Resolving Power Research Articles

Genetic diversity assessment of Palestinian safflower (Carthamus tinctorius L.) utilizing DAMD molecular markers.

The current knowledge about Palestinian safflower landraces is relatively limited in terms of phenotypic and molecular characterization, however, the purpose of this investigation was to determine the amount of genetic diversity in eighteen local safflower landraces using seven DAMD markers. The banding patterns for each primer were scored and compiled into a data matrix. Subsequently, the data matrix was analyzed using UPGMA cluster analysis to identify distinct genetic groups among the landraces. In total, 88 DNA fragments were found, and there were an average of 12.6 loci per assay unit observed. Resolving Power (RP) revealed an average of 7.09 was determined, with the highest RP value at 13.3. The dendrogram obtained from DAMD data divided the landraces into three main clusters, denoted as I, II and III. The first cluster (I) consisted of one genotype (PTUK.SA16). The second cluster (II) consisted of two genotypes (PTUK.SA13 and PTUK.SA10). The third cluster (III) was later partitioned into two distinct sub-clusters, which are III.a and III.b. Sub-cluster III.a comprised seven genotypes (PTUK.SA4, PTUK.SA9, PTUK.SA8, PTUK.SA7, PTUK.SA6, PTUK.SA5 and PTUK.SA3). While Sub-cluster III.b consisted of eight genotypes (PTUK.SA15, PTUK.SA18, PTUK.SA17, PTUK.SA14, PTUK.SA12, PTUK.SA2, PTUK.SA11, and PTUK.SA1). This research assess the genetic diversity of Palestinian safflower landraces using PCR-based DAMD markers. The remarkable level of polymorphism detected using DAMD markers demonstrated their effectiveness in distinguishing between Palestinian safflower genotypes.

Unveiling Genetic Diversity Among Bacterial Isolates Using SCoT Markers.

This study aimed to unveil the genetic diversity among 47 bacterial isolates from various species using start codon targeted (SCoT) markers. Six SCoT primers yielded 219 reproducible bands, with 89.04% exhibiting polymorphism. The amplification process generated 28 to 50 fragments per primer, with an average of 36.50. Genetic diversity was quantified using polymorphic information content (PIC) values ranging from 0.11 to 0.14, with SCoT32 showing the highest PIC (0.14) and SCoT23 the lowest (0.11). The resolving power (RP) index, used to assess primer discriminatory power, varied significantly, with SCoT23 demonstrating the highest RP (6.00) and SCoT29 the lowest (4.51). Comparative analysis with conventional markers like M13 and (GTG)5 revealed that certain SCoT primers exhibited superior PIC values, which indicates enhanced utility for interspecies differentiation. The high discrimination level achieved by SCoT primers underscores their effectiveness in genetic differentiation and biodiversity assessment within bacterial populations. This research highlights SCoT markers as powerful tools for microbial genetic studies, which offers valuable insights into bacterial diversity and provides a robust methodological framework for future investigations aimed at elucidating genetic variation and improving species identification. The application of SCoT markers represents a significant advancement in molecular techniques for bacterial characterization and phylogenetic analysis, demonstrating their potential to enhance our understanding of microbial genetics and evolution.

Taxonomic identification of Nigerian Terminalia superba and Terminalia ivorensis Combretaceae) using AFLP molecular markers

Terminalia superba and T. ivorensis are difficult to identify with morphological markers. Molecular characterization is very effective to correct the delimitation of timber species, especially when the discriminatory power of morphological markers is weak. In this study, four amplified fragment length polymorphism (AFLP) marker combinations were used to determine the taxonomic relationship among a total of 33 accessions of the genus Terminalia, consisting of two species, Terminalia ivorensis (12 accessions) and T. superba (21). The primer combinations produced a total of 740 fragments out of which 619 (83.6%) were polymorphic. Among all the primer combinations used, E-ACT/M-CTC was the most informative, which generated 11 unique markers for clear identification of the two species. The average polymorphic information content (PIC) ranged from 0.24 (E-ACT/M-CAT) to 0.28 (E-ACT/M-CTC) while the resolving power (RP) varied from 40.73 (E-AAC/M-CTA) to 63.76 (E-ACT/M-CTC). The genetic difference between the two species was significant (PhiPT = 0.610, p<0.001). All 33 accessions were delimited by both the UPGMA cluster and principal component analysis. Based on the results, it was concluded that E-ACT/M-CTC is the best among the marker combinations used for molecular study of the two tree species and used significantly to distinguish them. STRUCTURE analysis identified two accessions of Terminalia superba with alleles derived from T. ivorensis as well as revealed five putative hybrid accessions, which requires further genetic investigation to substantiate the finding.

