Polymorphism Information Content Values Research Articles

CDDP and ISSR markers-assisted diversity and structure analysis in Iraqi Mazu (Quercus infectoria Oliv.) accessions

Mazu, or oak gall (Quercus infectoria Oliv.), a member of the Fabaceae family, is an abundant tree species in Iraq. Because of ongoing habitat damage, this species is on the verge of extinction. However, the genetic diversity of wild oak populations has yet to be measured. Semi-arbitrary [Inter-simple sequence repeat (ISSR)] and gene-targeted [Conserved DNA derived polymorphism (CDDP)] markers were employed separately or in combination to investigate genetic diversity within and among 85 Iraqi Mazu (Q. infectoria) accessions based on geographic origin. A total of 88 polymorphic alleles were produced in this investigation utilizing nine CDDP primers, with an average of 9.78 alleles per primer. The mean values for the major allele frequency (MAF), polymorphism information content (PIC), and marker index were 0.23, 0.29, and 2.79, respectively. Twenty ISSR primers were used to amplify 195 alleles (9.75 bands per primer), with MAF, PIC, and MI values of 0.21, 0.28, and 2.72, respectively. All accessions were divided into two major groups with multiple sub-groups based on Ward clustering and structure analysis. Within-population variance was calculated to be 94.17% using CDDP markers and 92.97% using ISSR markers. As per the fixation index values derived from the STRUCTURE analysis, there was a significant difference within the population. Increased gene flow was found among populations. The correlation (r) between the CDDP-based genetic distance matrix and the ISSR-based genetic distance matrix was 0.54, with a p-value of 0.001. The genetic dissimilarity calculated by CDDP and ISSR data revealed a wide range of diversity, demonstrating substantial genetic variation across accessions originating from various populations. This investigation’s findings could aid in the conservation and further utilization of oak germplasm.

Phylogenetic Analysis of Ryegrass (Lolium rigidum) Populations and the Proliferation of ALS Resistance in Saudi Arabia

Morphological and simple sequence repeat (SSR) approaches were used to determine the genetic diversity of 29 ryegrass (Lolium rigidum) genotypes belonging to eight populations collected from several regions in Saudi Arabia. In this study, 50 in Silico-developed SSR markers derived from genomic and expressed sequence tag (EST) microsatellites were examined. Analysis of variance showed highly significant differences in all studied traits. Cluster analysis based on the morphological data of the 29 Lolium genotypes and using PAST (paleontological statistics) software was performed. According to the results, clustering was based mostly on genotype location. The sensitive genotypes for herbicide were clustered in one group. In addition, using EST-SSR markers, we observed the existence of a considerable number of genetic variations among Lolium genotypes. From these markers, only 31 produced reasonable amplification products. The results showed that 23 SSR markers revealed that 74.19% were polymorphic. The number of alleles detected per primer ranged from one to five in the primer LTC SSR1. The tested primers amplified 1434 bands across eight populations, with an average of 46.26 bands per primer. The polymorphism information content (PIC) values ranged from 0.11 to 0.76 for the primers LT EST-SSR5 and LTC SSR1. The unweighted pair group method with arithmetic average (UPGMA) clustering of the 29 genotypes representing eight populations was based essentially on their locations and herbicide-tolerance levels. Most of the populations formed into four clusters, together representing genotypes. Moreover, the tolerant populations were distinguished from the sensitive ones. The relationship between the genetic diversity and geographical source of Lolium rigidum populations of Saudi Arabia was revealed through this study. The results showed that the efficiency of developed SSR markers are transferable across species. They have been helpful to assess the genetic diversity of the ryegrass population as this could be applied to differentiate between tolerant and sensitive populations of ryegrass.

