Polymorphism Information Content Research Articles

Molecular Variations in Rabi Sorghum Varieties Using SSR Markers

Genetic diversity was assessed for 2 popular varieties and 5 promising lines of rabi sorghum by using11 SSR markers. The marker Xiabt312 reported 100% polymorphism rate followed by Xtxp15 (85.70%) and mSbCIR300 (85.71%). The sorghum varieties studied for this analysis showed the polymorphism information content (PIC) ranged from 0.25 to 0.87 with a mean of 0.67 indicates higher diversity within them. Clustering analysis based on the genetic dissimilarity grouped the 7 lines into 2 major and 4 sub clusters and grouping was in good agreement with pedigree. Cluster II was the largest cluster with 4 genotypes followed by cluster I with 3 genotypes. The rabi sorghum genotypes viz., M35-1, RSV-1876 and RSLG-2422 were placed in cluster I and Phule Anuradha, RSV-2371, RSV-1910 and RSV-1988 placed in cluster II. Clustering based on SSR molecular profile of the genotypes shows that there is a distinct variability among the genotypes under this study. The selected markers have great potential in DNA fingerprinting in sorghum which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.

Genetic diversity and population structure of maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers

Understanding germplasm’s genetic diversity is essential for developing new and improved cultivars with stable yields under diverse environments. The objective of this study was to determine the genetic diversity and population structure of 128 maize inbred lines sourced from the International Institute of Tropical Agriculture (IITA), the International Maize and Wheat Improvement Centre (CIMMYT), and the University of KwaZulu-Natal (UKZN) using 11,450 informative single nucleotide polymorphism (SNP) markers. The inbred lines revealed highly significant (p < 0.001) levels of variability for the key phenotypic traits. The SNP markers had a mean gene diversity (GD) and polymorphic information content (PIC) of 0.40 and 0.31, respectively, indicating the existence of substantial genetic variation across the germplasm panel. The model-based population structure analysis identified three subpopulations (K = 3) among the inbred lines. This corroborated the phylogenetic analysis using phenotypic traits and molecular markers which classified the inbred lines into three groups. The findings of this study identified considerable genetic diversity for the selection of inbred lines with favourable alleles for multiple traits and could be useful to initiate marker-assisted selection (MAS) to identify significant loci associated with agronomic performance and multiple-stress tolerance.

Establishment of AA-NAT, SCD, PROP1, and IGFBP3 gene frequency distributions in Karacabey Merino and Kivircik Sheep Breeds

Thus, the aim of the current study was to investigate the genotypic dispersion of AA-NAT, SCD, PROP1, and IGFBP3 genes in the target population. Primarily, the genomic DNA was isolated from blood samples by the phenol/chloroform method. The genomic analyses were performed on a total of 160 Karacabey Merino (KM) sheep (n=80) and Kivircik (n=80). The PCR-RFLP method was used to determine the genotype of the SNPs. Deviation from Hardy–Weinberg equilibrium (HWE) and population genetic assays such as observed (Ho) and expected (He) heterozygosities, effective allele numbers (Ne), and the polymorphism information content (PIC) were calculated for each gene in the population. As a result, there was no deviation from HWE was determined except SCD and PROP1 gene in KM. The most frequent genotypes were found AA (66,25% and 87,50%) for AA-NAT gene, CC (93,75% and 91,25%) for SCD gene and CC genotype (70,00% and 56,25%) for PROP1 gene in KM and Kivircik sheep. All breeds were detected monomorphic in terms of the IGFBP3 gene. In conclusion, the other regions of the IGFBP3 gene which were determined as monomorphic in the studied flock could be researched. Moreover, further studies should be necessary for defining the effects of investigated genes on related traits in KM and Kivircik sheep in terms of polymorphic genes specified.

Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Chilli Pepper Cultivar: Physiology and Molecular Approach

The fruit color of chili pepper is an important characteristic in identification and classification and is often used as the basis for determining consumer preferences. Information on the relationship between chili fruit color and its molecular profile is very important in supporting selection activities in plant breeding. This study aims to identify genetic diversity associated with the fruit color of three genotypes of chili (Capsicum frutescens L.): Cakra Hijau, HV-149 and G1/M8, using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). Morphological confirmation was carried out according to Capsicum descriptors. Nineteen RAPD markers and six SSR markers were used for genetic variability assessment. Genetic variation was analyzed using the unweighted pair group method with the arithmetic mean and the Jaccard similarity index. The three chili genotypes had different fruit colors at each maturation stage. The immature Cakra Hijau fruit is dark green and turns dark red as it ripens. The immature fruits of the G1/M8 line are light green and turn red when ripe. Finally, immature HV-149 fruits are dark green and yellow when ripe. The SSR markers used in this study were unable to show polymorphism. On the other hand, the RAPD marker successfully detected genetic variation in the three chili genotypes and resulted in a total of 49 alleles. The average value of polymorphic information content of the RAPD primers used ranged from 0 to 0.296, with the highest index indicated by OPA-1. The dendrogram shows the separation of the three genotypes into two main clusters, with the first cluster consisting of the HV-149 variety and the second cluster consisting of Cakra Hijau and G1/M8 lines. This study revealed that there are genetic variations based on the morphological characteristics of fruit color at each ripening stage and RAPD band profile. The RAPD marker was more effective than the SSR marker for identifying the genetic diversity of fruit color in the three chilies studied.

Characterization and development of 14 microsatellite markers for mountain stewartia (Stewartia ovata): an uncommon, Appalachian-endemic member of the tea family

ABSTRACT Mountain stewartia [Stewartia ovata (Cav.) Weatherby] is a rare, endemic understory tree native to the southeastern U.S.A. While found only in microsites across southeastern Appalachia, the species distribution spans from northern Alabama and Georgia to southern Kentucky and Virginia. However, most occurrences have been recorded in Tennessee. While recent distribution surveys and habitat suitability modeling conducted for this species have improved our understanding of the environmental parameters that constitute its fundamental niche, the ecological profile of S. ovata remains poorly understood. Consequently, its rarity has raised concerns as to the long-term resilience of this species in the wild. Faced with these challenges, the assessment of existing genetic diversity in S. ovata through genetically informative molecular resources is critical to understanding the adaptive potential and ecological resilience of the species. Microsatellites are cost-efficient molecular tools capable of addressing these concerns by elucidating trends in population structure, population demography, and inbreeding. To increase the available genetic resources for S. ovata, we screened 105 microsatellite loci for their suitability to assess these population features using capillary gel electrophoresis. The utility of these markers was evaluated by assessing polymorphism information content (PIC) and population statistics, which yielded 14 highly polymorphic microsatellite markers. These markers displayed an average PIC of 0.695 (PIC range of 0.538–0.851), which supports their ability to capture fine-scale genetic diversity within the species. We also report a low average observed heterozygosity of 0.375 (versus an expected heterozygosity of 0.645) among screened loci, which reinforces the need for broader genetic diversity assessments within this species.

Uncovering microsatellite markers associated with agronomic traits of South Sudan landrace maize.

Maize has great importance in South Sudan as the most cultivated cereal after sorghum; however, numerous challenges are encountered in its production. To raise maize production, it is critical to exploit the wealth of its genetic variation for grain yield enhancement. This study aimed to conduct association analysis to identify specific simple sequence repeat (SSR) markers associated with quantitative agronomic traits. Genetic variation and population structure were investigated among 31 maize accessions by association analysis using 50 SSR markers and seven quantitative agronomic traits. The genotypes exhibited abundant genetic variation, and 418 alleles were detected with an average of 8.4 alleles per locus. The average genetic diversity, major allele frequency, and polymorphic information content were 0.754, 0.373, and 0.725, respectively. The population structure based on 50 SSR markers divided the maize accessions into two main groups and an admixed group without considering their descent. Association analysis was performed using a general linear model (Q GLM) and a mixed linear model (Q + K MLM). Q GLM detected 44 trait-marker associations involving 23 SSR markers. Q + K MLM detected four marker-trait associations involving three SSR markers (umc2286, umc1303, umc1429) associated with days to tasseling, days to silking, leaf length, and leaf width. The detected significant SSR markers related to agronomic traits could be useful for future genetic studies. Additionally, markers affecting several agronomic traits and overlapped SSR markers require further testing on a wide range of genotypes prior to their consideration as candidate markers for marker assisted selection for South Sudan maize improvement.

