Unweighted Pair Group Method Of Arithmetic Averages Research Articles

Characterization of genetic diversity in Curcuma longa L. cultivars using Start Codon Targeted (SCoT) markers

Curcuma longa L. (Family- Zingiberaceae), commonly called turmeric, is one of the most important commercial spices. Being a center of turmeric's diversity, India boasts of more than fifty cultivars with variable agronomic characters and curcumin content. However, the quest for calibrating their genetic variability remains debatable as popular molecular marker-based studies have yielded inconsistent results. A promising PCR-based approach, known as the Start Codon Targeted (SCoT)-PCR system has been established to be more efficient than random DNA marker systems because this technique can generate more information on genetic polymorphism patterns. Hence, the present study proposes to use Start Codon Targeted (SCoT) markers to assess inter-cultivar genetic diversity of turmeric. We report an orthogonal L16 (45) design-based approach to investigate the influence of five crucial factors (dNTPs, Taq DNA polymerase, primer, template DNA and annealing temperature of primer) on the efficiency of the polymerase chain reaction (PCR) for development of an optimized Start Codon Targeted (SCoT) amplification protocol using twenty-seven different cultivars of C. longa. The optimized PCR protocol yields best results with a 20 uL reaction mixture, containing 10×PCR Buffer (with 15 mM MgCl2), 2.5 mM dNTPs, 10 mM SCoT primer, Taq polymerase (2 U), template DNA (50 ng), which was verified by using twenty-five SCoT primers. This standardized rapid protocol of SCoT-PCR reported here was employed to examine genetic diversity among twenty-seven Indian cultivars of turmeric, revealing high range of polymorphism ranging from 81.25 % to 100 %. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data segregated the twenty-seven cultivars into two main clusters. The first cluster comprised of nine cultivars (36 % of the cultivars) which was further divided into three sub-clusters and the second one consisted of eighteen cultivars (64 %) which further divided into four sub-clusters. From the results of this study, it can be inferred that the employment of SCoT markers can be an effective tool for analysing genetic variability, phylogenetic relationships and develop a rich genetic resource management system for C. longa cultivars.

Analysis of Genetic Variability of Potato Induced Mutants Using Simple Sequence Repeat (SSR) Markers

Aims: Potato (Solanum tuberosum L.) is ranked fourth amongst the world’s major stable food crop and second in Kenya after maize and thus plays a vital role in food and nutrition security and sustainable development. Despite its importance, potato production in Kenya is still low due to abiotic and biotic constraints. Traditional breeding and improvement have been difficult due to the narrow genetic diversity of the crop owed to the complex tetrasomic inheritance patterns. Induced mutation has been used to generate genetic variations in potato from which desired putative mutants are selected. In most cases the level of genetic variability is not known. The objective of this study was to determine the genetic variability of potato mutants using SSR markers. Study Design: The study involved three potato varieties; Asante, Kenya Mpya and Kenya Sherekea which are high yielding and commercially grown varieties in Kenya. Place and Duration of Study: Sample: They were irradiated at different dose rates of gamma rays at Co60 source at FAO/IAEA laboratories, Seiberdorf Austria in 2014. A total of 163 mutants were advanced to M1V4 generation at the University of Eldoret between 2015 and 2018. Methodology: Genomic DNA was extracted to assess the diversity with 20 SSRs markers. Results: All the 20 SSR primers were polymorphic with 6-19 bands amplified per primer and marker STM5127 showed the highest allele number (19) using PowerMarker software. The STRUCTURE analysis suggested that the potato mutants were clustered into six sub-populations based on the unweighted pair-group method of arithmetic averages (UPGMA) thus, the accessions were divided into three major clusters. Analysis of molecular variance (AMOVA) indicated that 8.6% of total molecular variance was attributed to diversity among sub-populations, while 91.4% of variance was associated with differences within sub-populations. Conclusion: This study highlights the most comprehensive investigation of the genetic diversity and population structure of potato mutants, and provides valuable information for genetic improvement, and systematic utilization.