Genetic diversity and population structure analysis of Grass pea (Lathyrus sativus L.) accessions collected from North-Western Ethiopia using SSR markers

Grass pea (Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to the presence of a neurotoxin that causes lathyrism in the crop, it has been neglected and underutilized. As a necessary first step towards, therefore, this investigation was undertaken to assess the genetic diversity and population structure that existed within grass pea accessions collected from North-West Ethiopia using simple sequence repeat markers. Twenty-five grass pea accessions collected from the Ethiopian Biodiversity Institute were planted at the College of Agricultural Science, Ebonyi State University, Nigeria. The genomic DNA was extracted using Quick-DNA™ ZR Plant/Seed Miniprep Kit and amplified in an ABI Veriti PCR machine with 10 pairs of SSR markers in IITA, Ibadan, Nigeria. Out of 10 SSR primers, only eight primers were polymorphic. A total of 41 alleles were detected with an average of 5.13. The Polymorphism Information Content and Gene Diversity values ranged from 0.074 to 0.944 with a mean of 0.474 and 0.536 respectively. The largest pairwise genetic distance (0.365) was detected between North Gondar and East Gojjam populations. The ФPT (analog of FST test) estimated through AMOVA were 0.24, 0.20, and 0.05 for within accessions, among regions, and population within regions respectively. The highest genetic differentiation value (76%) resides within accessions followed by 20% among regions. Both the population structure and cluster analyses grouped the 25 grass pea accessions into two distinct subgroups. This grouping pattern indicates the presence of gene flow among geographic regions. In general, the findings of this study indicate that despite few numbers of SSR markers it was possible to detect genetic diversity among grass pea accessions indicating the power of the SSR marker in picking up the existing genetic diversity within the studied accessions.

Insights into the genetic diversity of an underutilized Indian legume, Vigna stipulacea (Lam.) Kuntz., using morphological traits and microsatellite markers.

Vigna stipulacea (Lam.) Kuntz., commonly known as Minni payaru is an underutilized legume species and has a great potential to be utilized as food crop. To evaluate and select the best germplasm to be harnessed in the breeding programme, we assessed the genetic diversity of V. stipulacea (94 accessions) conserved in the Indian National Genebank, based on morphological traits and microsatellite markers. Significant variation was recorded for the morphological traits studied. Euclidean distance using UPGMA method grouped all accessions into two major clusters. Accessions were identified for key agronomic traits such as, early flowering (IC331436, IC251436, IC331437); long peduncle length (IC553518, IC550531, IC553557, IC553540, IC550532, IC553564); and more number of seeds per pod (IC553529, IC622865, IC622867, IC553528). To analyse the genetic diversity among the germplasm 33 SSR primers were used anda total of 116 alleles were detected. The number of alleles varied from two to seven, with an average of 3.52 per loci. The polymorphic information content values varied from 0.20 to 0.74, with a mean of 0.40. The high number of alleles per locus and the allelic diversity in the studied germplasm indicated a relatively wider genetic base of V. stipulacea. Phylogenetic analysis clustered accessions into seven clades. Population structure analysis grouped them into five genetic groups, which were partly supported by PCoA and phylogenetic tree. Besides, PCoA and AMOVA also decoded high genetic diversity among the V. stipulacea accessions. Thus, morphological and microsatellite markers distinguished V. stipulacea accessions and assessed their genetic diversity efficiently. The identified promising accessions can be utilized in Vigna improvement programme through introgression breeding and/or can be used for domestication and enhanced utilization of V. stipulacea.

Applicability of inter-primer binding site iPBS- retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm

Rosewood (Aniba rosaeodora Ducke), which has a great demand due to its essential oil globally, is an evergreen tree of the Amazon forests. Rosewood natural stands have been depleted through deforestation and the destruction of habitat. Currently, rosewood is included in the ICUN red list of endangered species. The 11 highly polymorphic primers amplified total 305 bands of which 301 (98.69%) were polymorphic. The number of effective alleles (Ne), Shannon's information index (I), overall gene diversity (Ht), gene diversity (h), and polymorphism information content (PIC) were (1.562), (0.505), (0.330), (0.337) and (0.343), respectively. These diversity indices explored high genetic diversity in rosewood germplasm. Among studied germplasm, the Santa Marta population was found most diverse by reflecting higher values of diversity indices while the Zungarococha population was found least diverse. The analysis of molecular variance (AMOVA) revealed that 79% of the genetic variation was within the populations. The STRUCTURE algorithm, unweighted pair group with arithmetic mean (UPGMA), and principal coordinate's analysis (PCoA) separated all germplasms into different population groups according to their geographic locations. Santa Marta population was found more diverse by reflecting higher values of diversity indices. The maximum genetic distance (0.868) was found between the Huajoya-10 and Nanay-3. In this investigation, iPBS- retrotransposon marker system was used to explore the genetic diversity of Peruvian rosewood germplasm. The results in this study such as higher genetic diversity indices, AMOVA (79%) within population and PIC value (0.343) showed the utility and reproducibility of iPBS-retrotransposons in this species successfully. The STRUCTURE algorithm separated the germplasms into six population groups according to their geographic locations. These results have valuable information for the conservation, management strategies and future breeding activities of rosewood.

Molecular Characterization of Sixty Local Mango Germplasm of Chapainawabganj

The experiment was conducted at Plant Genetic Resources Centre, Bangladesh Agricultural Research Institute (BARI) and the genotypes were collected from Chapainawabganj, the most mango variability rich district in Bangladesh. The molecular characters of mango germplasm were assessed by using six simple sequence repeat (SSR) markers. Polymerase chain reaction (PCR) amplification of the DNA isolated from 60 mango germplasm with 6 SSR primers was performed. The sizes of the alleles detected ranged from 112 to 221 bp. SSRs exhibited moderate values of polymorphic information content (PIC) range of 0.9405 to 0.6501. Genetic distances (D) between varieties were computed from combined data of the 6 primers, ranging from 0.5000 to 1.0000. Moderate degree of genetic diversity was obtained where the highest level of gene diversity value was noted 0.9433 in loci MIGA179 and the lowest level of gene diversity value was computed 0.6683 in loci MIGA253 with a mean diversity of 0.8842. The dendrogram generated from the unweighed pair group arithmetic average (UPGMA) cluster analysis broadly placed 60 mango cultivars into ten major clusters. The cluster size varied from 1 to 12 and cluster-VI was the largest cluster comprising of 9 cultivars. The tendency of clustering among mango cultivars revealed that they have strong affinity towards further breeding programme.

MUTAGENESIS FOR THE DEVELOPMENT OF SUBMERGENCE TOLERANCE RICE GENOTYPES in Indica BY GAMMA IRRADIATION-INDUCED MUTATION USING 60CO SOURCE ISOTOPE WITH MARKER ASSAY

The high selection pressure applied to rice breeding since it was domesticated thousands of years ago has initiated a narrowing its genetic variability. Obtaining new rice varieties therefore becomes a major challenge for breeders and the development of techniques to increase genetic variability has attracted the attention of various research groups. Understanding mutations and their application has paved the way for the interpretation of immersion tolerant rice. Creating variability through mutations has therefore become the most important tool for rice improvement. Gamma-rays were able to create genetic variables for abiotic stress tolerance, such as submergence tolerance as well as plant height, number of tillers, shoot and root weight, total biomass, and panicle length. Among the three parents of BRRI dhan52, Guti swarna and Mamun swarna, the highest average yield plant-1 (46.56 g) was produced by Mamun swarna (cont.) and the lowest (18.16 g) by BRRI dhan52. On the other hand, the group of all mutants, Mamun swarna-250 (M3) was more productive (39.30 g) and the maturation was 142.66 days from Guti swarna-300 (M3) (20.20 g) and maturity duration was 151.66 days. The first three principal components studied, including the Eigen value, explained 80.4% of the total variation in 11 rice genotypes for 9 quantitative traits. The gene diversity value of allele across 11 genotypes was 0.469. The value of polymorphism information content (PIC) was 0.359 (SC34 / RM23679) and the allele frequency (%) was 62. However, this assessment may be effective in developing reliable mutants for significant submergence stresses in rice.

Genetic polymorphisms of the 5' untranslated regions of the HSP70 gene in Indonesian cattle populations.

