Genetic variations among the isolates of Bipolaris Maydis based on phenotypic and molecular markers

Maydis leaf blight, caused by Bipolaris maydis, is an important disease of maize crop in Khyber Pakhtunkhwa (KP) Pakistan. Fifteen isolates of the pathogen, collected across KP, were studied for variability based on phenotypic and molecular markers. Significant variability among the isolates was observed when assessed using phenotypic traits such as radial growth, spore concentration, fungicide sensitivity and virulence. The isolates were classified into six culture groups based on colour, texture and margins of the colony. Conidial morphology was also variable. These were either straight or slightly curved and light to dark brown in colour. Fungicide test showed significant variation in the degree of sensitivity against Carbendazim. Isolate Bm8 exhibited maximum radial growth on carbendazim spiked plates. Conversely, isolate Bm15 showed the lowest radial growth. Variations in virulence pattern of the isolates were evident when a susceptible maize variety Azam was inoculated with spores of B. maydis. Genetic variability amongst the isolates was also estimated by RAPD as well as sequencing of ITS region. The RAPD dendrogram grouped all the isolates into two major clusters. Average genetic distance ranged from 0.6% to 100%, indicating a diverse genetic gap among the isolates. Maximum genetic distance was found between isolates Bm9 and Bm10 as well as Bm2 and Bm8. Conversely, isolates Bm13 and Bm15 were at minimum genetic distance. Phylogenetic dendrogram based on sequencing of ITS region grouped all the isolates into a single major cluster. The clusters in both the dendrogram neither correlate to the geographical distribution nor to the morphological characteristics.

Determination of Genetic Diversity Based on RAPD molecular Marker and ParARF3 Gene Expressions in some Apricot Genotypes in Iraq

Employing DNA markers allowed determining genetic diversity and relationships amongst five apricot genotypes. In this study, two relative gene expressions pertaining to ParARF3 gene, which could be distinguished from the genotypes that were exposed to various concentrations of marine alga treatments. As per our results, screening of seven primers with the DNA of 5 apricot genotypes was done, and six primers were generated while the primer OPN–16 gave negative results. The total quantity of fragments generated by 6 primers was 80 at an average of 13.33 fragments ̸primer. The highest unique percentage band depicted in U-17 touched 23%, and the total number of polymorphic bands touched 17 fragments with the average reaching 2.83 fragments ̸primer. The number of monomorphic lied in the range of 5 to 10, with a total of 47 monomorphic. Primer M 32 yielded the highest number of monomorphic bands reaching 10. Between Zaghenia and Zinni, a maximum genetic distance value of 0.8 was reached with less similarity value of 20%. A minimum genetic distance value of 0.44721 was noted between Kaisy and Baia while the high similarity value touched 55.3%. According to the cluster tree analysis, the genotypes were generally split into two key groups: A and B. The Zinni group, which included one apricot genotype, showed genetic similarity of 20% with the other genotypes present in B group. The B group was split into two sub-clusters B1 and B2 and the genetic similarity reached 44%. The ParARF3 relative gene expression pertaining to Zinni genotypes was second as well as convergent with that of gene expression for Zaghenia genotype results. Baia and Kaisy genotypes lied in between the lowest and highest ParARF3 value gene expression exposed to Marine Alga. These outcomes showed that RAPD markers offer an effectual alternative for the plant species genetic characterisation.

Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

Genetic Characterization of Swamp Eel of Bangladesh Through Dna Barcoding and Rapd Techniques