Agro-morphological, biochemical, and molecular markers of barley genotypes grown under salinity stress conditions

The aim of this study was to evaluate the impact of salt stress on morphological, yield, biochemical, and molecular attributes of different barley genotypes. Ten genotypes were cultivated at Fayoum Research Station, El-Fayoum Governorate, Egypt, during two seasons (2020–2021 and 2021–2022), and they were exposed to two different salt concentrations (tap water as a control and 8000 ppm). The results showed that genotypes and salt stress had a significant impact on all morphological and physiological parameters. The morphological parameters (plant height) and yield attributes (spike length, number of grains per spike, and grain yield per plant) of all barley genotypes were significantly decreased under salt stress as compared to control plants. Under salt stress, the total soluble sugars, proline, total phenol, total flavonoid, ascorbic acid, malondialdehyde, hydrogen peroxide, and sodium contents of the shoots of all barley genotypes significantly increased while the potassium content decreased. L1, which is considered a sensitive genotype was more affected by salinity stress than the tolerance genotypes L4, L6, L9, and Giza 138. SDS-PAGE of seed proteins demonstrated high levels of genetic variety with a polymorphism rate of 42.11%. All genotypes evaluated revealed significant variations in the seed protein biochemical markers, with new protein bands appearing and other protein bands disappearing in the protein patterns of genotypes cultivated under various conditions. Two molecular marker techniques (SCoT and ISSR primers) were used in this study. Ten Start Codon Targeted (SCoT) primers exhibited a total of 94 fragments with sizes ranging from 1800 base pairs to 100 base pairs; 29 of them were monomorphic, and 65 bands, with a polymorphism of 62.18%, were polymorphic. These bands contained 21 unique bands (9 positive specific markers and 12 negative specific markers). A total of 54 amplified bands with molecular sizes ranging from 2200 to 200 bp were produced using seven Inter Simple Sequence Repeat (ISSR) primers; 31 of them were monomorphic bands and 23 polymorphic bands had a 40.9% polymorphism. The techniques identified molecular genetic markers associated with salt tolerance in barley crop and successfully marked each genotype with distinct bands. The ten genotypes were sorted into two main groups by the unweighted pair group method of arithmetic averages (UPGMA) cluster analysis based on molecular markers and data at a genetic similarity coefficient level of 0.71.

Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers

Abstract. Boonsrangsom T, Fuenghoi C, Premjet D, Suvittawat K, Ratanasut K, Sujipuli K. 2023. Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers. Biodiversitas 24: 3758-3765. Edible bananas and plantains, belonging to the family Musaceae, genus Musa, represent one of the most important fruit crops, with an annual production of more than 65 million tons worldwide. Bananas have several hybrid variations since they are descended from the two species Musa acuminata Colla (AA genome) and Musa balbisiana Colla (BB genome). Different morphological traits divide almost hybrid bananas into various genomic groupings. Banana genome categorization and identification, however, have always been challenging issues. This study aimed to assess the genetic relationships and verify the genomes of Thai banana cultivars using random amplification of polymorphic DNA (RAPD) markers. Using the 15 selected RAPD markers, 149 RAPD bands were found, with sizes ranging from 0.2 to 3.2 kb, and 88.6% were polymorphic. Polymorphic information content (PIC) values ranged from 0.18 to 0.42, averaging 0.30. Based on the Jaccard coefficient, the unweighted pair-group method arithmetic average (UPGMA) analysis showed that the banana samples had a similarity range of 0.27 to 1.00 with a mean of 0.56, demonstrating an abundance of viability across six banana genomes. The dendrogram generated from RAPD data revealed that all 18 Musa samples could be divided into two main groups (Group I and II). Three additional subgroups were created for each primary group (A, B, and C). The accurate identification and genetic data on the available genetic resources for bananas will be beneficial for breeding and conservation programs.

Genetic diversity and proteomic analysis of vegetable soybean (Glycine max (L.) Merrill) accessions grown in mineral and BRIS soils

Knowledge of the molecular mechanisms of response to environmental stress is fundamental for the development of genetically stress-tolerant crops. This study aims to find vegetable soybean accessions tolerant to cultivation in stressful tropical environments. Fourteen accessions of the vegetable soybean (Glycine max (L.) Merrill) were grown in mineral and beach ridges interspersed with swale (BRIS) soils. The genetic diversity, estimated using inter-simple sequence repeat (ISSR) markers, revealed 42.50% polymorphism and was regarded as moderate. The unweighted pair-group method arithmetic average (UPGMA) analysis allocated the tested accessions into five major clusters at a similarity coefficient level of 0.43. The lowest values of the genetic distance were between IIUMSOY11 and IIUMSOY13 & IIUMSOY13 and IIUMSOY14, indicating that these accessions were more genetically distant from the other accessions. Ten differentially expressed proteins were identified in the three selected accessions IIUMSOY1, IIUMSOY11 and IIUMSOY14 using mass spectrometry, revealing a unique expression of the proteins involved in the storage, flavonoid metabolism, protein modification, oxidative stress defence, carbohydrate metabolism and respiratory chain. The findings may be valuable for the selection of genetically diverse accessions, to enhance the breeding of vegetable soybean genotypes suitable for stressful tropical environments.