Background and Aim:Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. HSP70 is a conserved, sensitive, and abundant gene associated with heat stress’s physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the HSP70 gene (5’ untranslated region [UTR]) in seven cattle populations in Indonesia.Materials and Methods:Polymerase chain reaction products (551 bp) of the HSP70 gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue x Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method.Results:Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy–Weinberg equilibrium (p>0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the HSP70 gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue x PO crossbred cattle were farther apart.Conclusion:The polymorphisms in the 5’ UTR of the HSP70 geneidentified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.

SSR Marker Based Genetic Diversity and Fusarium Wilt Resistance Screening of Tomato (Solanum lycopersicum L.) Genotypes

Fusarium oxysporum is one of the devastating diseases of tomato (Solanum lycopersicum L.) causing high yield losses in fields and commercial greenhouses, inferring necessity for development of disease resistance. An research experiment was laid out with 23 diverse genotypes including susceptible check at research farm during wet season-2018 for screening of tomato genotypes for fusarium wilt resistance. Phenotypic screening of 23 genotypes revealed varied disease resistance as highly resistant (AVTO1219 and EC631), resistant (Pant bahar, EC620428, EC620378, EC631369 and EC620503), moderately resistant (EC615055, EC620389, EC620394, EC620422, EC620406 and AVTO9803) and moderately susceptible (PKM1, EC620382, EC620427 and EC620395) over the highly susceptible checks (Pusa Ruby, Arka Vikas). Employing 95 SSRs for molecular profiling resulted in 33 polymorphic markers, 58 monomorphic markers and remaining 4 markers as unamplified. A total of 74 alleles were detected using 33 polymorphic markers with an average allele number of 2.24 for each marker. Two markers viz., TES60 and TGS633 produced maximum (4) alleles. The polymorphic information content (PIC) value ranged from 0.28 to 0.76 with an average of 0.53 and marker TGS633 was found to be the most suitable marker with the highest PIC value. Cluster analysis through UPGMA method classified twenty three genotypes into five clusters and the coefficient among 23 genotypes was varied from 0.5 to 0.86. Over all, EC631379, EC631369, EC620428, EC620378 and EC620503 were identified as new resistant genetic resources against Fusarium wilt at both phenotypic and genotypic level with the presence of I-2 gene loci. Based on the results, the identified genotypes can be further tested and be used in Marker Assisted Selection or gene pyramiding programs to develop disease resistant commercial cultivars.

Genetic diversity of oat accessions revealed by SSR markers

Oat is an important cereal crop for the food and feed industries. Genetic resources of oat are the basic materials for sustainable breeding programs. Microsatellites (SSR) are a useful tool for understanding the genetic background of oat germplasm resources. We used 83 SSR primer pairs to assess the genetic diversity of 286 oat accessions from five countries. The results indicated the presence of considerable variation among accessions. The number of alleles per SSR locus ranged from 2 to 8, with an average of 3.49; allelic frequencies ranged from 0.002 to 0.709; Nei’s genediversity was 0.67, ranging from 0.44 to 0.85; and polymorphism information content (PIC) values ranged from 0.37 to 0.83. Genetic distance estimated by the Jaccard model was compared between accession groups as well as among all accessions using all marker alleles. The principle coordinates analysis based on genetic dissimilarity also revealed distinct groups of accessions. We concluded that SSR markers are effective for identification of oat germplasm resources and use of germplasm from North America and Asia should lead to significant progress in Mongolian oat breeding programs.

