Polymorphic Fragments Research Articles

Ecological and genetical diversity of black fungus- Aspergillus sp. inhabiting stone monuments of Mughal dynasty in Agra (UP) analysed by RAPD method

Biodeterioration is an inevitable degradation inflicted to the soil of buildings by microbial colonisation. Due to their tremendous enzymatic behaviour and their capacity to cultivate fungi, sculptures, cement and other items used for ancient works of art may be occupied and decayed. Culture-independent techniques have been utilized globally today, and microbial work that focuses entirely on approaches to cultivation cannot be deemed accurate. Using RAPD analysis, the microbial variability and community characteristic of isolated microorganisms is identifiable. Our work aims to identify the filamentous fungi that colonize the different sampling sites using the RAPD method to explore the diversity and occurrence patterns of the filamentous fungi that colonize different stone monuments. Out of the fifteen primers used, the average number of fragments detected is 8.73 and 8.47 and average no. of polymorphic fragments is 6.80 and 6.06 for Aspergillus niger and Aspergillus fumigatus, respectively.

Association analysis of prolactin and prolactin receptor genes with selected productive and reproductive traits in Egyptian buffalo

A total of 266 records of buffalo raised in two experimental herds in Egypt were assessed to detect prolactin (PRL) and prolactin receptor (PRLR) genes’ polymorphism using PCR-Single Strand Conformational Polymorphism (SSCP) and PCR-Restricted Fragment Length Polymorphism (RFLP) techniques as well as to investigate their association with calf birth weight (BW), weaning weight (WW), lactation period (LP), total milk yield (TMY), stillbirth, calving ease (CE), gestation length (GL), postpartum interval to pregnancy (PPIP), calving interval (CI), and age at first calving (AFC). Predicted breeding values were estimated and used in the association with detected genotypes. A monomorphic pattern of the studied PRL 156 bp segment was recorded and absence of its polymorphism in buffalo was corroborated. We also determined polymorphism of PRLR reflected in three loci: PRLR2, PRLR4, and PRLR9. Significant differences among PRLP9 genotypes (AA, AB, and BB) were displayed for all studied traits as well as among PRLR2 genotypes, except for CE, while PRLR4 genotypes significantly differed only in BW, WW, TMY, stillbirth, GL, and AFC. In practice, strong associations among genotypes of the PRLR gene and the traits of interest candidate this gene to be selective in Egyptian buffalo breeding for improving both productive and reproductive traits.

Specific shoot formation in Miscanthus saccharif lorus (Poaceae) under different environmental factors and DNA passportization using ISSR markers.

The generic complex Miscanthus Anderss. (Poaceae) is a unique example among herbaceous plants characterized by high values of growth of aboveground vegetative mass and practical use as a valuable source of alternative energy. Miscanthus is one of the most eff icient solar energy accumulators, and since phytomeliorative use implies the cultivation of these resource plants in inconvenient and semi-shady areas, the question about the effect of insuff icient lighting on the productivity of Miscanthus arises. As a result of a long-lasing introduction effort, the Central Siberian Botanical Garden SB RAS created a population of Miscanthus saccharif lorus (Maxim.) Benth., which has good prospects for growing under the conditions of the forest-steppe area in Western Siberia. The goals of our study were: (1) to determine the peculiarities of shoot formation, (2) to assess the cellulose and lignin accumulation in M. saccharif lorus populations under different lighting conditions and (3) to perform a DNA passportization of the Miscanthus population by ISSR marking. Evaluation of shoot formation and the amount of accumulated cellulose and lignin in plants was carried out under different degrees of illumination: one variant was grown in a sunny area, and the other, in partial shade. As a result of analysis of variance, it was found that the number of shoots does not depend on environmental conditions, but on the age of the plant, while environmental conditions have a signif icant effect on plant height. Although the samples of both M. saccharif lorus variants were characterized by different rates of creation of a continuous projective cover, plants in semi-shaded areas formed up to 89.34 % of shoots compared to their peers in illuminated areas, which did not affect signif icantly the size of the aboveground mass and the cellulose content in it. As a result of ISSR-analysis of genomic DNA in the M. saccharif lorus population, unique molecular polymorphic fragments were identif ied, which can be used for identif ication and DNA passportization at the inter-population level. Thus, the complex use of M. saccharif lorus as a valuable meliorative and bioenergetic culture is due to the high adaptive potential of this species. It was found that the illumination factor has virtually no effect on the amount of the cellulose content in the shoot, and a reduced content of the technologically undesirable lignin was observed in plants growing in the partial shade conditions.