Genetic diversity and correlation network approach on cotton genotypes in southern of Minas Gerais

The cultivation of Cotton (Gossypium hirsutum) is trending in an upward expansion at Minas Gerais state, Brazil. Due this growth, the breeding program has been demanded for the knowledge about the genetic diversity and correlation between morpho-agronomic traits, to start interesting crosses. The objective of this work was to study the genetic diversity and the correlation network between morpho-agronomic traits of cotton genotypes. Two cotton accessions and five commercial cultivars: FM993, FMT701, FM910, DP604 and DP604BG were evaluated for 16 traits. The results revealed divergence between the genotypes. Unweighted pair-group method arithmetic average (UPGMA) analysis allocated the genotypes in three clusters, with DP604 and Accession 2 being the most divergent. The correlation network helped to visualize the association between traits, presenting a negative correlation between anthracnose with plant height (-0.465), plant vigor (-0.486) and main root length (-0.437). Also, even with some genotypes presenting a higher number of reproductive branches, the correlation for this trait with number of bolls showed a high significant value (0.68). Thus, the genotypes showed wide genetic diversity for the composition of future crosses in cotton breeding programs. The correlation network allowed the visualization of a medium to high correlation pattern for the morpho-agronomic traits.

Detection of Stachybotrys chartarum isolates from faba beans dust during threshing.

Stachybotrys(S.)chartarumhad been related to dangerous health problems in animals and humans that take place when exposure to S.chartarum toxins.S. chartarumhad been isolated from various substrates, ranging from inappropriately stored feed and culinary herbs to damp buildings. To evaluate the pathogenic potential of isolates, it is essential to identify them with different methods. The occurrence and genetic diversity ofS. chartarum isolatesfrom faba beans dust during threshing in Upper Egypt were investigated. Low counts of Stachybotrys were found (six isolates) and identified morphologically by single-spore isolation and molecularly by the amplification of the specific internal transcribed spacer (ITS) region and glyceraldehydes-3-phosphate dehydrogenase (gpd).The genetic diversity of the collected isolates was studied by specific genes random primer polymerase chain reaction (SGRP-PCR). The phylogenetic analysis of S. chartarum showed that the specific primers IT51 and StacR3 used by commercial laboratories for detecting S. chartarum were not able to differentiate species of S. chartarum from S. chlorohalonata and unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of SGRP fragments confirmed this result. The six isolates of S. chartarum were analyzed for the presence of trichodiene synthase (Tri5) gene, which needed in the early stage of the trichothecene synthesis path. All the tested isolates were positive for the Tri5 gene. Further study on the taxonomic status of the epithet S. chartarum is necessary and presence of sub species to S. chartarum might be acceptable depending on the variations of morphological characteristics which were confirmed by molecular techniques.

Morphologic and cytoplasmic assessments of bulb onion (Allium cepa L.) landraces

Today climate change threatens to reduce crop yield and harming the food security. Local landraces have adaptation skills to shifting climatic conditions. Using of this local source in plant breeding programs becoming an alternative strategy. In this study, 97 landraces were collected to initiate the bulb onion breeding program eligible for the current trends. Collected materials were morphologically characterized using 21 descriptors, derived from UPOV (International Union for the Protection of New Varieties of Plants). Clustering which was conducted by the NTSYS (Numerical Taxonomy and Multivariate Analysis System) program using UPGMA (Unweighted Pair Group Method of Arithmetic Averages) method, showed that the genetic similarity rate of the landraces was calculated between 0.06-0.96. Hybrid onion breeding program depends on the cytoplasmic-genic male sterility (CMS) system. Thus, the PCR-markers were applied to identify the cytoplasm types of the landraces. Among landraces N-cytoplasm was found in 78 accessions and S-cytoplasm was found in 19 accessions. At the end of the study, a qualified gene pool has been established consisted of characterized onion genotypes which will might be used in further breeding studies.