Revisiting Dissolved Organic Matter Analysis Using High-Resolution Trapped Ion Mobility and FT-ICR Mass Spectrometry.

The molecular level characterization of complex mixtures remains an analytical challenge. We have shown that the integration of complementary, high-resolution, gas-phase separations allows for chemical formula level isomeric content description. In the current work, we revisited the current challenges associated with the analysis of dissolved organic matter using high-resolution trapped ion mobility separation (TIMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). In particular, we evaluated the separation capabilities provided by TIMS-MS compared to MS alone, the use of ICR complementary data acquisition (DAQ) systems and transient processing strategies, ICR cell geometries (e.g., Infinity cell vs harmonized cell), and magnetic field strengths (7 T vs 9.4 T vs 21 T) for the case of a Harney River DOM sample. Results showed that the external high-performance DAQ enables direct representation of mass spectra in absorption mode FT (aFT), doubling the MS resolution compared to the default magnitude mode FT (mFT). Changes between half- vs full-apodization result in greater MS signal/noise vs superior MS resolving power (RP); in the case of DOM analysis, a 45% increase in assigned formulas is observed when employing the DAQ half (Kaiser-type)-apodization window and aFT when compared to the default instrument mFT. Results showed the advantages of reprocessing 2D-TIMS-FT-ICR MS data with higher RP and magnetic field chemical formulas generated list acquired (e.g., 21 T led to a 24% increase in isomers reported) or the implementation of alternative strategies.

Genetic characterization of white onion genotypes (Allium cepa L.) using ISSR markers

Understanding the genetic characteristics is crucial for preserving and developing Moroccan's white onion genotypes, with increased yield and quality as well as improved tolerance to biotic and abiotic stresses. In the present paper, inter simple sequence repeat (ISSR) markers were used to assess the genetic diversity and characteristics of white onion genotypes (Allium cepa L.) of Morocco. Based on the ISSR markers bands, 28 white onion genotypes were divided into four distinguished subgroups, with a genetic similarity value of 0.46 based on Jaccard index. Molecular markers analysis revealed that all ISSR markers were 100 % polymorphic with the white onions genotypes. Concerning markers performance, polymorphic information content (PIC) ranges from 0.051 to 0.39 with a mean of 0.301; however, the effective multiplex ratio (EMR) and marker index (MI) vary between 3–17 and 0.35–5.04, respectively. Based on resolving power (RP), it appears that the marker UBC825 has an efficient discriminatory power with an RP = 15.67. In contrast, the lowest RP value was detected with the marker UBC815 (RP = 1.58). Based on their high performance, markers UBC825, UBC835, UBC826, UBC840, and UBC811 ISSR seem to be specific and efficient for the identification of Moroccan white onion genotypes. Thus, given the genetic diversity shown by ISSR markers, the abundant resources of white onion genotypes in Morocco could be exploited in more valuable ways.

Molecular diversity of rice germplasms from Thailand characterized by different pericarp colors using Inter Simple Sequence Repeat (ISSR) markers

Abstract. Saengprajak J, Phetsom J, Sangdee A, Atichart P, Theerakulpisut P. 2024. Molecular diversity of rice germplasms from Thailand characterized by different pericarp colors using Inter Simple Sequence Repeat (ISSR) markers. Biodiversitas 25: 2839-2848. Studying genetic diversity in rice using molecular markers is necessary for varietal identification, better understanding of relationships and evolution, and conserving genetic resources. This study aimed to evaluate the genetic diversity of rice germplasms from Thailand characterized by different pericarp colors using ISSR markers. Thirty-two white and colored rice genotypes were assessed using 16 selected ISSR markers, which generated 179 alleles ranging from 210 to 1,374 bp, averaging 11.19 alleles per locus. The polymorphism percentage ranged from 40% to 100%, averaging 80%. The genetic similarity coefficient ranged from 0.458 to 0.855, while PIC values varied between 0.15 and 0.45, averaging 0.31. ISSR markers show a high Resolving Power (RP) of 12.15 and a Marker Index (MI) of 3.20, indicating their significant discriminatory power and effectiveness in detecting genetic diversity. The dendrogram grouped genotypes into five clusters: Cluster I included 5 red pericarp genotypes, Cluster II had 6 purple-black pericarp genotypes, Cluster III had 2 mixed white and purple-black pericarp genotypes, Cluster IV included 18 white pericarp genotypes, and Cluster V comprised 1 white pericarp genotype. PCA results corresponded to seed coat traits, forming eight grouping patterns similar to dendrogram clusters. These findings show that ISSR markers effectively assess genetic diversity and relationships in rice germplasms, providing valuable information for managing germplasm resources, developing variety-specific markers, and supporting rice breeding programs.