Identification of Major Brown Planthopper Resistance Genes in Indigenous Thai Upland Rice Germplasm Using Molecular Markers

Brown planthopper (BPH) is the most problematic insect in rice cultivation, as it decreases crop yields. In this study, 143 upland rice varieties were genotyped for five essential Bph resistance genes: bph2, Bph3, Bph14, Bph15, and Bph17. The gene frequencies of the five Bph resistance genes varied from 33.57% to 61.54%. The 139 varieties contained one to five Bph resistance genes. Polymorphism information content values ranged from 0.4460 to 0.4984 with an average of 0.4744. Cluster analysis supported the subpopulations identified by STRUCTURE. An analysis of molecular variance analysis identified 7% variance among and 92% variance within subpopulations, indicating a significant gene exchange between the two subpopulations. The evaluation of BPH resistance using the SEM system by IRRI showed that 2 varieties were resistant to BPH, 29 varieties were moderately resistant, and 112 varieties were susceptible. The Bph3, Bph14, and Bph15 genes and BPH resistance showed significant correlation. These findings provide important information regarding BPH-resistant varieties for future use in rice breeding programs.

De novo transcriptome profiling and development of novel secondary metabolites based genic SSRs in medicinal plant Phyllanthus emblica L. (Aonla)

Phyllanthus emblica (Aonla, Indian Gooseberry) is known to have various medicinal properties, but studies to understand its genetic structure are limited. Among the various secondary metabolites, ascorbic acid, flavonoids, terpenoids, phenols and tannins possess great potential for its pharmacological applications. Keeping this consideration, we assembled the transcriptome using the Illumina RNASeq500 platform, generating 39,933,248 high-quality paired-end reads assembled into 1,26,606 transcripts. A total of 87,771 unigenes were recovered after isoforms and unambiguous sequences deletion. Functional annotation of 43,377 coding sequences against the NCBI non-redundant (Nr) database search using BlastX yielded 38,692 sequences containing blast hits and found 4685 coding sequences to be unique. The transcript showed maximum similarity to Hevea brasilensis (16%), followed by to Jatropha curcas (12%). Considering key genes involved in the biosynthesis of flavonoids and various classes of terpenoid compounds, thirty EST-SSR primer sequences were designed based on transcriptomic data. Of which, 12 were found to be highly polymorphic with an average of 86.38%. The average value for marker index (MI), effective multiplicity ratio (EMR), resolution power (Rp) and polymorphic information content (PIC) was 7.20, 8.34, 8.64 and 0.80, respectively. Thus, from this study, we developed newly EST-SSRs linked to important genes involved in the secondary metabolites biosynthesis that will be serving as an invaluable genetic resource for crop improvement including the selection of elite genotypes in P. emblica and its closely related Phyllanthaceae species.

Only 11 Simple Sequence Repeats Needed to Identify Chinese Cabbage (Brassica rapa L.) Cultivars

Chinese cabbage is a popular leaf vegetable, and many cultivars have been developed for different regions and growing seasons. For the identification of the cultivars, many marker systems have been applied, but they usually require a large number of markers and expensive equipment. Therefore, it is necessary to develop an efficient and economical method for identifying Chinese cabbage cultivars. In this study, we aimed to develop a marker system with the minimum number of markers using simple PCR and gel electrophoresis. A total of 48 simple sequence repeats (SSRs) in a previous study were screened based on their chromosomal location and applied to 105 Chinese cabbage cultivars. The minimum number of markers was selected based on their genomic location, polymorphic information content, and allele frequency. To validate the cultivar identification capability of selected SSRs, they were applied to genetically similar cultivar pairs from a previous study. Eleven SSRs were finally selected, and they successfully identified cultivars with high genetic similarity, as well as all 105 Chinese cabbage cultivars tested. The proposed SSRs require only 11 primer sets, simple PCR, and gel electrophoresis, which need less time and resources compared to previous ones. These SSRs can be used not only in small seed companies and laboratories but also in large-scale seed companies.

Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (Juglans regia L.) in Middle Asia

The common walnut (Juglans regia L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this work, a total of 357629 SSR loci were searched based on previously published walnut genome sequences, with a density of 662.28 (SSRs/Mb). The majority of all these loci were found to be single nucleotide A/T (58.49%), followed by the dinucleotide AT (19.48%). Based on the results of genome-wide SSR site design, 22 effective primer pairs were designed and screened to analyze the genetic diversity of 48 wild walnut samples from three countries. Each locus had an average of 5.17 effective alleles (Ne), with an average polymorphism information content (PIC) of 0.71, average heterozygosity (He) of 0.52, and average genetic differentiation index (Fst) of 0.09. The analysis of 48 wild walnut samples from three countries (Kyrgyzstan, Tajikistan, and China) using the unweighted pairwise clustering method and arithmetic mean (UPGMA) along with principal coordinate analysis revealed the division of all samples into three groups. In summary, these novel SSR markers serve as a reference for the identification of wild walnut germplasm in Central Asia and for the development and utilization of wild walnut seed resources.

SSR marker based profiling and population structure analysis in peach (Prunus persica) germplasm

For breeding programmes to be successful and for germplasm conservation, it is essential to characterize and analyze the genetic diversity of available germplasm. The present experiment was conducted at Molecular Biology and Genetic Engineering Laboratory of Uttarakhand Council for Biotechnology, Haldi, Uttarakhand during 2022 to study the molecular profile of 41 peach [Prunus persica (L.) Stokes] accessions using 23 polymorphic SSR markers. The number of alleles detected ranged from 3 to 8 with an average of 4.65 alleles per locus (Na) and a total of 107 alleles were amplified. The average effective number of alleles (Ne) were 2.89 per marker. The SSR marker MA015a produced maximum number of 8 alleles followed by BPPCT 015 and CPPCT14 which produced 7 alleles each. The polymorphic information content (PIC) varied between 0.317–0.836 with a mean value of 0.563. The observed heterozygosity examined was lower (Ho = 0.02) and the expected heterozygosity (He = 0.61) ranged between 0.34 to 0.85. The presence of a higher Shannon’s information index (I) of 1.17 indicates higher diversity in the given set of peach genotypes. Jaccard’s similarity coefficient ranging from 0.533 to 1, indicated a pair-wise relationship among the peach accessions. The cluster dendrogram partitioned the accessions into two main clusters. However, the total accessions were stratified into 3 groups (K=3) based on population structure analysis which was further confirmed by Principal Coordinate Analysis (PCoA). The information generated in the study may have great implications in molecular characterization, fingerprinting and documentation of accessions in the peach improvement programme.

Genetic Diversity and Population Structure Analyses in Bitter Gourd (Momordica charantia L.) Based on Agro-Morphological and Microsatellite Markers.

Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity analysis using 10 quantitative traits, and 82 simple sequence repeat (SSR) markers. Out of 82 SSRs, 33 were polymorphic and the mean polymorphism information content (PIC) value was 0.38. Marker, JY-003 revealed a maximum (0.81) PIC value and, the number of alleles per locus ranged from 2 to 7 (average 3.46). The value of gene diversity showed the presence of a significant level of polymorphism among these genotypes. The unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into two major clusters of which Cluster I comprised mostly small and medium-fruited genotypes of both M. charantia var. charantia and M. charantia var. muricata, whereas Cluster II included mostly long and extra-long fruited genotypes. Furthermore, these genotypes were divided into six distinct groups based on population structure analysis. The diversity analysis based on 10 quantitative traits revealed that earliness and high-yielding ability were exhibited by the predominantly gynoecious line DBGS-21-06 followed by DBGS-48-00. The principal component analysis (PCA) revealed that the first two components exhibited more than 50% of the total genetic variation. The present study deciphered a higher magnitude of agro-morphological and genetic diversity in 96 bitter gourd genotypes. Therefore, trait-specific genotypes identified in this study could be utilized in breeding programmes directed towards the development of improved cultivars and hybrids of bitter gourd.