Assessment of genetic variability of passion fruit using simple sequence repeat (SSR) markers

Purple passion fruit (Passiflora edulis Sims) is the third most important fruit crop in Kenya that is produced for both local and export markets. In Uasin Gishu County, passion fruit had recently emerged as an important cash crop for the small-holder farmers. Understanding the structure and diversity of species is very important in plant breeding and in conservation of genetic resources related activities. This study was set out in 2017-2018 to determine the genetic diversity of purple passion fruits genotypes grown in Uasin Gishu County, Kenya using SSR markers. Among the 50 purple passion fruit accessions used in this study, the genetic distance coefficients among accessions ranged from 0.24 to 0.72, with an average of 0.48. The results of STRUCTURE analysis suggested that the 50 accessions could be grouped into five sub-populations. The clustering was based on the unweighted pair-group method of arithmetic averages (UPGMA) where accessions were divided into three major clusters. The UPGMA dendrogram revealed that accessions from identical or adjacent areas were generally, but not entirely, clustered into the same cluster. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population sub-divisions and the genetic relationships among accessions. Principal coordinate analysis (PCoA) with SSR markers revealed a similar grouping of accessions to the UPGMA dendrogram and STRUCTURE analysis. Analysis of molecular variance (AMOVA) indicated that 16% of the total was attributed to the diversity among sub-populations, while 84% was associated with differences within sub-populations. Overall, there was a considerable amount of genetic variability among passion fruit accessions grown in Uasin Gishu County of Kenya. The study represents the comprehensive investigation of the genetic diversity of passion fruit accessions which would be valuable for germplasm collection, genetic improvement, and efficient utilization.

Genetic diversity and population structure in Castanopsis fissa revealed by analyses of sequence-related amplified polymorphism (SRAP) markers

Improved understanding of the genetic structure and genetic variation patterns in natural populations is an essential element of breeding programs that focus on forest species. Castanopsis fissa is an important, fast-growing evergreen species in southern China, where it is used for reforestation. We sampled 28 different C. fissa populations from three provinces in southern China and investigated their genetic variation and genetic relationship through an analysis of sequence-related amplified polymorphism (SRAP) markers. We acquired 236 electrophoretic bands from the 241 individuals analyzed by SRAP; 195 bands were polymorphic. Analysis of molecular variance (AMOVA) detected significant genetic variation within and among the populations; genetic variation among populations was smaller than variation within populations (p < 0.001). The 28 populations of C. fissa were classified into three types by STRUCTURE analysis. The clustering by the unweighted pair group method of arithmetic averages (UPGMA) procedure divided the 28 populations into four groups that corresponded to the output of a principal coordinate analysis (PCoA). Improved understanding of the population structure and population genetic diversity of C. fissa will be an essential element of programs that aim to genetically improve and breed the species. Our information on the population structure and genetic diversity of C. fissa in three provinces in southern China will enable future development of a theoretical scientific foundation for genetically improving and breeding this species.

Morphologic and molecular assessments of cucumber (Cucumis sativus L.) landraces

In this study, 90 locally grown cucumber (Cucumis sativus L.) landraces were collected and morphologically characterized using 20 descriptors derived from UPOV (International Union for the Protection of New Varieties of Plants). Genetic diversity and relationships of the genotypes were revealed using 20 sequence-related amplified polymorphism (SRAP) marker combinations. The discrimination power of each polymorphic marker (estimated by the polymorphism information content) ranged from 0.15 to 0.99 with an average of 0.73. Dice's similarity coefficient ranged between 0.00-1.00. The cluster analysis that was conducted using the unweighted pair group method of arithmetic averages (UPGMA) for both molecular and morphologic data showed that all of the genotypes fell into two main groups and many subdivisions. According to morphological data, fruit length, diameter and weight of the genotypes were determined between 6.5 - 32.5 cm, 25 - 52 mm and, 28 - 625 g respectively. It is clear from the results, a moderate level of genetic diversity, which has the potential for broadening the genetic base, was observed among the Turkish cucumber landraces.