The freshwater air-breathing swamp eel Monopterus spp. are native to the freshwater of Bangladesh and throughout the Indian subcontinent. To identify the different swamp eel species and to check the genetic diversity among them, a total of twelve swamp eel specimens were collected from four districts (Tangail, Bogura, Bagerhat and Sylhet) representing the four division of Bangladesh. The extracted DNA from twelve fish samples was amplified by the PCR technique for DNA barcoding and RAPD analysis. Among 12 specimens, 8 specimens showed a 95-100% similarity with M. cuchia species published in the NCBI GenBank database and BOLD system. The studied mct3 (collected from Tangail region), mcs1, mcs2 and mcs3 (collected from Sylhet region) specimens showed about 83% homology with Ophisternon sp. MFIV306-10 as per BLAST search; whereas BOLD private database showed 99% similarity with Ophisternon bengalense (Bengal eel). From the phylogenetic tree analysis, 8 samples were clustered with M. cuchia and 4 samples showed similarity with Ophisternon sp. MFIV306-10 and Ophisternon bengalense _ANGBF45828-19. In RAPD-PCR based analysis, it was found that the maximum genetic distance (1.6094) was observed between mcba2 and mcs3, while between mct1 and mct2, the minimum genetic distance was 0.000. A total of 192 bands, of which 35 were polymorphic with 17.88% polymorphisms among swamp eel species and the size of the amplified DNA fragments ranged from 250 to 1800 bp. The information on DNA barcoding and RAPD analysis help measure the genetic diversity among swamp eel species, ensure the reliability of the published taxonomic information, and initiate proper management programs to conserve these vulnerable species to meet future export demand. Asiat. Soc. Bangladesh, Sci. 46(2): 117-131, December 2020

Molecular Characterization of Fusarium oxysporum Causing Chickpea Wilt by Internal Transcribed Spacer (ITS) Marker

Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris is one of the serious disease causes tremendous loss to crop throughout the world and has assumed serious proportions in the recent years. Wilt affected chickpea plant roots samples were collected from forty eight different regions of Maharashtra. The collected samples were characterized by designed ITS primers. The Fusarium oxysporum f. sp. ciceris (Foc) showed about 302 bp amplicon when subjected to PCR with these primers. Further the amplified product was digested with five restriction enzymes viz. AluI, EcoRI, HaeIII, MboI and MspI and restriction fragment length polymorphism (RFLP) pattern were analysed. A dendrogram derived from ITS-RFLP analysis of the rDNA region divided the Foc isolates into four clusters. The maximum genetic distance 0.75 exhibited by five Foc isolates viz. Foc-30, Foc-36, Foc-24, Foc-25 and Foc-48 belonging to Shahartakli, Shelur, Nashik, Satara, Kolhapur regions respectively and found to be more diverse among the other Foc isolates. Whereas isolate no. Foc-20, Foc-21 and Foc-8 from Ambajogai, Karjat and Rahata shown minimum genetic distance (0.13). This showed the genetic variability among the Foc isolates collected from different regions of Maharashtra.

A new black fly (Diptera: Simuliidae) species of the subgenus Asiosimulium Takaoka & Choochote from Thailand

A new black fly species of the subgenus Asiosimulium Takaoka & Choochote of the genus Simulium was recognized from northeastern Thailand based on morphology, mitochondrial DNA and ecology. This black fly species has similar morphological characteristics to Simulium oblongum Takaoka and Choochote that was also described from the same geographic region in all life stages. However, this new species could be distinguished at the adult stage by coloration of the maxillary palp and in the larval stage by the presence of a pigmented subesophageal ganglion that is lacking in S. oblongum. Genetic distance and phylogenetic analyses based on mitochondrial cytochrome c oxidase I sequences clearly differentiated the two species with minimum genetic distance of 3.51%. These species are also ecologically isolated as S. oblongum is found only at low elevation (<650 m above sea level) but the new species occurs only at high elevation (>1,100 m above sea level).

Report of high genetic diversity of filarial worm, Wuchereria bancrofti from endemic region of Eastern Maharashtra (India)

Summary “Filariasis free India” is National Health Policy’s vision. Currently, India has undertaken Mass Drug Administration drive (MDA) to eliminate the filariasis infection. Taking this into account, the emergence of new Wuchereria bancrofti resistant strains against the current choice of drugs cannot be ruled out. In this study, we report the genetic diversity of Wuchereria bancrofti from four districts (Amravati, Nagpur, Chandrapur and Wardha) of Vidarbha, a region in the eastern part of Maharashtra state of India and considered a hot spot of filariasis infections. The RAPD profiles were generated for 21 populations using nine random RAPD primers. The RAPD-PCR based distance matrix shows maximum genetic distance of 0.425 between the parasites from Nagpur and Amravati region and minimum genetic distance of 0.210 between the parasites of Wardha and Nagpur. The tree inferred by Neighbour-Joining (NJ) method shows four distinct clusters. With the single exception of isolates from Amravati, all other clusters show the intermingling of isolates with other districts. Further, the representation of isolates from Chandrapur in three out of four clusters revealed to be a founder and indicates towards the entry of the filarial worm into the Maharashtra state through southern route.

