UPGMA Analysis Research Articles

Determination of maize genotypes performance under water deficit using ISSR molecular index

Shortage of water is disastrous for crop production. The aim of this work is to obtain a group of maize inbred lines and hybrids that tolerates water deficit and collecting molecular characterizations for selection. This work was conducted in the 2019 and 2020. Five maize pure inbred lines B73, A132, NA30, S7 and DR-B1 were planted according to the design of half-diallel cross-breeding of the second Griffing method, and then 10 hybrids and 5 inbred lines were planted under the impact of irrigation intervals of 5, 10 and 15 days according to the Randomized Complete Block Design (RCBD) in split plot with 3 replicates. Results showed significance genotypes responses. The hybrid DR-B1 × S7 recorded the highest means of seed number per row (34.49 seed row-1), weight of 300 seed (80.77 g), and single plant yield (167.2 g). The shortest irrigation interval of 5 days recorded the highest number of seeds per row (35.39 seed row-1) and single plant yield (162.3 g). Similarity analysis showed a highest genetic diversity (lowest genetic similarity) was 0.83 between inbred 4 and 5. The highest genetic divergence (the least genetic similarity) between hybrids and inbred lines was 0.78 in inbred 4 and hybrid 3 x 2, while the highest genetic divergence of 0.92 was found between hybrids of 3 x 1 and 5 x 4. UPGMA analysis showed that inbred 5 (DR-B1) and inbred 4 (S7) in addition to 1×3, 1×2 and 1×4 hybrids high divergence. Therefore, yield components characteristics can be used for selection in breeding programmes and ISSR (inter simple sequence repeats) is a promising and efficient technique in identification of maize genotypes DNA molecular markers for water deficit tolerance selection.

Assessment of genetic diversity and population structure in local alfalfa genotypes using iPBS molecular markers

iPBS retrotransposon markers, in other words, inter-primer binding site markers based on retrotransposon, have been helpful for the determination of genetic diversity in several plants. The study was evaluated using 10 iPBS molecular markers on the level of genetic diversity and genetic structure of alfalfa genotypes. A total of 280 alleles in 50 alfalfa genotypes (48 local genotypes and 2 commercial varieties) were obtained by 267 polymorphic markers with an average of 28 per locus, ranging from 9 to 41 alleles. The rate of polymorphism of the markers ranged from 86.36 to 100% with an average of 93.71%. The average number of polymorphic bands per marker was detected as 26.7. The mean PIC value and Dice's similarity index were calculated as 0.14 and 0.50 respectively. The results of UPGMA analysis, principal coordinate analysis (PCoA), and STRUCTURE demonstrated that the 50 alfalfa genotypes could be classified into 4 subpopulations, namely the Q1, Q2, Q3, and Q4. The Nei’s genetic distances ranged from 0.0121 to 0.0359. iPBS markers and alfalfa genotypes used in this study may be used in studies of alfalfa breeding and germplasm conservation.

Genetic and nuclear DNA content variation of stevia (Stevia rebaudiana Bertoni) accessions grown in Turkey

The objectives of this study were to make morphological and molecular characterization of Turkish stevia accessions. The field data showed significant variations (P < 0.05) for all morphological parameters (plant height, number of main stems per plant, number of secondary stems, fresh and herb yields) exception with number of secondary stems. The primers of MtP5CS, AtNHX1, MtProDH, Mt-Actin MtSOS1and MtSOS2 genes were used as loci specific DNA markers. All markers were amplified in Stevia genome and provided a mean of 74.16% polymorphism rate. Flow cytometer analysis showed no statistically significant differences (P < 0.16) for 2C DNA content with a mean of 1.62 pg. The UPGMA analysis revealed that Samsun accession was distinctly separated from the others and had the lowest 2C DNA content (1.52 pg). This study first time showed that the stevia accessions grown in Turkey have limited genetic and no nuclear DNA content variations. The results also revealed that gene targeted functional markers associated with salt and drought tolerance have a great potential to be used as DNA markers to determine the genetic variation in plants

Development and genomic characterization of EMS induced mutant population of Zea mays L.

AbstractMaize is among major field crops which provides food, fodder and various byproducts to the industry. Development of better performing varieties is very important to enhance and strengthen the maize production system. In this study ethyl methanesulfonate (EMS) is used to induce genetic variation in maize. Mutant population was derived from two genotypes 100,003 and 100,004. EMS was applied under three different concentrations of 25, 50 and 75 mM. 25 mM was found as an ideal concentration resulting in maximum survival rate. Total 10 SSRs were used in this study, which amplified 28 alleles with average of 2.7 alleles. Analysis of molecular variance showed significant differences present among individuals. Average heterozygosity for mutants derived from 100,003 and 100,004 was 0.58 and 0.53, respectively. UPGMA analysis characterized the mutants into two main and many sub clusters. According to the principal component analysis, PC 1 and 2 contributed to 64.2% variability with eigenvalue greater than 1. Statistics showed maximum coefficients of variance in traits of leaf area, cobb height and plant height. Promising mutants were also identified and recommended for future breeding programme. In conclusion, EMS mutagenesis is an effective technique to develop novel mutants that can be exploited in future breeding programmes.

Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS.

Natural populations of Rhanterium eppaposum Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local Rhanterium plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of Rhanterium. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (FST = 0.029; p = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel’s test returned a very weak correlation coefficient of r2 = 0.101 (p = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation.

Morphological Variation in the Wing Mite Periglischrus paracaligus (Acari: Spinturnicidae) Associated With Different Moving Strategies of the Host Leptonycteris yerbabuenae (Chiroptera: Phyllostomidae)

We evaluated the morphometric variation of wing mite Periglischrus paracaligus Herrin and Tipton, along with the distribution of their host Leptonycteris yerbabuenae Martinez and Villa, in Mexico. A total of 115 female and 96 male specimens of P. paracaligus were used to conduct linear and geometric morphometric analyses. We assessed the influence of the geographic distribution of the migratory and nonmigratory populations of its bat host species on changes in size and shape on these parasites. Both analyses revealed high intraspecific variation in P. paracaligus, but subtle geographic differentiation. None of the approaches used identified a consistent pattern that separates unambiguously migratory from nonmigratory populations. Females presented more phenotypic variation than males and UPGMA analyses showed southern and northern colonies grouped in two distinct clades. Males on the other hand showed randomly grouped colonies with no geographic concordance. Interestingly, the most differentiated colony was the north Pacific colony of Jalisco. For both, males and females, isolation by distance (IBD) was not observed. We discuss these results as a possible scenario of contact between migratory populations located in northern Mexico with nonmigratory populations in other localities in central and southern Mexico conforming to a panmictic population along with their distribution range.

Genetic diversity analysis among late leaf spot and rust resistant and susceptible germplasm in groundnut (Arachis hypogea L.)

Abstract Groundnut is an important oilseed crops with high nutritional values. Yield of groundnut is constrained owing to diverse biotic and abiotic factors. Amongst biotic stresses two foremost foliar fungal diseases viz., late leaf spot and rust are universal and sparingly significant. Both conventional and modern breeding methods may be applied for improvement of groundnut. The current investigation was carried out to recognize genetic variability present among different groundnut germplasm with the use of morphological characters and SSR markers with the screening of resistant to leaf spot and rust resistant genotypes. In morphological examination, the analysis of variance divulged highly substantial differences among 48 germplasm lines. Initial screening of Germplasm was tried with the use of 125 SSR markers. But, based on banding pattern, 21 markers were found to be the best and selected for amplification of whole set of genotypes. Out of 21 markers, 16 were found to be highly polymorphic. Highest PIC value (0.8196) was detected for marker S021 representing 81% diversity. SSR Markers viz., PM42, PM204, PM377, S052, S076, S078 and S078 have PIC value more than 0.5, confirms their superiority in detection of polymorphism among studied germplasm lines. UPGMA analysis assemblage all the germplasm lines into three major clusters. Most of the foliar disease resistant genotypes were grouped together with higher genetic resemblance. Polymorphic markers identified in the study may be utilized further for molecular diversity analysis and the identified resistant genotypes may be employed further for the improvement of the crop.

Genetic diversity analysis of the wild edible mushroom Termitomyces heimii by using RAPD markers

To identify the genetic diversity of wild edible Termitomyces heimii (T. heimii) mushrooms, they were collected from three geographical locations in Baleswar, Kendujhar and Mayurbhanj districts in the North Odisha of India and were assessed using RAPD markers. 5 primers produced 43 scorable bands with 100% of the polymorphism. Polymorphic banding patterns with the number of amplified fragments varied from 6 (OPT 5 and OPT 12) to 11 (OPT 1) with an average of 8.6 per primer. The PIC values ranged from minimum value of 0.30 to maximum of 0.44 with an average value of 0.38. The heterozygosity (H) varied from 0.29 to 0.43 with an average of 0.36. The number of effective alleles (Ne), Shannon’s information index (I) and Nei’s gene diversity (h) were observed at population level as 1.604, 0.542 and 0.361 respectively whereas at species level the values were observed as 1.675, 0.684 and 0.459 respectively. These results showed the abundant genetic variability in the wild T. heimii. Nei’s gene diversity investigation showed that the genetic diversity was mainly found within geographical populations. The results of Mantel tests, UPGMA analysis, PCoA and PCA showed that geographical isolation is an important factor for the observed genetic differentiation.

The Phylogeography of Rhizophora in Peninsular Malaysia: High Genetic Variation between West and East

Geographic history of Rhizophora species and hybrid is effect on their genetic structure. In addition, determining population genetic variation is essential for phylogeography research. For this phylogeography investigation, Four natural population of Rhizophora were collected from five different regions in peninsular Malaysia for this phylogeography study. This study aims to evaluate the genetic diversity of Rhizophora species namely Rhizophora apiculata , Rhizophora mucronata , Rhizophora stylosa and hybrid R. × lamarcki and clarify their genetic structure of its populations using Nucleotide polymorphism in chloroplast intergenic spacer between trnL and trnF genes was studied.The populations of Rhizophora species and hybrids were divided into two groups: the east coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili; and the west coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili. The population of the west coast was the second cluster. This result was supported by UPGMA analysis using MEGA5 software.