Molecular, morphological, palynological and biochemical characterization of six accessions of two Mangifera indica L cultivars (Keitt and Ewais) native to Egypt

Accurate characterization of crops or fruits leads to successful improvements in breeding programs. Mango (Mangifera indica L.) is the second most common fruit in Egypt. It is a heterozygous plant; consequently, the possibility of incorrect characterization is significant. Therefore, this study used six accessions of two M. indica cultivars, ‘Keitt’ and ‘Ewais’, to produce precise molecular characterization and prove their genetic relatedness using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers. Pollen morphology was studied for the first time for these two Egyptian cultivars to determine their correlation. Morphological traits were quantitatively and qualitatively investigated. In addition, phytochemical analyses were performed to correlate the six mango accessions. One of these accessions (accession 3) was commercially identified as ‘Ewais’ cv., but the obtained result revealed that it does not belong to ‘Ewais’ cv. This finding was proved molecularly using ISSR and SCoT markers and morphologically. Similarly, phytochemical analyses revealed a difference between accession 3 and the other accessions under investigation. Polymorphic information content (PIC) and resolving power (RP) data revealed that the SCoT technique was more informative than ISSR for studying these genotypes of mango. Accordingly, the present findings prove the necessity for molecular, morphological, palynological, and biochemical investigations for accurate characterization of mango genotypes and genetic relatedness for improving breeding programs.

Genetic diversity of maize resources revealed by different molecular markers

Maize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance.

Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022-2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

Evaluation of Some Local and Registered Safflower (Carthamus tinctorius L.) Varieties Based on SRAP Markers

Safflower (Carthamus tinctorius L.), a member of the Asteraceae family, is an important plant grown in the world as a source of vegetable oil. In addition, it is a versatile crop that is also used as biodiesel, animal feed, spice, dye, and medicinal plant. In this study, SRAP markers were used to determine the genetic diversity and relationships between four local and three registered safflower cultivars for use in cross-breeding programs. The twelve primer combinations yielded a total of 101 bands, including 33 polymorphic bands. The level of polymorphism of SRAP markers which were represented by the average number of total bands (NTB) (8.4), the average number of polymorphic bands (NPB) (2.8), polymorphic band ratios (PBR%) (34.5%), resolving power (RP) (1.48), effective multiplex ratio (EMR) (1.17), and marker index (MI) (0.43) was low. Conversely, polymorphism information content (PIC) (0.35), Nei’s gene diversity (h) (0.36) and Shannon's information index (I) (0.55) showed a significant genetic variation in the safflower genotypes studied. The polymorphism information content of the SRAP primer combinations used in the study ranged from 0.24 to 0.46, with an average of 0.35. Genetic similarity was calculated according to Dice similarity and varied from 0.12 to 0.92, with a mean genetic similarity (GS) of 0.58. The cophenetic correlation between the Dice similarity matrix and corresponding dendrogram obtained by SRAP (r = 0.95) revealed very good compliance. The genetically close genotypes were Remzibey05 - TR64702 and TR49119 - TR42630 (GS=0.91). Also, Dinçer5-118 and Yenice5-38 were the most genetically distant varieties (GS=0.12). Dinçer5-118 was very different from other genotypes (GS=0.29).

