Percentage Of Polymorphic Bands Research Articles

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Genetic diversity in see-see partridge (Ammoperdix griseogularis, Galliformes) populations from sub-Himalayan Mountain ranges of Pakistan

We used Random Amplified Polymorphic DNA (RAPD) markers to investigate the genetic structure of two populations of see-see partridge (Ammoperdix griseogularis, Galliformes) from the Suleiman range, in the Pakistani Himalayan region. The see-see partridge is a vulnerable species with a distribution in the Middle East and central Asia. The percentage of polymorphic bands (94.05%), Shannon Index (H = 0.455) and Nei’s average gene diversity (I = 0.298) of A. griseogularis at species level were rather high when compared with other avian species. 17% of polymorphic loci showed statistically significant differences in their allelic frequencies. The G (Nei’s coefficient of genetic variation) values indicated low levels of differentiation (G = 0.08). A genetic distance D of 0.05 indicated that both populations were to some degree in isolation but their differentiation was not significant. Overall, our genetic data can support action plans aiming to locally preserve differentiated genetic resources that, in the future, could potentially result in ecologically and behaviourally differentiated populations. In view of the rapid environmental changes that the Himalayan region has been experiencing in the last decade, this study could help in conservation plans.

Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d’Orbigny) in Con Dao and Phu Quoc islands, Vietnam

BackgroundBigfin squid is one of the economically important seafood resources in Vietnam’s fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box–derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. ResultsCon Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. ConclusionsFor the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.

Plant Traits of Tilia tomentosa Moench, Fraxinus excelsior L., and Pinus nigra J.F.Arnold as a Proxy of Urbanization

Linden, ash, and pine are ubiquitous ornamental trees due to their ability to adapt to the urban environment. They have been key species in urban green infrastructure from more than hundreds of years and play an active role in maintaining ecosystem services. The urbanization rate in recent decades, combined with global climate change, has led to dynamic changes in the environmental factors which pose new challenges to urban vegetation. Hence, the aims of this study were as follows: (i) to track changes in the content of some elements in plant leaves after transplanting them into an urban environment; (ii) to investigate the relationship between urbanization intensity with plant traits (leaf injuries, photosynthetic activity, transpiration, stomatal conductance, and molecular changes); and (iii) to provide recommendations for improving the management and ecological functions of urban trees. To address these aims, data on urbanization intensity (according to the percentage of built-up area and traffic volume), plant performance, and intraspecific variations of silver linden (Tilia tomentosa), European ash (Fraxinus excelsior), and European black pine (Pinus nigra) were collected at four experimental plots in the city of Plovdiv (Bulgaria) during 2015–2020. The initial concentrations of some potentially toxic elements (As, Cd, Cr, Cu, Mn, Pb, V, and Zn) in the tree leaves at the beginning (prior to planting into the urban environment) and at the end of the experiment were also measured. We illustrate that the growth of urbanization intensity increased the concentrations of potentially toxic elements in tree leaves, caused leaf injuries, and enhanced the maximum photosynthetic rate but decreased the transpiration rate and stomatal conductance. At the molecular level, the percentage of polymorphic bands was also found to depend on urbanization intensity. High similarity was observed between the trees in the first three experimental plots (subjected to urbanization load), with the lowest similarity in the control plot. These findings are of high practical value for urban planners regarding how to build a new green infrastructure and how to preserve plant diversity in urban areas across urbanization gradients.

Genetic diversity analysis using SSR marker in Naga King chilli (Capsicum chinense Jacq.) genotypes

The present investigation has been undertaken with the objective to study the genetic variability and diversity among the Naga king chilli genotypes using SSR marker at Medziphema during kharif season of 2018. All total 89 bands were produced by 30 primers, 37 bands being polymorphic and producing average percentage polymorphic bands of 41.66 %. The Primer CAMS-826 showed highest percentage of polymorphic bands (75%), followed by primer CAMS 032, CAMS-117, CAMS- 864 and CAMS-647 which revealed (66.66 %) and primer CAeMS 009, CAMS 163, CAMS 871, HmpsE 047 AND HpmsE 014 exhibited 50% polymorphism which indicates that the primer can be used for genetic diversity study of C. chinense genotypes. Genetic parameters analyzed using Popgene® software indicated that Peren population has higher diversity among the four region populations. Jaccard’s similarity coefficient between the genotypes ranged from 0.64 to 0.96, indicating moderate variation between the genotypes. Clustering analysis depicted three clusters where germplasm collected from Peren and Medziphema showed close relatedness and Principal Coordinate Analysis (PCo A) plot obtained also supports cluster analysis data. Germplasm evaluation is of immense important for genetic crop improvement.