Morphological variation of plantain squirrel Callosciurus notatus (Boddaert, 1785) (Rodentia: Sciuridae) population in West Sumatra, Indonesia

Abstract. Tjong DH, Sari RM, Roesma DI. 2020. Morphological variation of plantain squirrel Callosciurus notatus (Boddaert, 1785) (Rodentia: Sciuridae) population in West Sumatra, Indonesia. Asian J For 21: 54-60. A study about the morphological variation of plantain squirrel among several populations in West Sumatra has been done in West Sumatra. There were 38 specimens of C. notatus collected from Padang, Lubuk Basung, Sangir, and Baso by using a survey and direct collection method. The morphometric measurement was conducted in the Laboratory of Genetic and Biomolecular, Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University. Morphological measurement data based on 21 external characters and 35 skull characters were analyzed by the Kruskall Wallis test, Principal Component Analysis (PCA), and Unweighted Pair Group Method Arithmetic Average (UPGMA). The result showed that there was morphological variation in ten body characters and nine skull characters. It is necessary to do further research to determine what environmental factors specifically influence certain morphological characters.

Diversity analysis of Sweet Potato (Ipomoea batatas[L.] Lam) genotypes using morphological, biochemical and molecular markers

Sweet potato [Ipomeabatatas(L.) Lam.]is a nutritious food crop primarily grown by small and marginal farmers. successful breeding and germplasm conservation programs demands characterization of its germplasm. Here, we tried to determine genetic diversity among 21 sweet potato genotypes using morphological, biochemical and molecular markers. Ten morphological traits were studied and subjected to analysis of variance (ANOVA). Mean square due to germplasm were highly significant as well as wide mean range performance was observed for tuber number per plant, individual tuber weight, tuber fresh yield per plant, tuber dry yield per plant, tuber yield per plot and tuber length. UPGMA (Unweighted Pair Group Method Arithmetic Average) cluster analysis based on morphological traits separated the germplasm into three groups. The genotypes Gautam, Shree Arun, RS-92 and CO-3-4 appeared promising with regard to yield characters. Total phenol was maximum in in V-12 genotype (1.39 mg), while minimum was recorded in Samrat genotype (0.95 mg). The highest total antioxidant was observed in the genotype Samrat (0.30 mg), while minimum was recorded in the genotype Navsari Local (0.16 mg). Molecular diversity analysis was carried out using 25 RAPD (Random Amplified Polymorphic DNA) primers, out of which 13 primers produced 117 reproducible amplicons (106 polymorphic, 7 monomorphic and 4 unique amplicons). UPGMA dendogram based on RAPD data separated the genotypes into two major clusters having the similarity coefficient ranged from 0.56 to 0.76. The results can be used for sweet potato crop improvement through molecular breeding and marker assisted selection of for desired traits in future.

Molecular genetic variability of Juglans regia L. and Juglans sigillata D. as revealed by fluorescent amplified-fragment length polymorphism

Juglans regia L. and J. sigillata D. have a long cultivation history in China. With the purpose of detecting interspecific and intraspecific genetic variation, 35 clonal cultivars of J. regia, J. sigillata, J. sigillata×J. regia and J. hopeiensis Hu. (J. mandshurica Maxim. ×J. regia) were selected from a broad geographic range and applied in amplified-fragment length polymorphism (AFLP) analysis. Clear-cut AFLP profiles were produced using 9 EcoR I/Mse I primer combinations. As for J. regia, J. sigillata and their hybrids, the percentages of polymorphic bands (PPBs) averaged 93.86%, 93.94% and 60.46%; the observed number of alleles (Na) averaged 1.5370, 1.6389 and 1.2593; the effective number of alleles (Ne) averaged 1.2582, 1.2543 and 1.1646; Nei's gene diversity (H) scored 0.1560, 0.1556 and 0.0951; Shannon’s information index (I) averaged 0.2402, 0.2459 and 0.1414, respectively. These results implied a moderate level of genetic diversity within the investigated species. The total gene diversity (Ht = 0.1596) can be distributed into intra- (Hs = 0.1356) and inter- (Dst = 0.0240) species gene diversity. The proportion of the distributed genetic diversity among populations (Gst ) was 0.1505, indicating that only 15% of the total gene diversity was attributed to differences between species. The factorial correspondence analysis (FCA) and unweighted pair-group method of arithmetic averages (UPGMA) analysis revealed a close genetic distance between these two species.