Molecular Variation in Some Taxa of Genus Astragalus L. (Fabaceae) in the Iraqi Kurdistan Region

Astragalus L. is one of the main genera of blossoming plants, and its diversity of species and forms is well known. The Astragalus L. taxa make a significant contribution to the mountainous and steppe ecosystems of the Kurdistan region of Iraq. Although the species within this genus have been the subject of several molecular studies, the evolutionary relationships among these species remain unidentified. Despite extensive research, little is known about the phylogenetic relationships among the various subgenera of Astragalus. This research is intended to investigate the molecular variation of 33 species of the genus Astragalus L. found in the Kurdistan area of Iraq. For molecular validations, three separate techniques (nuclear ribosomal DNA (rDNA), inter simple sequence repeats (ISSR), and conserved DNA-derived polymorphism (CDDP)) were used. With respect to Astragalus L. indentations, universal ITS1 and ITS4 gene sequencing was used, and the discovered sequences were subjected to BLAST searches in the NCBI database. A phylogenetic tree was generated with two main clades. Regarding detecting genetic diversity between the taxa, 24 molecular markers (14 ISSR and 10 CDDP) were used. High values of polymorphic materials and gene diversity were detected. ISSR markers had an average of 22.71 polymorphic bands per primer, while CDDP markers had the highest mean values for polymorphic information content (0.37), Shannon’s information index (0.27), expected heterozygosity (0.19), and unbiased expected heterozygosity (0.23). Cluster and principal coordinate analyses divided the Astragalus L. taxa into four main groups using the two molecular data sets. According to the results of the molecular variance analysis, the highest variation was detected within sections, with values of 92.01 and 89.48% for ISSR and CDDP markers, respectively. These outcomes suggest the effectiveness of molecular markers and the ITS region in determining and identifying genetic correlations between Astragalus species.

The potential of gamma irradiation on antioxidant capacity and genomic alterations in Calendula officinalis

There are lines of evidence that ionizing radiations such as gamma rays can cause different biological effects on plants. Marigold (Calendula officinalis L.) is a member of the family Asteraceae. It possesses profound amounts of active ingredients. The aim of this study was to evaluate the changes imposed upon different dose levels of gamma radiation on some features of Calendula officinalis such as antioxidant activity, total phenolic compounds and flavonoid contents, antibacterial activity and genomic alterations. Calendula officinalis seeds were exposed to different doses of Gamma radiation (0, 10, 15, 20 and 25 GY). Total phenolics, flavonoids, antioxidant activity (measured by DPPH assay) using methanolic extracts of plants and antibacterial activity measured by the disc diffusion assay showed significant differences to the control samples. The samples treated with 10 GY gamma rays showed the highest total phenol and flavonoid contents. Antioxidant activity significantly differed between Gamma rays dose levels and it was the highest at 25 GY. Four bacterial strains including E. coli, Bacillus subtilis and Pseudomonas aeroginosa were used for the antibacterial assay. Extracts from plants treated with 25 GY gamma rays showed the highest antibacterial activity against the 4 bacterial strains. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the genetic variation. The polymorphism information content (PIC) for RAPD primers ranged from 3% to 13% and ranged from 6 to 13% for ISSR primers. Results indicated that ISSR markers were more efficient than RAPD markers, as they detected 25.57% polymorphic DNA bands compared to 21.31% polymorphism for RAPD markers.