Population Differentiation and Gene Flow of Salicornia persica Akhani (Chenopodiaceae)

The genus Salicornia (Amaranthaceae) was established by Linnaeus. Commonly known as ‘glassworts’, the species of the genus are articulated succulent herbs with cortical palisade, opposite decussate scale-leaves, thyrsoid cymes, flowers packed in cauline depressions and the diaspore composed of l-seeded utricle. Therefore, due to the importance of the plant species, we performed a combination of morphological and molecular data analyses on this species. A total of 72 randomly collected plants from 8 natural populations in 2 provinces were evaluated using ISSR markers and morphological traits. Analysis of molecular variance (AMOVA) test revealed significant genetic difference among the studied populations, and also showed that 45% of total genetic variability was due to the diversity within the population, while 55% was due to the genetic differentiation among populations. A total number of 158 bands were detected by ISSR primers, of which 144 (89%) bands with an average of 14.4 bands per primer were polymorphic. The Percentage of Polymorphic Bands (PPB) ranged from 70% (ISSR-7) to 100% (ISSR-1, ISSR-4 and ISSR-5). The average Polymorphic Information Content (PIC), Shannon’s Information index (I), and Number of effective alleles (Ne) were 0.49, 0.28, and 1.09, respectively.

Identification of purple nutsedge (Cyperus rotundus L.) ecotypes and the effect of environmental factors on tuber sprouting in China

AbstractPurple nutsedge (Cyperus rotundus L.) is a widely distributed weed. To evaluate the effect of environmental factors on tuber sprouting in different ecotypes, an inter‐simple sequence repeat (ISSR)‐based genetic analysis approach was used to assess the genetic relatedness among 24 purple nutsedge populations collected in China. Twenty‐one ISSR primers were selected to generate 167 scorable bands. The percentage of polymorphic bands (PPB) was 97%, indicating a high level of genetic diversity, and the cluster results largely coincided with the geographical locations. Three ecotypes, HN‐1, HB‐1 and SD‐1 (collected from Hai'nan Island, central China and northern China, respectively), with large genetic and geographic distances from each other, were selected to assess variation in the purple nutsedge sprouting trait. Compared with the other ecotypes, ecotype SD‐1 showed the highest sprouting capacity at constant 15°C and at 10/20°C, and the shortest time to reach 80% sprouting (t80) at constant 20°C and at 15/25 and 20/30°C. The sprouting percentage was very high (95%–98.8%) and without significant differences between the three ecotypes over a pH range between 5 and 9. The osmotic potentials that caused 50% inhibition of the maximum sprouting percentages of HN‐1, HB‐1 and SD‐1 were −0.37, −0.43 and −0.44 MPa respectively. Ecotype SD‐1 appeared to maintain a slightly higher sprouting percentage under osmotic stress, but the difference was not significant. These findings suggest that the higher tolerance to lower temperatures and drought of ecotype SD‐1 might be an adaptation to lower winter temperature and drier climatic conditions in North China. Abundant genetic diversity may be a potential factor that endows purple nutsedge with strong environmental adaptability.

Population genetic diversity of Huperzia chinensis (Herter ex Nessel) Ching. in Northwest region of Vietnam revealed by ISSR and SCcoT markers

Genetic diversity of natural Huperzia chinensis population in Northwest region of Vietnam was analyzed based on the DNA fingerprint data induced by ISSR and SCoT methods separately and combined data from both methods. The genetic diversity parameters and genetic distances among individuals based on SCoT technique were higher than ISSR technique [expected heterozygousity (HeS) was 0.2812; Shannon index (IS) was 0.4153; Percentage of polymorphic bands (PPBS) was 75.44%; Genetic similarity coefficients (GSCsS ) were in range of 0.561 - 0.947 with the average value (AGSCS) of 0.758 revealed by SCoT technique compared to HeI was 0.2394; II was 0.3515; PPBI was 60.87%, GSCsI were 0.551 - 0.986 and AGSCI was 0.860 revealed by ISSR technique. Combined data showed that genetic diversity level of investigated population (He was 0.2583; I was 0.3804; PPB was 67.46%, higher than genetic diversity level of Huperzia serrata population in the same distribution area which was previously evaluated by the same markers. Combined data also indicated the genetic similarities among individuals (GSCs) were 0.579 - 0.960 with the average (AGSC) of 0.814. ISSR method reflected more loci in the investigated plants than SCoT method but SCoT method could differentiate the tested samples better and reflects genetic diversity at higher level than ISSR method.