Assessment of genetic diversity, population structure, and phylogenetic relationships among the Northeast Indian and South Indian commercially released tea cultivars using TE-AFLP markers

Commercially cultivated tea clones from Northeast and Southern India were analyzed using TE-AFLP markers. Analysis of molecular variance (AMOVA) and structure analysis showed high genetic variance (74%) within five distinct populations. This study also confirmed that Assam and UPASI (Nilgiri) tea clones have originated from two different tea populations introduced from imported China tea seeds by British. We evaluated the genetic variation and population structure in 30 tea clones of Tea Research Association (TRA), Tocklai Experimental station (Tockali ES), Jorhat, from North Eastern India and 30 clones of United Planters Association of South India (UPASI), Valparai, from South-India, released for commercial plantations and four C. japonica accessions (Total 64) used as outliers using Three Endonuclease-AFLP markers. Six primer combinations were selected from the best 10 primer combinations that were used on a set of 24 tea accessions as a standardization procedure. Dendrograms were constructed by using Jaccard’s similarity coefficient and Unweighted Pair Group Method of Arithmetic Averages (UPGMA) clustering method based on high coefficient correlation ratios obtained. High level of genetic diversity and clustering of accessions according to morphological proximity was established with minor aberrations. Analysis of molecular variance (AMOVA) showed highest genetic variance (79%) within five populations whereas the lowest variance (21%) was found among populations. These values change to the highest 87% and the lowest 13% when Camellia japonica accessions were removed from the analysis. Population structure analyses were performed to establish the genetic diversity and exact type each clones vis-a-vis to their molecular and morphological characteristics at present. Attempts were made to find out the population structure of Northeast and Southern India tea germplasm with their relatedness to existing morphological type. These analyses confirmed that all tea clones were genetically diverse and grouped based on their morphological characteristics and geographic regions.

Genetic diversity in Astragalus argaeus, a critically endangered species from Turkey

Astragalus argaeus is critically endangered endemic species growing only on Erciyes Mountain in Kayseri. Inter simple sequence repeat (ISSR) markers were chosen to detect the genetic diversity in four populations of A. argaeus. Ten primers were used to assess the diversity among 96 genotypes collected from the four localities in Erciyes Mountain. A total of 78 bands were scored, of which 44 (55.8%) were polymorphic. The unweighted pair group method arithmetic average (UPGMA) and principle component analysis (PCoA) showed moderate genetic diversity at the species and population level. The percentages of polymorphic bands (PPB) ranged from 53.8 to 61.5 (58.01% ± 3.2) and average gene diversity (h) at the population and species level was estimated to be 0.17 and 0.23, respectively. The Shannon’s information index (SI) ranged from 0.24 to 0.29 at the population level and was 0.35 at the species level. The determined gene flow (Nm) was 1.83. The UPGMA tree indicated that the four populations were not genetically distinct obviously. In analysis of molecular variance (AMOVA), the percentage of the variance was 38.72% among populations and 61.28% within populations. The data which small population size, habitat fragmentation and moderate levels of genetic diversity demonstrate that A. argaeus possess threat of extinction if its narrow habitat is destroyed.

Characterization of the Genetic Diversity of Acid Lime (Citrus aurantifolia (Christm.) Swingle) Cultivars of Eastern Nepal Using Inter-Simple Sequence Repeat Markers.

Acid lime (Citrus aurantifolia (Christm.) Swingle) is an important fruit crop, which has high commercial value and is cultivated in 60 out of the 77 districts representing all geographical landscapes of Nepal. A lack of improved high-yielding varieties, infestation with various diseases, and pests, as well as poor management practices might have contributed to its extremely reduced productivity, which necessitates a reliable understanding of genetic diversity in existing cultivars. Hereby, we aim to characterize the genetic diversity of acid lime cultivars cultivated at three different agro-ecological gradients of eastern Nepal, employing PCR-based inter-simple sequence repeat (ISSR) markers. Altogether, 21 polymorphic ISSR markers were used to assess the genetic diversity in 60 acid lime cultivars sampled from different geographical locations. Analysis of binary data matrix was performed on the basis of bands obtained, and principal coordinate analysis and phenogram construction were performed using different computer algorithms. ISSR profiling yielded 234 amplicons, of which 87.18% were polymorphic. The number of amplified fragments ranged from 7–18, with amplicon size ranging from ca. 250–3200 bp. The Numerical Taxonomy and Multivariate System (NTSYS)-based cluster analysis using the unweighted pair group method of arithmetic averages (UPGMA) algorithm and Dice similarity coefficient separated 60 cultivars into two major and three minor clusters. Genetic diversity analysis using Popgene ver. 1.32 revealed the highest percentage of polymorphic bands (PPB), Nei’s genetic diversity (H), and Shannon’s information index (I) for the Terai zone (PPB = 69.66%; H = 0.215; I = 0.325), and the lowest of all three for the high hill zone (PPB = 55.13%; H = 0.173; I = 0.262). Thus, our data indicate that the ISSR marker has been successfully employed for evaluating the genetic diversity of Nepalese acid lime cultivars and has furnished valuable information on intrinsic genetic diversity and the relationship between cultivars that might be useful in acid lime breeding and conservation programs in Nepal.

