPK-16 (5’-GAGCGTCGAA-3’), produces a specific band of approximately 290 bp which is only found in female plants. It is assumed that this band is related to gene(s) controlling sex determination in N. adrianii. The RAPD marker can be used for the sex determination of young N. adrianii seedlings.

Assessment of Genetic Stability of Micropropagated Bambusa balcooa Roxb. using RAPD Marker

Bambusa balcooa Roxb. was in vitro propagated by optimizing protocol using nodal segment from secondary branches with 100% success in MS liquid media containing 100 mg/l Myo-inositol, 3% sucrose supplement with 4.4 - 26.64 μM BAP for shoot multiplication, and 2.69 - 32.26 μM NAA for root induction. The highest shoot multiplication (14.53 ± 0.33 folds), shoot length (5.9 ± 0.6 cm), shoot number per explants (4.0 ± 0.24), and rooting (89.3 ± 0.33%) was obtained in MS liquid media supplement with 13.32 μM BAP (shooting) and 26.88 μM NAA (rooting) and 1% aqueous leaf extract of Artemisia vulgaris L. (EAV). Twenty RAPD (Random amplified Polymorphic DNA) primers were used individually to amplify DNA of tissue culture-raised plants and the mother plant where 8 primers yielded monomorphic banding patterns with reproducible, clear, scorable bands (2.8 per primer) ranging from 250 to 1800 bp respectively which revealed the micropropagated plants of B. balcooa retained their genetic stability. Plant Tissue Cult. & Biotech. 31(1): 81-95, 2021 (June)

Genetic analysis of Sperata sarwari (Singharee) population fragmentized by Physical barriers in the Indus drainage system of Punjab, Pakistan.

Physical barriers like head works, dams barrages are main cause of fragmentation and declining of freshwater fish population in natural habitat. Present study focused on RAPD marker technique to assess the genetic variability among and between the populations of endangered sperata sarwari (Singharee) inhabited in the Indus drainage system of Punjab. Total eight populations (80 speciemen) of S. sarwari were collected from the up and downstream of four Rivers (Chenab, Jhelum, Ravi and Indus) of Punjab. Genomic DNA isolated from muscle tissue of adipose side and ten RAPD marker were used, which produced 50 scorable bands with average band ranging from 250–1050 bp which used for further genetic analysis of S. sarwari. Downstream Indus population of S. sarwari showed highest values of observed alleles (na), effected alleles (ne), Nei’s diversity (h), Shannon index (I) and polymorphism which indicated that downstream Indus population was more genetically variant. The genetic variability (0.5124) and genetic flow (0.4758) among the eight population S. sawari was observed. The up and downstream population showed the highest genetic distance (0.5738) and lowest genetic similarities (0.5634) which indicated complete isolation of Ravi population from other six population. Dendrogram showed that up and downstream Ravi population was completely isolated from the other six up and down stream population of S. sarwai. Overall results indicated that the presence of high fragmentation in River Ravi caused the destruction of habitat and decline in population of S. sarwai in the River Ravi.

Molecular Markers (RAPD and SSR) Based Characterisation of Genetic Diversity and Population Structure of Moss Hyophila Involuta

Genetic relationships among 24 genotypes of Hyophila involuta collected from five different natural populations of Mount Abu (Rajasthan) is analysed using RAPD and SSR markers. Based on efficiency parameters calculated for each marker system such as polymorphic information content (RAPD = 0.34; SSR = 0.66), marker index (RAPD = 2.78; SSR = 2.62) and resolving power (RAPD = 8.13; SSR = 2.23), the RAPD marker system shows higher values for some indices but microsatellites are more accurately reproducible than RAPD. Moreover, in case of the SSR, the average number of alleles was almost twice compared to RAPD. Mean coefficient of genetic differentiation between populations with RAPD was Gst = 0.269, while with SSR marker was Fst = 0.224. The UPGMA cluster analysis assembled genotypes into two main clusters with diverse levels of sub-clustering within the clusters. Also, the Mantel test showed no significant correlation between geographical and genetic distances. The observed moderately high genetic variability can be explained by efficient spore dispersal. Other factors such as reproductive mode, somatic mutation, continuous propagule recruitment and high degree of intermingling have great impact on the level of genetic variability in moss populations.