Androgenic ability and plant regeneration potential in some tomato varieties

Aiming to evaluate the in vitro regeneration potential, five varieties of tomatoes (Solanum lycopersicum) were studied for their response in anther culture. Anther explants at an early stage of microspore development were inoculated onto three culture media. The first differentiation processes were recorded during the first three weeks of culture, in darkness. The statistical analysis of the data recorded during the anther culture showed significant differences between genotypes regarding their specific response to culture conditions and the significant influence of the initiation medium composition in triggering the differentiation processes. Under the tested conditions were induced: the embryogenic potential in three genotypes (ʻȘtefănești 22ʼ, ʻCostate 21ʼ and ʻChihlimbarʼ) and the indirect organogenesis in two genotypes (ʻArgeș 20ʼ and ʻCostate 21ʼ). Morphological characteristics of anther-derived plants from ʻArgeș 20ʼ variety, grown in greenhouse conditions (growth rate, features of leaf, flower, and fruit), as well as analyses with nine SSR markers (banding patterns, the coefficient of genetic similarity, and the polymorphism information content) in DNA samples from each regenerant and the donor variety, provided clear evidence of the occurrence of spontaneous genetic variation during in vitro anther culture, and of the existence of somaclonal variation in regenerated plants. The amplified products obtained with SSR primers revealed a total number of scorable bands of 160 and a mean percentage of polymorphic bands of 21.09%. Two out of the nine tested primers, SSR63 and SLM6-7 proved to be efficient in detecting genetic differences not only among regenerants but also between them and the donor genotype.

Biological effects of gamma-ray radiation on tulip (Tulipa gesneriana L.).

Tulip, being an important ornamental plant, generally requires lengthy and laborious procedures to develop new varieties using traditional breeding methods requires. But ionizing radiation potentially accelerates the breeding process of ornamental plant species. The biological effects of γ-ray irradiation on tulip, therefore, were investigated through establishing an irradiation-mediated mutation breeding protocol to accelerate its breeding process. ISSR-PCR molecular marker technique was further used to identify the mutants of phenotypic variation plants. This study showed that low irradiation doses (5 Gy) stimulated bulb germination to improve the survival rate of tulip, while high irradiation doses (20 to 100 Gy) significantly (P < 0.05) inhibited its seed germination and growth, and decreased the flowering rate, petal number, flower stem length and flower diameter. More than 40 Gy significantly (P < 0.05) decreased the total chlorophyll content and increased the malondialdehyde (MDA) content in tulips. Interestingly, three types of both stigma variations and flower pattern variations, and four types of flower colour variations were observed. With increasing the irradiation dose from 5 to 100 Gy, the anthocyanin and flavonoid contents continuously decreased. Scanning electron microscopy (SEM) analysis evidenced that high irradiation doses altered the micromorphology of leaf stomata. Microscopic observations of tulip root apical mitosis further showed the abnormal chromosomal division behaviour occurring at different mitotic phases under irradiation treatment (80 Gy). Increasing the irradiation dose from 20 to 100 Gy enhanced the micronucleus rate. Moreover, the suspected genetic variation in tulips was evaluated by inter-simple sequence repeat (ISSR) analysis, and the percentage of polymorphic bands was 68%. Finally, this study concludes that that 80 Gy may be an appropriate radiation does to better enhance the efficiency of mutagenic breeds in tulip plants. Using γ-ray irradiation, therefore, is expected to offer a theoretical basis for mutation breeding in tulips.

ISSR marker based genetic diversity in Morinda spp. for its enhanced collection, conservation and utilization

Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia L. and Morinda tomentosa B. Heyne exRoth collected from different regions of India were investigated using inter simple sequence repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity and mean Shannon’s information index in M. tomentosa and M. citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20) and (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in M. tomentosa compared to M. citrifolia. These diversity rich genotypes of M. tomentosa can be evaluated for nutraceutical, nutritional and other nonfood purposes to identify trait specific genotypes for its enhanced utilization. ISSR markers based Structure, and UPGMA cluster analysis placed the M. tomentosa and M. citrifolia genotypes into well-defined separate clusters. Further, distinct ecotypes within a particular species could also be inferred. Priority regions identified can be earmarked for exploration and collecting substantial number of genotypes for ex-situ conservation. In-situ conservation of Morinda genotypes in hotspots to preserve the diversity in their natural habitats vis-à-vis evolution and increased adaptation of newer diversity with respect to changing environment was also emphasized.