Genetic and Chemical Diversity of Edible Mushroom Pleurotus Species.

The genus Pleurotus is one of the most widely cultivated and edible mushrooms with various cultivators. Three molecular characteristics were used to evaluate the genetic diversity of 132 tested samples. Phylogenetic analysis showed five clades for tested samples of the genus Pleurotus by the combined ITS and LSU sequences with strong bootstraps and Bayesian posterior probability supports. A total of 94 polymorphic fragments ranging from 10 to 100 bp were observed by using an intersimple sequence repeat (ISSR) marker. The DNA fragment pattern showed that P. ostreatus cultivator (strain P9) was clearly distinguished from wild strain based on their clear banding profiles produced. DNA GC content of the genus Pleurotus varied from 55.6 mol% to 43.3 mol%. Their chemical composition was also determined, including sugar, amino acid, polar lipid, mycolic acid, quinone, and fatty acid, which presented some high homogeneity. Most of the tested samples contained mycolic acid; glucose and arabinose as the main sugars; aspartic acid, arginine, lysine, tyrosine, and alanine as the main amino acids; and C16:0, C18:0, C18:2cis-9,12, anteiso-C14:0, and summed feature 8 as the main fatty acids. In addition, their polar lipid profiles were investigated for the first time, which significantly varied among Pleurotus species. The genus Pleurotus contained menaquinone-6 as the sole respiratory quinone, which showed a significant difference with that of its closely related genera. These results of this study demonstrated that the combined method above could efficiently differentiate each Pleurotus species and thus be considered an efficient tool for surveying the genetic diversity of the genus Pleurotus.

Exploring single nucleotide polymorphisms in GH, IGF-I, MC4R and DGAT1 genes as predictors for growth performance in dromedary camel using multiple linear regression analysis

Understanding the genetic factors influencing the growth traits of animal is very important for an accurate selection and genetic improvement of these quantitative traits. Therefore, the aim of this study was to identify polymorphisms in growth hormone (GH), insulin-like growth factor-I (IGF-I), melanocortin-4 receptor (MC4R) and diacylglycerol O-acyltransferase 1 (DGAT1) genes and their association with body weight and daily gain in dromedary camels. Blood samples were collected from seventy camels using vacutainer tube containing EDTA as an anticoagulant for DNA extraction. PCR-DNA sequencing approach was performed to investigate polymorphisms in fragments for 5’ UTR of GH (286-bp) and part of coding sequence (CDS) of IGF-I (462-bp), MC4R (512-bp), and DGAT1 (390-bp) genes. Results revealed that there were single nucleotide polymorphisms (SNPs) in the investigated genes between the enrolled camels except for IGF-I gene that elicited a monomorphic pattern. The identified SNPs allocated camels into different groups according to which animal harbored the explored SNPs. Using multiple linear regression analysis (MLR), identified SNPs had a significant effect on body weight and weight gain at different age stages. Determination coefficients (R2) value indicated that variability in the phenotypic measurements of growth performance might be correlated with the identified SNPs in growth related genes. The area under the ROC curves was higher in the case of DGAT (0.793-1.0), followed by GH (0.736-0.866) and then MCR (0.410-0.545). DGAT anticipates body weight and weight gain traits better than GH and MCR. As a pilot study, single nucleotide polymorphisms in the investigated genes could be used as proxy predictors and genetic markers that permit a marker assisted selection for growth traits in dromedary camels.

The Efficiency of Long Primers Compared to The Short Primer for RAPD Technique in Date Palm

Random Amplified Polymorphic DNA (RAPD) applies single arbitrary short primers (8-12nucleotides) to produce many amplified discrete DNA. Limited reports and studies were done onthe use of long primers (over 12 bases). This study was performed to investigate the potential valueof long primers (15-21 bases) for generating RAPD polymorphisms. We compared both short andlong primers in RAPD assays of two date palm cultivars grown in Malaysia: Ajwa and Barhi. Thenumber of produced polymorphic fragments ranged in order from 2 and 38 bands for short andlong primers in Ajwa. Meanwhile, more polymorphic fragments were generated by long primersin Barhi, which were 50 and only five bands for short primers. 18-mer GY107 and 20-mer CO4primers yielded 100% polymorphism in Ajwa and Barhi, respectively. Moreover, long primersproduced more DNA fragments and a wider range of DNA fragment sizes (from 140-1600 bp,with respect to 300-1000 bp obtained with 10-mer primers). Hence, a significant correlation wasobserved between primer length and the number of polymorphic fragments within the long primergroup, suggesting that increasing primer length above 15 bases may demonstrate enhancedproduction of more polymorphism.