Molecular characterization of mutant lines of Ayvalik olive cultivar obtained by chemical mutation

This research was carried out with the aim to detect the mutagenic effect of three different doses (15, 20 and 25 mM) of Ethyl Methane Sulphonate on the Ayval?k olive cultivar (Olea europaea L.), to detect the variation and to identify whether individuals are genetically different from Ayval?k olive cultivar using molecular marker technologies. 23 mutant lines were screened using 28 SSR markers and a total of 138 alleles were detected and the number of alleles per primer ranged from 2 to 9 with an average of 4.9 alleles per primer. The polymorphism information content (PIC) value was changed between 0.4-0.98. The genetic similarity between Ayval?k olive cultivar and mutant lines was found between 5.5% and 78%. The mutant lines 15mM-12, 15mM-11 and 25mM-3 were found similar to Ayval?k cultivars at the rate of 78, 63 and 55%, respectively. Whereas, 20mM-5, 15mM-4 and 15mM-15 mutant lines were found distant to Ayval?k cultivar at the rate of 5.5, 5.6 and 8% genetic similarity, respectively. Ethyl Methane Sulphonate was successfully used in this study to extend the genetic diversity of the Ayval?k olive cultivar. Mutants might be screened for agricultural and quality traits and promising lines might be registered.

Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.

Morphological and molecular characterization of cowpea (Vigna unguiculata L. Walp.) genotypes

Cowpea [Vigna unguiculata (L.) Walp.], is a legume and one of the most ancient crops known to man and grown in tropical and subtropical regions. Cowpea seeds have a high nutritional value containing high amount of protein (20-25%). Despite of its importance, the utilization of genetic diversity and germplasm characterization in cowpea breeding program has not been fully exploited. Therefore, twelve morphological characters and six polymorphic microsatellite/simple sequence repeat (SSRs) markers were used to analyze genetic diversity in thirty-eight cowpea genotypes. The dendrogram was constructed using UPGMA algorithm and Gower?s dissimilarity values (ranged from 0.0601 to 0.5589) derived from twelve morphological characters. It was grouped in seven clusters showing the most diverse genotypes were CGD 1246 and CGD 1311 (Gower?s distance: 0.5589) and the most similar genotypes were GC 1501 and GC 1601 (Gower?s distance: 0.0601). In molecular characterization, a total of 14 amplicons were detected with a ranged from two to three with an average 2.33 alleles per loci. The mean values of polymorphic information content (PIC) and heterozygosity was 0.319 and 0.399, respectively which are measures of the efficiency of markers for studying polymorphism level available in the cowpea genotypes. Total 224 amplicons were considered for to derive Jaccard?s similarity matrix for the construction of dendrogram (having six clusters) and 2-D PCA (Principal Component Analysis) plot. The morphological characters and SSR markers can be used in diversity analysis and characterization of cowpea genotypes. The per se performing genotypes for individual character can be exploited in population/genotype development of cowpea for the improvement of that particular character. This will provide information to plant breeders for selection of parents to develop populations in cowpea breeding programs.

Development and application of a duplex simple sequence repeat panel for outcrossing fertility evaluation in red clover (Trifolium pratense) under open-pollination conditions†

Context Red clover (Trifolium pratense L.) is an important legume forage in temperate agricultural zones. Evaluation of self- and cross-pollination fertility is important for setting up an effective breeding-program scale. However, the outcrossing rate of red clover under open-pollination conditions is not certain. Development of a reliable and time-saving marker system is needed to quantify and characterise outcrossing rates. Aim We aimed to develop a duplex PCR-based protocol based on a genome-wide simple sequence repeat (SSR) screen, and to determine the outcrossing rate of red clover under open-pollination environments. Methods We screened 209 SSR markers with pooled DNA samples of 60 plants from 20 red clover accessions, and selected 185 SSR markers that produced clear scorable bands for testing with 24 individual DNA samples to determine polymorphism. We selected 70 primer pairs, and then assembled a core set of 24 loci into 12 sets of duplex markers, which were used for outcrossing behaviour analysis of 60 maternal parents and their respective 22 half-sib progenies. Key results Mean polymorphic information content (PIC) for the 70 markers was 0.490 (range 0.117–0.878). Minimum, mean and maximum PIC values for the 24 markers constituting the 12 duplexes were 0.226, 0.594 and 0.781, respectively. The outcrossing rate was identified as 99.4% for red clover in a natural environment. Conclusion We successfully developed a duplex SSR-based PCR protocol consisting of 24 markers. This SSR system was applied to determine the outcrossing rate of red clover in a natural environment.