Morphological and molecular markers based assessment of genetic diversity of a valuable endemic plant Lasiurus sindicus Henr. in the arid region of Rajasthan, India

Morphological and molecular markers are useful in genetic diversity assessment and improvement of plants. In the present study, five morphological traits, random amplified polymorphic DNA (RAPD) and Start codon targeted (SCoT) markers were used for genetic diversity evaluation of Sewan grass (Lasiurus sindicus Henr.), a valuable endemic plant of Indian Thar desert. Accessions collected from 14 different sites were used for measuring morphological traits, namely plant height (PH), number of tillers (NT), number of nodes (NN), leaf length (LL) and spike length (SL) which showed large variations among populations; particularly PH, NT and LL. Ward’s linkage hierarchical cluster analysis exhibited two major clusters and Cluster I contained two minor clusters. The percentage polymorphic bands (PPB) produced were 89.64% and 64.51% for RAPD and SCoT respectively. RAPD markers based dendrogram revealed three clades while there was no clear clade formation with SCoT markers. Single primer amplification reaction (SPAR) analysis with combined data of RAPD + SCoT showed more similarity with SCoT than with RAPD clusters. AMOVA revealed higher variation within population (90%) than among populations (10%) of L. sindicus. The Principal coordinate analysis (PCoA) also supported this result. There was no correlation between morphological and molecular data confirming environmental impact on morphological variation. SCoT and SPAR markers have clearly identified a novel genotype (LS JS 3) which has high values of PH, NN and LL. This study suggests that morphological data combined with molecular data can alone help in the identification of novel genotypes of L. sindicus among its populations.

Population genetic structure of Gymnospermium scipetarum subsp. eddae (Berberidaceae), an endangered Forest endemic from the Southern Apennines (Italy)

Assessing genetic diversity of narrow endemic plants is essential for their conservation. Gymnospermium scipetarum subsp. eddae (Berberidaceae) is an Italian endemic limited to a narrow forest area in the southern Apennines. Here we used random amplified polymorphic DNA (RAPD) markers to investigate population genetic differentiation and diversity in relation to distribution and microhabitat conditions. In all five extant populations and 134 individuals analysed we found a relatively low level of population genetic diversity (average Shannon-Weaver diversity index = 0.280; mean percentage of polymorphic bands = 57.45%; mean Nei’s gene diversity He = 0.187). Percentage of polymorphic bands (PPB) at species level was higher than at the population level (83.33%), while total species diversity (He = 0.210) was comparable to that found in the two southernmost subpopulations. AMOVA revealed a weak differentiation among populations, which shared three genetic pools in their genetic structure. The estimated gene flow among populations was relatively high (mean Nm = 5.320), while the Mantel test revealed no significant correlation between geographical and genetic distances at the population level. We argue that information on genetic diversity of G. eddae have important implications for conservation programmes, particularly for the establishment of ex-situ collections and restocking conservation actions.

EST-SSR marker-based genetic diversity and population structure analysis of Indian Curcuma species: significance for conservation

Protection and utilization of plant genomic resources are greatly perceived these days. The possibility of their dwindling genetic diversity along with the augmented demands for the resources has necessitated immediate concern for their conservation and sustainable plant utilization. The genus Curcuma (family Zingiberaceae) is well known for its valuable multipurpose products for medicine, spices, food, fragrance, flavoring agents, condiments as well as ornamentals. Because of the resurgence of curiosity in the commercial development and conservation of Curcuma, it has become essential to precisely characterize the existing genetic diversity at the species level. In the present study, 109 EST-SSR markers showed cross-transferability among 9 Curcuma species, among which 33 showed polymorphism. These 33 polymorphic EST-SSRs were utilized to assess genetic resemblance and distance among Curcuma species. The results of cluster analysis and principal coordinate analysis highly correspond to each other. AMOVA showed higher genetic variation among Curcuma species. The population genetic study revealed the genetic differentiation of species. The mean values of Nei's gene diversity (H), Shannon's information index (I), polymorphic information content (PIC), percentage of polymorphic bands (PPB), and resolving Power (RP) were found to be 0.3314, 0.49, 0.66, 88.57% and 7.24, respectively. Values of Nei's gene diversity in C. longa indicated the need for its large-scale cultivation and conservation prioritization of wild taxa of C. caesia, C. aromatica and C. amada. These SSR markers could also be utilized to identify morphologically similar Curcuma species.