Comparison of horned, polled Bali cattle and Banteng based on microsatellite markers

Bali cattle (Bos javanicus) are domesticated cattle from Banteng. Bali cattle have unique characteristics that is the white sock. In the Maiwa breeding center, Enrekang district, South Sulawesi Province, polled Bali cattle are being kept in large quantities, both male and female. The microsatellites are widely used in the study of population genetics and quantitative trait locus. Therefore, the study aims to observe genetic diversity and determine whether microsatellites can distinguish horned Bali cattle, polled Bali cattle, and Banteng as their wild relatives. DNA was isolated from blood samples of 57 Bali cattle from two different populations: horned Bali (n=20) from Nusa Penida Island Bali province, polled Bali cattle (n=37) from Maiwa Breeding Center, South Sulawesi province, and 20 samples of Banteng from Ragunan Zoo (n=10), Jakarta Province and Surabaya Zoo (n=10), East Java Province. Genotyping was done using 11 microsatellite markers. The size of each microsatellite marker was determined using GeneMapper version 5.0. The observed heterozygosity value (Ho), expected heterozygosity value (He), the heterozygote deficit within the breed (Fis), gene flow (Nm), Hardy-Weinberg equilibrium (HW), and allele frequency were performed using CERVUS version 3.0.7 program. The FSTAT 2.9.4 was performed to obtain Fis value from two different populations.Similarly, bayesian clustering assignments were analyzed using STRUCTURE version 2.2. The polymorphism information content of eleven microsatellite markers ranged from 0.390-0.879. Moreover, we found Fis values of all markers which depicted that there is no inbreeding in horned and polled Bali cattle populations. We also found that polled Bali cattle have more private alleles than horned Bali cattle. Using Bayesian analysis, we found different genetic structures between polled Bali and horned Bali cattle with the K optimal at K=3. Findings indicated that ILST6 allele 288, TGLA53 allele 132, and TGLA227 allele 70 can be considered as the private allele to differentiate between the horned, polled Bali cattle and Banteng.

Genetic Diversity Analysis of Onion (Allium cepa L.) from the Arid Region of Tunisia Using Phenotypic Traits and SSR Markers

The present study was carried out to evaluate and characterize, for the first time, the genetic potential of a collection of onion (Allium cepa L.) local accessions from the arid region of southern Tunisia. The genetic diversity among 135 onion individuals, belonging to 23 accessions, was evaluated using microsatellite (SSR) markers and phenotypic information. A total of 35 alleles were generated with 11 SSRs. The polymorphic information content (PIC) value ranged from 0.08 to 0.95, with an average PIC of 0.43. The expected heterozygosity averaged 0.37, and the observed heterozygosity averaged 0.42. The analysis of molecular variance (AMOVA) revealed that 79% of genetic variation existed within individuals. Structure and cluster analysis grouped the accessions into two major clusters: landraces and pre-breeding lines. For the phenotypic traits evaluated, field trials were conducted in two different environments. Significant differences among accessions were shown, and for most traits, there was also a significant environmental effect and a significant interaction between environment and accession. Great variability was found for all the traits that could be exploited to create new varieties of onion adapted to local conditions by selecting appropriate parents in hybridization breeding.

SSR diversity on rice landraces collected from Yogyakarta Province

In Indonesia, rice is the most common food, and many areas have a lot of rice landraces. Therefore, characterization is very important to be done to identify potential gene sources to be used for the breeding program. The current study aims to learn more about the genetic diversity of rice landrace accessions collected from Yogyakarta province using simple sequence repeat (SSR) markers. A total of 56 accessions of rice landraces originated from Yogyakarta province, and 7 accessions of standard varieties, were used in the study. The DNA sample was extracted from young leaves and isolated for further molecular analysis by using eleven SSR markers. Data analysis was conducted using Power Marker v3.25 for genetic analysis, and DARwin v6.0.021 for cluster analysis and dendrogram visualization. The results of the genetic analysis showed that the average values of major allele frequency, number of alleles, gene diversity, heterozygosity, and polymorphic information content (PIC) were 0.27, 10.1, 0.83, 0.15, and 0.80, respectively. All eleven SSR markers were highly informative (PIC>0.50), as their PIC values ranged from 0.69 to 0.85. These markers have great potential to be used for marker-assisted selection of the germplasm collections. The result of cluster analysis showed that all the rice landrace accessions were separated into three different groups, each consisting of 29, 28, and 6 accessions.