Genetic diversity analysis in different genotypes of black gram [Vigna mungo (L.) Hepper] using RAPD marker

Amongst the various DNA fingerprinting methodologies, randomly amplified polymorphic DNA (RAPD) was used to estimate genetic diversity and relationship amongst 22 black gram genotypes. A total of 25 randomly selected decamers were screened, out of which only 16 got amplified. A total of 133 amplified bands were obtained, out of which 120 were polymorphic. The average percentage of polymorphism was 90.23. The total number of amplified bands varied between 3 (primer OPK-03) and 15 (primer OPC-08) with an average of 9 bands per primer. The overall size of PCR amplified products ranged between 200 bp to 2600 bp. The average PIC was 0.30 ranging from 0.17 to 0.43. Five unique bands (ranging from 200-1200 bp) were detected in four genotypes using 5 RAPD primers. Jaccard's similarity coefficient values for RAPD primers ranged from 0.58-0.85 with an average of 0.71. Based on dendrogram generated through UPGMA method and PCA, most of the genotypes got divided into three main clusters. Genotypes U-17 and STY-2289 were lying close and thus showed minimum genetic distance while genotypes UH-177 and IPU99-233 had minimum similarity value of 0.42, thus showing maximum divergence. Thus, these results could be used to assess other black gram accessions in the Vigna germplasm pool that can provide useful information towards molecular classification and the genetic marker assisted breeding for crop improvement.

Assessment of Genetic Diversity in Bamboo Accessions of India Using Molecular Markers

Bamboo is an important grass with wide scale applications in paper industries, medicines, constructions industries. It is potential feedstock for advanced biofuel production due to its favourable characteristics, natural abundance, rapid growth, perennial nature and higher CO2 sequestration. The objective of this study is to understand genetic diversity between the bamboo accessions with respect to geographical origin to correlate molecular information with feedstock characterization and adaptation to abiotic stress. In this study, genomic DNA was extracted from twenty bamboo accessions collected from different regions of India and genetic variations were assessed by inter simple sequence repeat (ISSR) based molecular marker approach using 8 primers. Maximum genetic distance was observed between Bambusa wamin-Itanagar & B. ventricosa-Durg (0.48221) & minimum genetic distance between Bambusa balcooa-Modasa & Bambusa balcooa-Tripura (0.00787). Bambusa balcooa and Bambusa vulgaris were genetically similar as compared to other accessions. The genetic distance is independent of geographical distance for the bamboo accessions considered in this study. The findings of this study will help to understand the degree of differences between bamboo accessions under the same environmental conditions and to identify the representative accessions that can be used for abiotic stress resistance studies. The information can be explored for screening of closely related bamboo accessions for abiotic stress resistance screening trials.Int J Appl Sci Biotechnol, Vol 3(2): 330-336 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12587

The genetic variability of Hungarian Tsigai sheep

Microsatellite analysis was used to estimate the genetic origin, differences, relationship within 10 Hungarian Tsigai populations. The number of alleles was 262 at the 16 examined locus. Fifteen population specific alleles were detected. The mean number of alleles detected per locus ranged from 4.3 (OarAE119) to 11.9 (MAF70). Genetic distance values were calculated from Nei’s minimum genetic distance (DA) formula. Phylogenetic tree was constructed using UPGMA algorithm. The results indicated that the genetic difference was negligible between the following populations pair-wise: two Hungarian indigenous populations (Kardoskút1-IN and Kardoskút2-IN); the Hungarian indigenous population Soltszentimre-IN and the Milking Tsigai population Akasztó-ZO; the Hungarian indigenous population Csanádpalota-IN and the transitional type population Makó-Rákos-TR. Microsatellite genotyping prooved to be efficient tool for examing the genetic relationships among Hungarian Tsigai populations.