Genetic Diversity Analysis, Population Structure and Gene-flow Estimates among Citrus Macroptera Mont. Collections from Garo Hills, Meghalaya using SPAR Approach

North East India is extremely rich in natural resources and is a biodiversity hotspot. Many plant species, including Citrus are known to have originated from this region. Citus macroptera Mont. is a wild, endangered species which have been found to exist naturally in various parts of this region, including Meghalaya. To access the genetic variability among genotypes and their phylogeny, 30 genotypes of wild C. macroptera Mont. were collected from Garo Hills of Meghalaya. Single primer based DNA markers viz. RAPD, ISSR, DAMD were utilized to ascertain genetic diversity. The percentage polymorphic bands for RAPD, ISSR, DAMD were found to be 97.71%, 94.67% and 100% respectively. ISSR showed the highest values for both RP (7.67) and MI (5.03) highlighting its efficacy in determining genetic variations. A concatenated approach, Single Primer Amplification Reaction (SPAR) was also followed to assess their genetic diversity. Dendogram generated from SPAR data showed that the South-West Garo Hills population is the most recently evolved amongst all others while West Garo Hills collections retain an ancestral position in the evolutionary time-frame. Population genetics parametres such as Gene flow (Nm) and the diversity among populations (GST) were found to be 1.9894 and 0.2009 respectively. Gene flow estimates (Nm&gt;1) suggests appreciable gene flow in the populations. AMOVA data further supported this with high percentage of variations (92%) within populations whereas variations among populations were about 8% only. Shannon’s information index (I) values and Nei’s gene diversity (h) varied between 0.303-0.423and 0.201-0.285 respectively. The use of SPAR method yields a clear and concise picture of the underlying genetic variabilities, and a detailed and comprehensive data analysis will help conceive efficient and sustainable conservation strategies for this important plant.

Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

GENETIC DIVERSITY OF NATURALLY DISTRIBUTED Rhododendron moulmainense Hook. f. POPULATIONS IN LAM VIEN PLATEAU, VIETNAM REVEALED BY ISSR AND SCoT MARKERS

Genetic diversity and variation of three naturally distributed Rhododendron moulmainense populations in the Lam Vien Plateau of Vietnam were analyzed using ISSR and SCoT markers separately and data from the two types of markers were then combined to show the overall results. Based on combined data, the genetic diversity parameters of the Tuyen Lam population were percentage of polymorphic bands (PPB) = 28.79%; genetic heterozygosity (He) = 0.1041; Shannon index (I) = 0.1552. The corresponding parameters were PPB = 37.88%; He = 0.1434; I = 0.2131 in the Hon Nga population, and PPB = 46.21%; He = 0.1857; I = 0.2709 in the Bidoup population. At the species level in Lam Dong province, the corresponding parameters were PPB = 62.12%; He = 0.1747; I = 0.2756. The average of pairwise genetic similarity coefficients among investigated individuals of Tuyen Lam population was 0.973, of Hon Nga population was 0.911, and of Bidoup population was 0.895. The genetic differentiation and the number of migrants per generation among investigated populations were GSTS = 0.1735 and Nm = 2.3824 individuals, respectively. Genetic distance between Tuyen Lam and Hon Nga populations was 0.0399, between Tuyen Lam and Bidoup populations were 0.0621, and Bidoup and Hon Nga populations were 0.0670. Data generated by both marker types and the combined revealed similar trends of genetic diversity levels among the studied populations. The SCoT data showed higher values of genetic diversity and population gene differentiation than did the ISSR data, but the latter showed higher gene differentiation among sampled individuals in the study populations. Comparing the values of Polymorphism Information Content (PIC) for discriminatory ability; Effective Multiplex Ratio (EMR) for several revealed loci and/or efficiency of the primer-marker system; Marker Index (MI) for the efficiency of used method; and Resolving Power (Rp) between used techniques indicated that discriminatory ability, efficiency, and ability of the ISSR primer combinations were higher but using SCoT marker system was more efficient than ISSR marker system for evaluating genetic diversity.

Meta-analysis of genetic representativeness of plant populations under ex situ conservation in contrast to wild source populations.