Genetic diversity and population structure of Chinese natural bermudagrass [Cynodon dactylon (L.) Pers.] germplasm based on SRAP markers.

Bermudagrass [Cynodon dactylon (L.) Pers.], an important turfgrass used in public parks, home lawns, golf courses and sports fields, is widely distributed in China. In the present study, sequence-related amplified polymorphism (SRAP) markers were used to assess genetic diversity and population structure among 157 indigenous bermudagrass genotypes from 20 provinces in China. The application of 26 SRAP primer pairs produced 340 bands, of which 328 (96.58%) were polymorphic. The polymorphic information content (PIC) ranged from 0.36 to 0.49 with a mean of 0.44. Genetic distance coefficients among accessions ranged from 0.04 to 0.61, with an average of 0.32. The results of STRUCTURE analysis suggested that 157 bermudagrass accessions can be grouped into three subpopulations. Moreover, according to clustering based on the unweighted pair-group method of arithmetic averages (UPGMA), accessions were divided into three major clusters. The UPGMA dendrogram revealed that accessions from identical or adjacent areas were generally, but not entirely, clustered into the same cluster. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among accessions. Principal coordinate analysis (PCoA) with SRAP markers revealed a similar grouping of accessions to the UPGMA dendrogram and STRUCTUE analysis. Analysis of molecular variance (AMOVA) indicated that 18% of total molecular variance was attributed to diversity among subpopulations, while 82% of variance was associated with differences within subpopulations. Our study represents the most comprehensive investigation of the genetic diversity and population structure of bermudagrass in China to date, and provides valuable information for the germplasm collection, genetic improvement, and systematic utilization of bermudagrass.

Characterization of pearl millet hybrids and their parental lines by seed storage protein markers

The variability of seed storage-proteins of 21 pearl millet genotypes were analyzed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Electrophorogram for 21 Pearl millet genotypes (seven hybrids, six female parent, five male parent and three Open Pollinated Variety(OPV)) were scored and Jaccard‘s similarity index (JSI) was calculated. Genetic diversity of Pearl millet genotypes was evaluated by constructing the dendrogram with Unweighted Pair Group Method Arithmetic Average (UPGMA) algorithm using NTSYSPC version 2.01 software. Six mobility bands that were polymorphic (Rm=0.33, 0.39, 0.43, 0.51, 0.69 and 0.75) were used for genotyping. Though it proved an efficient method to distinguish a few genotypes (H 90/4-5, H77/833-2, G 73-107, H 77/29-2, ICMA 95222A, HHB 146, MS 843A and ICMA 89111A) based on banding pattern. Intensity of bands were also some extant helped to differentiate genotypes especially Band with Rm value of 0.43 was light for H 77/29-2, band with Rm value of 0.51 was very light for G73-107 and band with Rm value of 0.75 was medium intensity for H 90/4-5. It is concluded that seed storage protein profiles could be useful markers in the studies of genetic diversity and classification of Pearl millet genotypes.

English

Safflower (Carthamus tinctorius) is an oilseed crop with high quality vegetable seed oil. A set of 55 accessions from different geographical origins were introduced to constitute a breeding program germplasm. These materials were characterized by inter-simple sequence repeat (ISSR) as a simple method to reveal polymorphism among them. ISSR analysis was carried out with 13 primers. After agarose gels analysis, ISSR banding patterns were converted into binary data of presence-non presence and matrices were processed. Genetic distances between all pairwise combinations of the accessions were calculated using similarity of simple coefficient matching (SCM). Dendrogram of studied accessions was constructed using the UPGMA (unweighted pair group method arithmetic average) method. A high number of reproducible ISSR bands exhibited a high percentage of polymorphism (69.64%), indicating a high genetic diversity among the material studied. The lowest similarity coefficient was 0.462, observed between accessions 109 and 135, whilst the highest one was 0.962, observed between accessions 68 and 126, with an average of 0.726. Dendrogram similarity relationships revealed some clusters according to different genetic pools. The ISSR markers were very informative and exhibited a high level of polymorphism. The findings of this study would be useful for safflower breeding program in Morocco as well as in other countries of the world. © 2016 Friends Science Publishers