DNA PROFILE OF COMMERCIAL PINEAPPLES IN MALAYSIA BY USING SSR MARKERS

Nine commercial varieties of pineapples in Malaysia (Josapine, Maspine, MD2, Sarawak, Gandul, N36, Moris, Crystal Honey and Yankee) were collected from various places in Peninsular Malaysia and analysed for cultivar identifications using nine simple sequence repeat (SSR) markers. A total of 27 alleles have been observed which ranged from 2 to 5 with an average of 3 alleles per locus. The polymorphic information content (PIC) value ranged from 0.3426 (Acom_82.8) to 0.6561 (Acom_67.2) with a mean of 0.4524 while the heterozygosity value ranged from 0.1097 (TsuAC021) to 0.8010 (TsuAC039) with a mean of 0.5481. The pairwise Nei’s genetic distances had also been calculated and the value ranged from 0.0562 (Gandul and Josapine) to 0.6383 (MD2 and Yankee) with an average value of 0.3169. The above data emphasised a moderate level of polymorphisms among the nine varieties. A dendrogram was constructed by using the unweighted pair group method with arithmetic mean (UPGMA) which showed all the nine successfully differentiated pineapple commercial varieties. A principal coordinate analysis (PCoA) was also had been generated which revealed an agreement with the dendrogram output. Therefore, these nine SSR markers can be used to identify the nine selected commercial varieties to ensure pure planting materials.

Characterization and Genetic Diversity of Photoperiodic among Mutant Kenaf (Hibiscus Cannabinus L.) Using EST-SSR Markers

ABSTRACT Information on molecular genetic diversity among Hibiscus cannabinus L. lines is crucial for developing a new variety from the existing germplasms based on consumer demand. Based on this premise, the allelic diversity of thirty-one kenaf genotypes were assessed using polymorphic EST-SSR. From the 72 EST-SSR primers tested, 10 showed sharp and clear polymorphic bands ranging from 4 (137 to 225 bp) to 7 (182 to 382 bp) alleles with a mean value of 5.2 per primer. The Polymorphism Information Content (PIC) value ranged from 0.531 to 0.737, with a mean of 0.610, indicating that the genotypes are genetically diverse. Shannon index estimation varied from 0.982 to 1.515, whereas 0.123 to 0.405 was recorded within the groups. Genetic differentiation ranged from 0.67 to 1 alongside the average gene flow (Nm) of 0.024. The AMOVA revealed 76% variation within the population, while the population gain recorded was 24%. UPGMA dendrogram indicated the relationship and categorized the evaluated kenaf mutants into five major groups. This study revealed the existence of significant variation in kenaf mutants based on EST-microsatellites. These results could be used for future breeding programs and conservation of germplasms to enhance Hibiscus cannabinus L. genotypes.

Investigation of population structure and molecular genetic diversity under coastal agro-ecosystem in rice (Oryza sativa L.)

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Thirty nine simple sequence repeat (SSR) markers were selected in order to evaluate the genetic diversity in 88 genotypes. A total of 115 alleles were detected in 39 SSR polymorphic markers. The number of alleles per marker ranged from 1 to 5, with an average of 3 alleles per locus. An average polymorphism information content value of 0.5615 was recorded. It ranged from zero (RM431, RM379 and RM262) to 0.6476 (RM324), indicating significant genetic diversity among and within the rice accessions of the present study. The average observed heterozygosity was 0.1136, while the average expected genetic diversity was 0.6105. A dendrogram constructed using the Unweighted Pair Group Method with Arithmetic means (UPGMA), grouped the 88 rice genotypes into three well differentiated major clusters. The structured program without prior information provided support for the existence of three genetically distinct clusters (K=3). Key words: Cluster analysis, SSR marker, Oryza sativa, Rice breeding, Variability.