Ex-situ conservation is widely used to protect wild plant species from extinction. However, it remains unclear how genetic variation of ex-situ plant collections reflects wild source population diversity. Here, we conduct a global meta-analysis of the genetic representativeness of ex-situ populations by comparing genetic diversity (i.e. AR, allelic richness; HE , expected heterozygosity; PPB, percentage polymorphic bands; and SWI, Shannon-Winner index), inbreeding coefficient (FIS ), and genetic differentiation between ex-situ plant collections and their wild source populations. Genetic diversity (i.e., HE , PPB, and SWI) was significantly lower in ex-situ populations than their wild source populations, while genetic differentiation between ex-situ and wild populations (ex-situ-wild FST ), but not that among ex-situ populations, was significantly higher than among wild populations. Outcrossing species, but not those with mixed mating system, had significantly lower genetic diversity in ex-situ populations, and significantly higher ex-situ-wild FST . When the collection size for ex-situ conservation was ≥30 or 50, PPB, HE , and ex-situ-wild FST were not significantly different between ex-situ and wild populations, indicating a relatively high genetic representativeness. Collecting from the entire natural distribution range and mixing collections from different sources could significantly increase the genetic representativeness of ex-situ populations. Type of ex-situ conservation (i.e., planting or seed bank) had no effect on genetic representativeness. The effect size of HE decreased and the effect size of ex-situ-wild FST increased with the duration of ex-situ conservation. Our results suggest that current ex-situ plant collections do not effectively capture the genetic variation of wild populations. Low genetic representativeness of ex-situ populations was caused by both initial incomplete sampling from wild populations and genetic erosion during ex-situ conservation. We emphasize that it is necessary to employ more thorough sampling strategies in future collecting efforts and to add new individuals where needed. Article impact statement: Low genetic representativeness of living plant collections is a worldwide problem in ex situ conservation. This article is protected by copyright. All rights reserved.

Molecular diversity of the Fusarium fujikuroi species complex from maize

Random amplified polymorphic DNA (RAPD) markers were used to estimate genetic relationship and diversity of Fusarium species associated with pink ear rot of maize. Three Fusarium species – F. verticillioides, F. temperatum and F. subglutinans sensu stricto were collected from contaminated corn kernels. A collection of 41 randomly selected Fusarium isolates (16 F. verticillioides, 16 F. temperatum and nine F. subglutinans sensu stricto) was screened for polymorphism with thirty decamer primers. Seventeen primers that had generated a high number of polymorphic loci were used for the analysis of genetic diversity. The primers yielded a total of 146 polymorphic loci, an average of 8.59 polymorphic bands per primer. The percentage of polymorphic bands (%P) was 46.1%. The RAPD-based UPGMA analysis demonstrated that although F. temperatum and F. subglutinans s.s. form two distinct groups they are more similar to each other than to F. verticillioides. Fusarium verticillioides was the most heterogenous species (Nei’s genetic diversity 0.180), while the least heterogenous one was F. subglutinans s.s. whose genetic diversity was 0.098. The analysis of the translation elongation factor 1-α and β-tubulin gene sequences as well as the mating type ratio were employed to support the RAPD data.

&lt;p&gt;&lt;strong&gt;Species relationship and population structure analysis in &lt;em&gt;Allochrusa&lt;/em&gt; (Caryophylloideae, Caryophyllaceae) using ISSR molecular markers&lt;/strong&gt;&lt;/p&gt;

Allochrusa is a genus of subfamily Caryophylloideae comprising about 8 species distributed in Turkey, Central Asia, Afghanistan, Caucasus, and Iran. Four species of A. versicolor, A. bungei, A. lutea, and A. persica occur in Iran and show overlaps in morphology, which make critical their identification. In this study, we used 49 randomly collected specimens belonging to seven populations. AMOVA test provide important genetic variation among the examined populations and showed that 70% of the overall genetic difference was due to within population diversity, while 30% is because genetic population variability. Overall, 150 groups were distinguished through ISSR marker, in which 137 (90%) bands with a normal of 13.7 bands marker were polymorphic. Percentage of Polymorphic bands (PPB) ranging from 77% (ISSR-7) to 100% (ISSR-1, ISSR-4 and ISSR-5). The average Polymorphic Information Content (PIC), Shannon’s Information index (I), and Number of effective alleles (Ne) were 0.59, 0.27, and 1.8, respectively.