Association study between some cultivated species and their wild relatives from Apiaceae, Asteraceae and Brassicaceae families based on molecular and DNA barcoding in Egypt

Concerns about food security worldwide have been raised due to the adverse impacts of climate change on agricultural productivity. Utilizing wild relatives of cultivated plants in breeding schemes is a potential solution to address the abovementioned challenges. Wild relatives refer to indigenous plant species that share genetic ancestry with recently cultivated plants. The capacity of plants to withstand abiotic stresses and enhance crop yield stability in cold and arid environments renders them a valuable prospective resource for breeding programs. Molecular markers are employed to assess the genetic variability of cultivated plants and their wild relatives under investigation. This study employed a set of five primers derived from ISSR (Inter Simple Sequence Repeats) and SCoT (Start Codon Targeted) to assess comparative research between cultivated species and their wild relatives from three families: Apiaceae (Apium gravolens L., A. leptophyllum (Pers.) F.Muell., Daucus carota L.& D. litoralis Sm.), Asteraceae (Lactuca sativa L. & L. serriola L.) and Brassicaceae (B. oleracea L., Brassica tourneforttii Gouan., Raphanus sativus L. & R. raphanistrum L.). The ISSR technique yields approximately 206 bands, whereas the SCoT primers generate approximately 207 bands. The ISSR primers yielded 169 polymorphic bands, exhibiting a polymorphism rate of 82.04%, whereas the SCoT primers produced 169 polymorphic bands with a polymorphism rate of 81.64%. The Brassicaceae has been found to exhibit the highest resolving power (RP) of 48.25, as determined by ISSR. The primary objective of DNA barcoding is to create a communal database of DNA sequences that can be utilized to identify organisms and clarify their taxonomic classification. The findings indicate that the internal transcribed spacer (ITS) regions exhibit high efficacy as a DNA barcoding tool. Overall, the results obtained from two molecular markers and DNA barcoding analyses suggest a significant degree of genetic diversity and relatedness among the cultivated taxa and their wild relatives examined in this study.

Evaluation of the growth, yield traits and the genetic diversity of some Brassica napus genotypes under Egyptian conditions

BackgroundCanola (Brassica napus L.) is considered an alternate oilseed plant. Therefore, this study aimed to evaluate some growth parameters, yield, chemical parameters and genetic diversity among thirteen canola genotypes including a collection of Chinese, German, French, and local genotypes under Egyptian conditions.ResultTrapper genotype recorded the highest values of plant height (47.12 and 89.75 cm) and dry weight/plant (8.54 and 28.19 dry weight/plant) at 60 and 90 days from sowing, respectively. Data from the field experiments showed that significant differences were recorded among tested genotypes for all yield and its component parameters (i.e., plant height (cm), branches/no. plant, siliquas and seed weight (g/plant) and seed oil %. The genetic diversity and the relationships among the thirteen canola genotypes were evaluated utilizing sequence-related amplified polymorphism (SRAP) and simple-sequence repeats (SSRs) markers. The allelic frequency of the different SRAP and SSR markers tested has differed among the thirteen canola genotypes. The SRAP and SSR analyses showed 659 out of 742 and 15 out of 45 markers, respectively, were detected as polymorphic markers (88.8% and 33.33%) among the tested wheat cultivars In addition, the polymorphism information content (PIC), marker index (MI) and resolving power (RP) parameters were computed to assess the effectiveness of the markers. The results indicated the occurrence of a considerable genetic variation between Chinese, European and Egyptian genotypes.ConclusionThese markers are of considerable value and can be utilized to screen large canola populations. The results of the comparison between the two molecular markers showed that the most effective marker that showed the genetic diversity between canola genotypes was SRAP (88.8%) polymorphism. It could be concluded that the tested canola genotypes could be cultivated under the Egyptian condition with high performance especially Trapper, Agamax and Topas genotypes. Therefore, it could be suggested that these three genotypes seem to be promising for oil gap reduction and need further evaluation for the expansion under new reclaimed regions.

Molecular profiling of therapeutically important Alpinia and Kaempferia species using RAPD, ISSR, and SSR markers