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ&gt;LN&gt;SY&gt;SZ&gt;TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame (Sesamum indicum L.) plays a crucial role in Ethiopian agriculture, serving both subsistence and commercial purposes. However, our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited. To address this knowledge gap, we genotyped 368 Ethiopian sesame germplasms, categorizing into four distinct breeding groups: Accessions, landraces, improved varieties, and wild types, using a comprehensive set of 28 polymorphic markers, including 23 simple sequence repeat (SSR) and five Insertion-Deletion (InDel) markers. These markers ensured robust genomic representation, with at least two markers per linkage group. Our results unveiled substantial genetic diversity, identifying a total of 535 alleles across all accessions. On average, each locus displayed 8.83 alleles, with observed and expected heterozygosity values of 0.30 and 0.36, respectively. Gene Diversity and Polymorphic Information Content (PIC) were recorded at 0.37 and 0.35. The percentage of polymorphic loci varied significantly among breeding groups, ranging from 8.00% to 82.40%, indicating high diversity in accessions (82.4%), moderate diversity in improved varieties (31.20%) and landraces (29.60%), and limited diversity in wild types (8.00). Analysis of Molecular Variance (AMOVA) results emphasized significant genetic differentiation among populations, with substantial diversity (P ​< ​0.001) within each population. Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations, while the larger proportion of genetic diversity (92%) resided within each individual sesame population, showcasing heightened diversity within each group. Our study's findings received support from both Bayesian clustering and Neighbor-joining (NJ) analysis, reaffirming the credibility of our genetic structure insights. Notably, Population structure analysis at its highest Δk value (k ​= ​2) revealed the existence of two primary genetic clusters, further subdivided into four sub-populations at k ​= ​4. Similarly, NJ analysis identified two prominent clusters, each displaying additional sub-clustering. In conclusion, our research provides a comprehensive understanding of genetic groups, subpopulations, and overall diversity within Ethiopian sesame populations. These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections. This genetic richness holds promise for breeding and conservation efforts, highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Enhancement of some barley (Hordeum vulgare L.) resistance for nematode (Heterdra avanae) using DNA fingerprinting analysis

Background Heterodera avenae, the cereal cyst nematode or European cyst nematode, is a plant pathogen and an obligate parasite of cereal crops including barley, oats, wheat, and rye. Cereal crops infected with this nematode are more susceptible to infection by fungal diseases such as Rhizoctonia root rot. Objective The main objective of the present study was to map Heterodera avenae resistance and to compare seven different species. This study also aimed to increase the efficiency and precision of standard procedures for testing the resistance of barley toward root-lesion nematodes. Materials and methods The genetic variability analysis of seven barley genotypes, of Egypt was achieved using 7 Inter simple sequence repeat (ISSR) primers. Phylogenetic relationships of seven accessions of (Hordeum vulgare L.) collected from different region of Egypt were assessed. The soil was sterilized in an autoclave of each pot was planted in the comparison experiment, as well as in the treatment experiment with nematode Heterdra avanae infected soil brought from an infected field, and this soil was added to the treated pots. Also (ISSR) molecular marker technique was used for DNA fingerprinting and assessing genetic diversity and phylogenetic relationships in barley germplasm. Results and conclusion A significant correlation was observed between the Jaccard’s dissimilarity matrices based on ISSR markers, as revealed by Mantel test using the Pearson correlation coefficient (r = 0.69; P &lt; 0.05). The results showed that ISSR primers produced 37 bands their size ranged between 100-2000 bp with (87.5%). polymorphism percentage. Polymorphic information content PIC was 0.74 for ISSR. Unweighted Pair Group Method with Arithmetic (UPGMA), Dendrogram was divided into two clusters by morphological traits and ISSR analysis. Genetic similarity matrix was examined with Jaccard’s coefficient, maximum similarity was found between Giza126 and Giza127 (99%) with morphological analysis both and lowest similarity between Giza123 and Giza126 (6%) with ISSR analysis. Determination of genetic diversity between barley is of major importance for characterization of barley germplasm, breeding programs and conservation purposes. Morphological traits and ISSR analysis are effective tools for detecting genetic variations. The results showed that H. vulgare have high ratio of variation. This study may be considered as reference study for further studies on H. vulgare and may contribute to species concept and breeding programs.