Cevizde açık tozlanmış tohumlardan elde edilen genotiplerde fenolojik ve moleküler karakterizasyonun belirlenmesi üzerine bir araştırma

This research was carried out to reveal the phenological and genetic differences between the S-1/1 walnut genotype and its 94 progenies. In the phenological observations made, it was observed that budburst in genotypes took 52 days, leafing 50 days, leaf yellowing 31 days, and defoliation date 27 days. When the mother plant (S-1/1) and the genotypes were compared, it was found that there was a phenological variation of 75.54% in budburst, 73.41% in the leafing, 34.05% in leaf yellowing, and 93.62% in defoliation date, while the average variation was 69.15%. In the dendrogram obtained using phenological data, 2 main and 5 subgroups were obtained. In molecular genetic analyzes, 7 ISSR primers were used to determine genetic variations, as a result, 7 monomorphic and 45 polymorphic bands were obtained, and the rate of polymorphism was found to be 86.53%. The average number of alleles was calculated to be 7.42. In genotypes, the polymorphism information content (PIC) value varied between 0.48 and 0.95, while the average PIC value was calculated to be 0.73. As a result of cluster analysis, it was seen that genotypes were divided into 2 main clusters and 2 subsets. At the end of the study, it was determined that the S-1/1 and its progenies have a significant variation both phenologically and genetically.

Marker based genetic variability analysis of rice (Oryza sativa L.) landraces for drought tolerance

Under the present study, assessment of genetic variability of 60 numbers of rice landraces was carried out under morphological and molecular level for selection of promising drought tolerant genotypes under upland ecosystem of North East India. Predominance of additive gene action on characters like leaf rolling index, root: culm ratio, grain yield and other yield contributing traits like plant height came out as effective parameters for selection of drought stress tolerant landraces. Molecular analysis revealed moderate genetic diversity with average Polymorphic Information Content values of 0.44 across the rice landraces. No specific clustering patterns of landraces against some morphological traits numbers of productive tillers per plant, numbers of filled grains per plant etc were found. This signifies the polygenic nature of the quantitative characters and influence of environment on them. Precise correlation between the morphological performance of the landraces and their clustering pattern under molecular analysis was found to be effective in identifying suitable landraces like Chikanswarikabar as a promising parent for future breeding programme and also to formulate efficient strategies for sustainable management of rice landraces under rain fed ecosystem.

Biodiversity of some fig cultivars in Southern Syria

This research has been conducted in the Biotechnology Laboratory in Damascus University_ Damascus, Syria where the genetic diversity of fourteen cultivars of figs (Ficus carica L.) growing in Swaida governorate which located in the south region of Syria were investigated using (Simple Sequence Repeats) SSRs technique, where 4 cultivars of them were genotypes scattered in the local fields without any scientific taxonomy and farmers did not classify them properly. Eight pairs of SSRs markers were used depend on their ability to separate between fig cultivars as mentioned in previous studies, six pairs of them gave amplified products in the polymerase chain reaction (PCR), while MFC3 and MFC6 primers did not give any amplification products. A total of 17 alleles were detected at six SSRs loci. The alleles number per locus ranged from 2 to 4 with an average of 2.83 alleles/locus. The observed heterozygosity (Ho) was 0.33, while the expected heterozygosity (He) was 0.17. The mean value of genetic similarity was 0.69 where fig cultivars has separated into two clusters in Cluster Analysis, which confirms a significant genetic similarity between most of the cultivars. MFC1 and MFC2 loci gave about 0.67 and 0.61 PIC (Polymorphism Information Content) values respectively, which confirms their ability to study the genetic diversity of fig cultivars more than other loci. F1 and F2 cultivars greatly affect the quality of the fruits as paternity traits as Caprifigs. Tammozi cultivar has low values of its genetic similarity with the rest of the cultivars which reflect great difference between it and other cultivars. Generally, the challenges in this study were in characterizing unrecognized fig cultivars in southern Syria to distinguish between them as they were not certified in agriculture ministry in Syria because the lack in studies related to the same topic as these cultivars were not studied before, thus, we managed to make a significant contribution in certifying fig cultivars in Syria using SSR technique.