Alpinia and Kaempferia species require precise identification and diversification to improve the accuracy in drug discovery and industrial demands. In this current study, four Alpinia species (Alpinia malaccensis, A. nigra, A. galanga and A. calcarata) and three Kaempferia species (Kaempferia galanga, K. rotunda and K. parishii) were selected for molecular profiling analysis. Three types of molecular markers (PCR based) such as RAPD, ISSR, and SSR were used to increase the accuracy of analysis. About 91 polymorphic loci were amplified in these 7 species using 9 RAPD primers out of 30. The resolving power (RP) was varied from 4.56 to 10.06 and the polymorphic information content (PIC) ranged between 0.8 and 0.93. Out of 40 ISSR primer 13 primers showed total 118 polymorphic loci. The maximum RP and PIC were 9.36 and 0.97 respectively. In case of SSR analysis, only 11 SSRs out of 35 showed 201 polymorphic loci. The RP were found between 3.12 and 17.86. The PIC in SSR primers were in between 0.78 and 0.97. This study indicated that unique banding pattern was observed in specific primers of each marker. D20, D18, and D8 primers were found as the best RAPD markers. (GA)8T, (GA)9T, and (GTGC)4 were the best ISSR markers which can produce distinct banding pattern. SSR2 and SSR14 have also successfully amplified in Alpinia and Kaempferia species with distinct banding pattern. Although SSR marker is more advance than other two but multiple markers based molecular profiling would have enough significance. This present study has enormous importance towards DNA fingerprinting study of different species of Alpinia and Kaempferia. The unique banding pattern in specific primer could be efficiently useful for species identification and future improvement of the taxa.

Genotypic diversity and abiotic stress response profiling of short-grain aromatic landraces of rice (Oryza sativa L. Indica)

This study evaluated the physiological responses and genetic diversity of selected short-grain aromatic rice landraces of Northern Eastern Ghats of India to multiple abiotic stresses. Results revealed that drought, salt and flooding stress remarkably declined plant biomass, relative growth index (RGI), relative water content (RWC), leaf photosynthesis, PSII activity, SPAD relative index, and elevated effect was found in susceptible IR64 (susceptible check) variety. We employed molecular marker analysis to characterize 21 rice genotypes using 32 SSR primers related to drought, flooding and salinity tolerance QTLs. Our analysis suggests significantly high polymorphism (93.12%) in 96 loci. The mean value of polymorphism information content (PIC), marker index (MI) and resolving power (RP) and heterozygosity index (HI) were 0.326, 1.037, 1.558 and 0.420 respectively. The Jaccard’s similarity coefficient ranged from 0.158 to 0.846 with a mean genetic dissimilarity of 0.647. According to neighbor-joining method of clustering, all genotypes were grouped into two major and five sub-clusters which is concurrent with a very broad genetic base (K = 5) obtained with STRUCTURE analysis. Taken together, six aromatic genotypes Basubhoga, Dudhamani, Kalajeera, Laktimachi, Kuyerkuling and Tulasi are genetically very close to drought-tolerant (N22) and flooding tolerant (FR13A) cultivar whereas, salt-tolerant (Pokkali) very close to Sapuri and Muktabali. The degree of genetic variants obtained from this profiling could be useful for landrace conservation, selection and global implications for multiple abiotic stress tolerance.

Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers.

Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into "rounded" and "nearly elongated". Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.

Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

BackgroundCapsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers. ResultsOut of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index (I), expected heterozygosity (He), Nei’s gene diversity, total diversity among species (Ht), diversity within species (Hs), respectively. Further, the coefficients of gene differentiation (Gst) and gene flow (Nm) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA). ConclusionISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.

Assessment of the genetic variations of sago palm Metroxylon sagu in three regions of Sarawak, Malaysia using amplified fragment length polymorphism (AFLP) marker

BackgroundSago palm (Metroxylon sagu) is an important staple crop in the rural area of Sarawak, Malaysia. The palms grow well in the rough, swampy peat, from low flooded areas to uplands and acidic to neutral soils. Among the starch-producing crops, this palm is the most productive and promising, where it can store a significant amount of carbohydrate in the trunk. Due to the lack of molecular study of sago palm, the work described here aimed to develop molecular markers for identifying M. sagu and accessing the genetic variations of sago palm in different locations of Sarawak.ResultsAmplified fragment length polymorphism was employed to determine the genetic variations of sago palm between fifteen populations collected from three different locations: Mukah, Pusa and Samarahan. Based on 35,016 polymorphic fragments generated from 32 primer combinations, polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.269, 0.005157 and 51.52039 per primer combination, respectively, were obtained, signifying the effectiveness and accuracy of the AFLP marker. Mukah showed higher diversity (I = 0.428, H = 0.232), while Pusa showed the lowest (I = 0.367, H = 0.240). The average value of the Shannon information index was 0.404. AMOVA showed 99% of the variation was found within the population. The Mantel test was performed with 9999 permutations. A significantly positive correlation (r = 0.220, p = 0.010) was observed between the genetic divergence of the population (Nei genetic distance) with the geographical distance.ConclusionsOur study considered AFLP is as an effective and reliable method to assess the genetic variations and the identification of M. sagu.Graphical