Molecular characterization of traditional mango germplasm of coastal Andhra Pradesh using RAPD markers

A study was conducted at Horticultural research station, Venkataramannagudem for evaluating the variability of mango germplasm to conserve the elite ones and to identify the superior genotypes using molecular markers for future crop improvement. Genetic variation and relationship among 34 traditional mango germplasm were analyzed using Random Amplified Polymorphic DNA (RAPD) markers. Fifteen out of the twenty primers screened were informative and 177 amplified DNA bands with sizes ranging from 100 - 5000 bp were selected as RAPD markers. The number of amplified fragments varied from 3 (OPG 13) to 20 (OPX 04) with an average of 11.8 polymorphic fragments per marker. Specific RAPD markers for some mango germplasm were identified. Unweighted Pair Group Method using Arithmetic means (UPGMA) cluster analysis grouped all the germplasm into two clusters with a genetic similarity coefficient range of 0.67 to 0.88. The accessions within the germplasm i.e., Banganapalli -1, Banganapalli -2 and Banginapalli-3 showed genetic similarity which is in good agreement from a single ancestor with their putative pedigrees. The genotypes Panukula Mamidi and Rajamamidi were closely clustered since these two genotypes are native to the Vizianagaram district. Similarly, the genotypes Nuzividu Tiyya Mamidi and Nuzividu Rasalu occurred in the same cluster indicated that these genotypes also originated from the same geographical area, it can be concluded that they were separated into the cluster based on geographic origin. This study showed clearly that germplasm from coastal Andhra Pradesh unveiled maximum diversity and indicated the potential of RAPD markers for the identification of mango germplasm for breeding purposes. Keywords: Cluster analysis, Dendrogram, Mango, Polymorphic information content and RAPD markers

Genetic diversity analysis of Moroccan saffron (Crocus sativus L.) of different origins based on intermicrosatellite markers

Saffron (Crocus sativus L.) is an autumnal herbaceous triploid plant; it is the source of saffron spice, recognized as the most expensive spice in the world. In this study, genetic diversity among 14 saffron accessions collected from different ancestral geographic areas in Morocco, Greece and France, has been assessed using inter-simple sequence repeats (ISSRs) markers system. Ten ISSR primers were amplified, a total of 143 fragments of which 44.05 % are polymorphic with an average of 6.3 polymorphic fragments per each primer and average of polymorphic information content (PIC) of 0.236. ISSR markers proved to be a powerful tool for assessment of genetic diversity among saffron accessions. Cluster analysis using unweighted pair group method with arithmetic mean (UPGMA), based on Jaccard’s similarity coefficient and supported by the principal coordinate analysis (PCoA), divided the studied accessions into three major groups, and showed that genetic distance is independent of geographical distance. In this paper, we report for the first time the level of genetic diversity among Moroccan saffron; this information allows an unequivocal development of a suitable approach for the conservation of C. sativus germplasm and reduce its genetic erosion.

DNA polymorphisms of FGFBP1, leptin, κ-casein, and αs1-casein genes and their association with reproductive performance in dromedary she-camels

In livestock, selection programs on reproductive traits are time consuming due to long generation interval and low heritability; however understanding the genetic factors that influence reproductive performance facilitates an accurate selection and genetic improvement of these quantitative traits. Therefore, the aim of this study was to identify the effect of lactation order and polymorphisms of FGFBP1, leptin, κ-casein, and αs1-casein genes on reproductive performance in dromedary she-camels. Blood samples were collected from one hundred she-camels using vacutainer tube containing EDTA as an anticoagulant for DNA extraction. PCR-DNA sequencing approach was performed to investigate the polymorphisms in fragments for coding sequence (CDS) parts of FGFBP1 (539-bp) and leptin (359-bp), 5′-flanking region of κ-casein (488-bp) and intervening non-coding fragment spanning from exon 4 to exon 6 (924-bp) of αs1-casein genes. Results revealed that there were single nucleotide polymorphisms (SNPs) in the investigated genes between enrolled she-camels except for leptin gene that elicited a monomorphic pattern. The identified SNPs allocated camels into different groups according to which animal harbored the explored SNPs. Multiple linear regression analysis (MLR) reveled that identified SNPs and parity order had significant effects on age at first calving (AFC), days open (DO), calving interval (CI), number of services/conception (NS/C) and milk yield traits. Determination coefficients (R2) value indicated also that variability in the phenotypic measurements of studied traits might be correlated with the identified SNPs in the reproduction related genes. This study highlights that parity order has a remarkable effect on reproductive performance. Single nucleotide polymorphisms in the investigated genes could be also used as proxy predictors and genetic markers that permit a marker assisted selection for reproductive performance traits in dromedary she-camels.