Assessing the molecular variability in Ustilaginoidea virens, the rice false smut pathogen with ISSR markers

Rice false smut disease is gaining importance because of its impact on the grain yield and its toxin production ability. Fifty-eight isolates of Ustilaginoidea virens were collected from different rice-growing regions of India. DNA of U. virens was isolated by the CTAB method and fifty ISSR primers were screened for molecular variability studies. Twelve primers viz., UBC series 807, 808, 809, 810, 811, 812, 834, 835, 836, 840, 841, and 842 were selected to study the genetic variability. Different parameters of tested primers viz., heterozygosity (Hn), polymorphism information content (PIC), effective multiplex ratio (EMR), marker Index (MI), and resolving power (RP) were calculated. Primers UBC 812 and UBC 809 recorded maximum heterozygosity (Hn). The PIC values ranged from 0.10 to 0.27 and UBC 807 recorded the maximum value of 0.27. The EMR value varied from 6.75 to 24.0, Similarly, UBC 807 recorded the highest value of MI (24) and RP (8.55). A dendrogram was generated using the DARwin software (version 6.0.21A) based on the unweighted neighbor-joining cluster method. All the fifty-eight U. virens isolates were grouped into three major clusters. Clusters I and II had 21 and 35 U. virens isolates respectively. Cluster III had only two isolates. The isolates showed genetic variations and there was no specific grouping based on the geographical distance.

Fine Structure in Isotopic Peak Distributions Measured Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: A Comparison between an Infinity ICR Cell and a Dynamically Harmonized ICR Cell

The fine structure of isotopic peak distributions of glutathione in mass spectra is measured using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) at 12 and 15 T magnetic field, with an infinity cell and a dynamically harmonized cell (DHC) respectively. The resolved peaks in the fine structure of glutathione consist of 2H, 13C, 15N, 17O, 18O, 33S, 34S, 36S, and combinations of them. The positions of the measured fine structure peaks agree with the simulated isotopic distributions with the mass error less than 250 ppb in broadband mode for the infinity cell and no more than 125 ppb with the DHC after internal calibration. The 15 T FT-ICR MS with DHC cell also resolved around 30 isotopic peaks in broadband with a resolving power (RP) of 2 M. In narrowband (m/z 307–313), our current highest RP of 13.9 M in magnitude mode was observed with a 36 s transient length by the 15 T FT-ICR MS with the DHC and 2ω detection on the 15 T offers slightly higher RP (14.8 M) in only 18 s. For the 12 T FT-ICR MS with the infinity cell, the highest RP achieved was 15.6 M in magnitude mode with a transient length of 45 s. Peak decay was observed for low abundance peaks, which could be due to the suppression effects from the most abundant peak, as result of ion cloud Coulombic interactions (space-charge).

Molecular characterization and genetic structure analysis of Coffea arabica and Coffea canephora cultivars from India using SCoT markers

Coffee is the second most traded community after oil and provides a livelihood for more than 125 million people worldwide. It is cultivated in 80 countries spreading over Africa, Asia and Latin America. In recent years, there is an increasing demand for high quality planting material because of the changing dynamics of pests and disease occurrence possibly triggered by climate change. This calls for a better understanding of the existing genetic diversity and its utilization in the breeding program. In this study, we investigated the molecular characterization and genetic structure of twenty coffee cultivars predominantly bred and cultivated in India using Start Codon Targeted (SCoT) molecular markers. Thirty-six SCoT primers amplified 368 bands of which 192 (52.17%) are polymorphic. The mean values of PIC, Resolving power (RP), mean effective multiplex ratio (EMR) and marker index (MI) were 0.27, 16.04, 3.26 and 1.12 respectively indicating the usefulness of these markers for the genetic analysis of coffee cultivars. Four cultivars produced 17 unique bands due to their specific genetic constituents and these bands could be useful for fingerprinting diagnostics. UPGMA clustering based on SCoT markers separated the accessions into two major clusters which accommodated five sub-clusters which are supported by the principal coordinate analysis (PCoA). The STRUCTURE analysis showed K = 5 as the optimum number of groups and completely separated the cultivars mainly according to their development and genetic constitution. Our results represent the first-of-its-kind attempt to shed light on the genetic diversity among coffee cultivars grown in India using the functional marker.