Development of Molecular Markers Associated with Resistance to Gray Mold Disease in Onion (Allium cepa L.) through RAPD-PCR and Transcriptome Analysis

Onions (Allium cepa L.) are one of the most consumed vegetable crops worldwide and are damaged by several fungal diseases in the field or during storage. Gray mold disease caused by the necrotrophic pathogens Botrytis cinerea and Botrytis squamosa is a disease that reduces the productivity and storage life in onions. However, it is difficult to control gray mold disease in onions by using physical and chemical methods. Breeding resistant onions against gray mold disease can reduce the damage caused by pathogens, reduce the labor required for control, and reduce environmental pollution caused by fungicides. However, onions have a large genome size (16Gb), making them difficult to analyze, and have a biennial cycle, resulting in a very long breeding period. Therefore, in this study, markers were developed to shorten the onion breeding period. First, random amplified polymorphic DNA (RAPD) was performed to confirm the genetic relationship between the gray mold disease-resistant and -susceptible lines through a dendrogram. In addition, the sequence characterized amplified region (SCAR)-OPAN1 marker to select resistant lines was developed using a polymorphic RAPD fragment. Second, the RNA-seq of the gray mold-resistant and -susceptible onion lines were analyzed using NGS technology. Using the RNA-seq results and DEG and GO analyses were performed, and the variants, such as SNPs and indels, were analyzed to develop a selectable marker for the resistant line. This study developed the SNP-3 HRM marker for selecting gray mold disease-resistant lines by using the SNPs present in the aldo-keto reductase (AKR) gene with high expression levels in these lines. The SCAR-OPAN1 and SNP-3 HRM markers developed in this study could be used to select gray mold disease-resistant onions in breeding programs to reduce the damage caused by gray mold disease.

ISSR genotyping of Phoenix theophrasti natural populations in Turkey and Crete (Greece) and P. dactylifera

Intraspecific and interspecific diversity between Phoenix theophrasti individuals (92 from Turkey and 70 from Crete, Greece) and P. dactylifera specimens (28 from Turkey) were investigated by inter‐simple sequence repeat (ISSR) analysis. A total of 45 polymorphic fragments, 360–3454 bps long, were produced. Intraspecific diversity for P. dactylifera was 26.63% and similarities ranged between 0.5 and 1. In the constructed dendrogram, P. dactylifera specimens clustered together in the first main group, outside branches consisting of P. theophrasti samples that generated the second main group. The intraspecific diversity for Turkish P. theophrasti populations was found to be 18.60% and for Cretan populations 13.45%. Antalya–Kumluca–Karaöz samples were grouped outside the branches of the remaining P. theophrasti samples. All three Cretan populations formed their own, separate branch. Datça–Eksera Stream samples together with two Datça–Hurmalıbük specimens constituted a group excluding Datça–Hurmalıbük and Bodrum–Gölköy specimens. Five Bodrum–Gölköy genotypes were clustered separately. Gene flow (Nm) values among populations were estimated from 0.157 to 59.615. AMOVA analysis revealed the percentages of variance among and within Phoenix populations: 73% and 27%, respectively. The first three principal coordinate components accounted for 37.60, 29.32 and 20.04%, respectively, thus the total variance obtained from the first three principal coordinate components was 86.96%. A positive correlation between geographic and genetic distances of populations was detected by Mantel tests (Rx,y = 0.44, p = 0.04). The populations were classified into four clusters by STRUCTURE analysis, supported the PCoA data. To conclude, ISSR results support that P. dactylifera and P. theophrasti are different species. Moreover, the findings not only revealed relationships between natural Phoenix theophrasti populations but also supported the identification of the P. theophrasti individuals that are phenotypically differentiated in the divided Bodrum–Gölköy population (P. theophrasti subsp. golkoyana).

Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers

BackgroundRosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. ResultsFourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. ConclusionCluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.

Study of Genetic Diversity of the Aphid Predator Hippodamia variegata (Goeze) in Different Areas of Syria Using SRAP markers

This study was conducted in 2020 at the Laboratory of Biotechnology, Agronomy Department and Research Center for Biological Control Studies, Faculty of Agriculture, Damascus University. This study aimed to determine the genetic diversity of the variegated ladybug aphid predator Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae) collected from different regions in Syria using the SRAP technique (Sequence-related Amplified polymorphism). The number of amplified fragments was 101 bands, 99 of which were polymorphic with a polymorphism rate of 97.99%. The number of polymorphic fragments ranged between two bands by using the primers pair SRAP-12 and 13 bands by using the primers pair SRAP-1, with an average of 6.6 bands for each primers pair. The lowest polymorphism rate was 83.33% for primers pairs SRAP-4 and SRAP-9, whereas the highest polymorphism rate was 100% for the rest of the primers pairs. The results obtained on the degree of genetic diversity of the predator's individuals H. variegata showed that the highest value for percent disagreement values was 0.904 between samples from Damascus and Latakia (Fedio) and Homs and Latakia (Fedio), whereas the lowest value for percent disagreement values was 0.271 between samples from Damascus and Sweida. The phylogenetic tree showed that the studied populations were divided according to their geographical distribution into two main groups; the first group included samples collected from the regions of Damascus, Sweida, and Homs with a genetic distance of 15.51, whereas the second group included samples collected from the regions of Tartous, Jabla (Beit Yashout), and Lattakia (Fedio) with a genetic distance of 11.08. This is the first study to determine genetic diversity of H. variegata in Syria. Keywords: Genetic diversity, predator, Hippodamia variegata, SRAP, Syria

Molecular detection of Rickettsia in ectoparasites (Siphonaptera and Phthiraptera) of domestic and feral pigs from Argentina.

Rickettsioses are distributed among a variety of hematophagous arthropods, and represent an emergent threat. The presence of rickettsial bacteria in ectoparasites collected from pigs from Argentina is still unknown. This study investigated the presence and identity of Rickettsia spp. in fleas, Pulex irritans, and sucking lice, Haematopinus suis, of domestic and feral pigs, Sus scrofa, from Central-Northern Argentina, through the genes gltA and ompB. Rickettsial bacteria were detected in 50% of fleas and 24% of lice. The BLASTn analysis of the ompB gene fragments in P. irritans samples showed identities 99% and 100% with R. felis. Positive samples of H. suis were 99% similar with species from the spotted fever group, future amplifications of a more polymorphic fragment of the ompB gene will allow to corroborate the identity of the Rickettsia species present in these lice samples. The Rickettsia spp. reported in the present study are having eventually been associated with cases of human diseases, and the circulation of these agents in arthropods has already been reported in several countries. Therefore, the identification of circulating pathogenic agents, such as reported in this study, is crucial for development of preventive measures for the control of ectoparasite-borne rickettsiosis diseases. Further studies, using serology techniques, will be allow to explore the ability of pigs as a possible Rickettsia reservoir and its role as part of transmission cycle of Rickettsia spp. in the studied scenarios.

Genotypic–phenotypic diversity and distinctiveness among Magnaporthe grisea isolates from rice and weed Echinochloa colonum

AbstractRice blast disease caused by Magnaporthe grisea (Hebert) Barr is a serious biotic stress causing worldwide yield loss in cultivated rice. As high as 75% to 100% crop damage has been recorded in India. The disease is manifested by the appearance of lesions of various colours, size and spore liberation ability. The pathogen also infects 50 other hosts including weeds and grasses as secondary hosts. Information on genetic diversity, host specificity and phenotypic characters of the pathogens needs to be explored for better management of the disease. Therefore, fourteen M. grisea isolates from rice host and six isolates from weed host Echinochloa colonum were collected from three locations of coastal Odisha. Culture studies revealed that most isolates from virulent lesions had both black colour mycelia and pigmentation (B/B pattern). All the twenty M. grisea isolated produced bigger conidia with size ranged from 21.1–33.0µm to 7.6–12.7µm (length and breadth). Isolates from virulent lesions produced higher number of conidia. Isolates from weed had long and slender type conidia. Molecular genetic studies based on repetitive element Pot2 and random amplified polymorphic DNA (RAPD) could separate isolates on the basis of host plant and virulence of source lesion. Isolates from weed were consistently placed in separate group where presence and absence of bands specific to this group were observed. Rep‐PCR based on Pot2 amplified polymorphic DNA fragments where bands at 1750bp were specific to isolates from weed. Similarly, amplification specific to weed isolates was obtained at 1200bp by primer OPB10 in RAPD PCR. Amplification at these base pairs may be used for the development of markers to distinguish M. grisea from rice and weed. This is the first report of utilization of rep‐PCR and RAPD to distinguish M. grisea among rice and Echinochloa colonum in this region.

Diversity and genetic structure in a mini-garden of Dalbergia nigra: A tree threatened with extinction in the Atlantic Forest

Maintaining genetic variability within rare or threatened species is essential for the development of conservation and restoration strategies. Therefore, the objective of this study was to characterize the diversity and genetic structure in Dalbergia nigra mini-garden. DNA samples from 90 individuals of D. nigra originated from seeds collected in Linhares-ES and Viçosa-MG were analyzed using Inter Simple Squence Repeat (ISSR) markers. For this, eleven primers were selected, which generated 180 fragments (70.76% polymorphism). The polymorphic information content (PIC) for the markers used averaged 0.38, considering them as moderately informative. The number of ISSR fragments to obtain desired precision in genetic diversity analyses was shown to be 122 polymorphic fragments, which was attained by examining 11 ISSR markers with clear amplification patterns. It was observed that for the origin of Linhares the number of alleles observed (Ao) was 1.99 and the number of effective alleles (Ae) was 1.60. For the origin of Viçosa, the values of Ao and Ae were 1.92 and 1.57, respectively. High genetic diversity was found with parameters Shannon index (I* = 0.5538) and genetic diversity of Nei (H* = 0.3742) for all populations sampled; from Viçosa, these parameters were 0.4963 and 0.3334, respectively, and from Linhares, they were 0.5328 and 0.3563. In the graphic representation of genetic distances, 10 groups were formed, three of them with only one genotype in each group. Among the individuals from Viçosa, the presence of five groups was revealed, one of which was isolated. For comparisons between individuals from Linhares, grouping by the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method revealed seven groups, two of which contained only one individual. Molecular variance analysis (AMOVA) for D. nigra populations indicated moderate genetic differentiation (ΦST = 0.118). The ΔK statistic corroborates the analysis of the structure, indicating the convergence of two Bayesian groups (K = 2). The ISSR markers were efficient in detecting genetic diversity in D. nigra. The populations of D. nigra present moderate genetic differentiation, with the highest proportion of genetic diversity within the populations. Mini-stumps have high diversity and, therefore, have the potential to be used as matrices for the collection of propagules in the production of seedlings for conservation purposes.

Molecular Systematic Investigations of Three Fin Fish Cichlid Species of Oreochromis niloticus (Nile Tilapia), Genetically Improved Farmed Tilapia (GIFT) and Astronotus ocellatus (Oscar Cichlid)

Fisheries in India contribute significantly to the total GDP of agriculture and earn significant foreign exchange. Aquaculture is playing an important role in India and is bestowed with a huge biodiversity of aquatic organisms. India ranks second in total fish production in the world. Nile tilapia has become the world’s second most popular farmed fish, after carps. Oscars is a popular aquarium fish around the world. In the present study, efforts were made to analyze the extent of divergence or similarity among three cichlid finfishes (Nile Tilapia, GIFT Tilapia, and Oscar Cichlid) using molecular biology techniques such as Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP). The Phylogenetic tree was constructed using PhyElph software to study the evolutionary relationship between the three cichlid finfish species. The Phylogenetic or evolutionary relationship was established for the three fishes, Nile tilapia, GIFT, and Oscar cichlid, with the Phylogenetic tree. It was found that Nile tilapia and GIFT share a recent common ancestor, while Oscar cichlid does not share any evolutionary relationship with Nile tilapia and GIFT.

Elucidating Mitochondrial DNA Markers of Ogura-Based CMS Lines in Indian Cauliflowers (Brassica oleracea var. botrytis L.) and Their Floral Abnormalities Due to Diversity in Cytonuclear Interactions.

Mitochondrial markers can be used to differentiate diverse mitotypes as well as cytoplasms in angiosperms. In cauliflower, cultivation of hybrids is pivotal in remunerative agriculture and cytoplasmic male sterile lines constitute an important component of the hybrid breeding. In diversifying the source of male sterility, it is essential to appropriately differentiate among the available male sterile cytoplasms in cauliflower. PCR polymorphism at the key mitochondrial genes associated with male sterility will be instrumental in analyzing, molecular characterization, and development of mitotype-specific markers for differentiation of different cytoplasmic sources. Presence of auto- and alloplasmic cytonuclear combinations result in complex floral abnormalities. In this context, the present investigation highlighted the utility of organelle genome-based markers in distinguishing cytoplasm types in Indian cauliflowers and unveils the epistatic effects of the cytonuclear interactions influencing floral phenotypes. In PCR-based analysis using a set of primers targeted to orf-138, 76 Indian cauliflower lines depicted the presence of Ogura cytoplasm albeit the amplicons generated exhibited polymorphism within the ofr-138 sequence. The polymorphic fragments were found to be spanning over 200–280 bp and 410–470 bp genomic regions of BnTR4 and orf125, respectively. Sequence analysis revealed that such cytoplasmic genetic variations could be attributed to single nucleotide polymorphisms and insertion or deletions of 31/51 nucleotides. The cytoplasmic effects on varying nuclear-genetic backgrounds rendered an array of floral abnormalities like reduction in flower size, fused flowers, splitted style with the exposed ovule, absence of nonfunctional stamens, and petaloid stamens. These floral malformations caused dysplasia of flower structure affecting female fertility with inefficient nectar production. The finding provides an important reference to ameliorate understanding of mechanism of cytonuclear interactions in floral organ development in Brassicas. The study paves the way for unraveling developmental biology of CMS phenotypes in eukaryotic organisms and intergenomic conflict in plant speciation.

DNA barcoding of commercial fish products using dual mitochondrial markers exposes evidence for mislabelling and trade of endangered species

Fish fraud has been extensively reported in world fish trade. The fraud includes IUCN Red List and CITES-listed species. Hence, there is a growing need to identify the trade of endangered and threatened species that has been misused to satisfy consumer needs. Here, we apply DNA barcoding by using dual mitochondrial marker; cytochrome b (Cytb) polymorphic fragment and cytochrome c oxidase subunit I (COI) to authenticate 50 commercial fish products collected from the Malaysian market. The dual marker system improves species detection in tested fish products even in highly processed food and exposes the trade of one critically endangered (also CITES-listed) and three endangered or near threatened species under the IUCN red-list status. Our result also indicates that 36% of fish products in the Malaysian market is mislabelled and might cause concern for food safety. The newly developed Cytb primer pair also shows a higher success rate by identifying 92% of the tested samples compared to 40% for COI primer. This work suggests the dual-marker DNA barcoding approach is more effective in detecting food mislabelling and is indeed a promising tool to help regulatory bodies obtain a clearer standpoint for monitoring endangered fish trade to prevent further biodiversity loss.

ISSR and RAPD primers selection for assessing genetic diversity of Enhalusacoroides (L.f.) Royle

Inter Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) are common PCR-based molecular markers used to study genetic diversity both between and within species. One of important steps in ISSR and RAPD analyses is primer selection to obtain bright PCR products. The aim of this study was to select ISSR and RAPD primers that produced scorable fragments of PCR product for genetic diversity evaluation of seagrass Enhalusacoroides (L.f.) Royle. The study also aimed to compare ISSR and RAPD technique in producing informative fragments. Enhalusacoroides is one seagrass species widely distributed in Indonesia. Seagrass samples were collected from Sanur Coastal Water and from Nusa Dua Coastal Water. DNA was extracted using CTAB method. Ten ISSR primers and eight RAPD primers were tested. Results showed that RAPD was more informative than ISSR. Among ten ISSR primers, only four primers resulted in scorable fragments in all samples, and only one among those primers gave polymorphic pattern. As many as 15 fragments have resulted from three ISSR primers and only 1 fragment was polymorphic. All RAPD primers produced scorable products, and three primers resulted in polymorphic fragments. A total of 42 RAPD fragments were produced and 4 from them were polymorphic fragments