The Phylogeography of Rhizophora in Peninsular Malaysia: High Genetic Variation between West and East

Geographic history of Rhizophora species and hybrid is effect on their genetic structure. In addition, determining population genetic variation is essential for phylogeography research. For this phylogeography investigation, Four natural population of Rhizophora were collected from five different regions in peninsular Malaysia for this phylogeography study. This study aims to evaluate the genetic diversity of Rhizophora species namely Rhizophora apiculata , Rhizophora mucronata , Rhizophora stylosa and hybrid R. × lamarcki and clarify their genetic structure of its populations using Nucleotide polymorphism in chloroplast intergenic spacer between trnL and trnF genes was studied.The populations of Rhizophora species and hybrids were divided into two groups: the east coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili; and the west coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili. The population of the west coast was the second cluster. This result was supported by UPGMA analysis using MEGA5 software.

Development of DNA molecular ID card in hog millet germplasm based on high motif SSR

<p id="C3">In order to identify hog millet (<italic>Panicum miliaceum</italic>) germplasm rapidly, to establish a big data management platform, to provide a theoretical basis for germplasm identification and traceability management, 130 germplasms from four ecological cultivation areas were used as materials to construct a molecular ID based on 35 high-motif SSRs (21, 10, and 4 with four-, five-, and six-nucleotide repeats, respectively). The results showed that 30 out of the 35 SSRs could be used as core markers for the construction of molecular ID cards. Ninety allelic variants were detected; effective allelic variants (<italic>Ne</italic>) ranged from 2.3186 to 2.9982 with an average of 2.7607; Shannon diversity index (<italic>I</italic>) ranged from 0.9158 to 1.0873 with an average of 1.0472. The observed heterozygosity (<italic>Ho</italic>) was 0.5000-0.8678 with a mean of 0.7168; the expected observed heterozygosity (<italic>He</italic>) was 0.5710-0.6691 with a mean of 0.6386; the Nei’s gene diversity index (<italic>Nei</italic>) was 0.5687-0.6665 with a mean of 0.6360; the polymorphism information content (PIC) was 0.5151-0.7898, with a mean of 0.6966. All accessions were divided into three groups (Group I, II, and III) according to UPGMA analysis. In terms of Shanxi accessions, landraces and breeding varieties were classified into Group I and III, respectively, and farmers materials were distributed into three groups. Based on PCA analysis, all accessions were classified into four clusters, which were related to their geographical origin. As for the rule that the most germplasms were determined using the least markers, 3 markers were excluded due to their high similarity coefficient with others, namely RYW23, RYW49, and RYW51. Screening the remaining 27 markers, the combinations of 17 SSR (RYW35, RYW40, RYW37, RYW18, RYW30, RYW16, RYW20, RYW19, RYW8, RYW5, RYW3, RYW7, RYW1, RYW14, RYW9, RYW6, and RYW10) could identify all hog millet accessions. The DNA molecular identifications of character strings, bar code, and quick response (QR) codes were constructed via ID analysis 4.0, software online of bar code and QR codes technique (<uri>http://barcode.cnaidc.com/app/html/bcgcode128.php</uri> and <uri>https://cli.im/</uri>).

First Report of Fusarium oxysporum Causing Coriander Wilt Disease in North China.

Coriander or cilantro (Coriandrum sativum L.) is extensively used as a fresh herb in China. During the summer of 2019 in Tianjin, China, coriander plants showed a previously unknown wilt in commercial fields. In severely infected fields, approximately 85% of the plants at vegetative stages were stunted, chlorotic, wilted or dead. Vascular tissues of the main stem and root were discolored. Soil samples were collected from five fields with a history of severe wilt disease in Tianjin since the fall of 2019. Seeds of coriander cultivar "ansemi" were sown in soil from the five fields, and cultured in a greenhouse at 22°C/20°C (12 h /12 h, light/dark) and 75% relativehumidity. After50 days' cultivation, infected seedlings exibited similar symptoms to those of plants in the field. Twenty symptomic seedlings from each of the collected field soil samples were harvested and washed for 3 min under running water. Then the vascular tissue fragments (3 mm2) of stem and root at the boundary of the symptomatic area were excised, and placed on improved Komada's medium, which is selective for Fusarium sp. (Komada 1975). After incubation at 25°C for 5 days in the dark, 70% of the isolates generated white to pale pink aerial hyphae on PDA (Fig. S1). Microconidia were single-celled, hyaline, non-septate and ovoid, and measured 5.6 to 14.1 μm long and 2.1 to 3.8 μm wide (n = 40). Macroconidia were three to five-septate, slightly curved at apex, and ranged from 11.2 to 38.6 μm long × 3.2 to 4.5 μm wide (n = 40). Based on morphological characteristics, these fungi were preliminarily identified as F. oxysporum (Leslie and Summerell 2006). For molecular identification, the ITS gene, TEF1-α gene and mtSSU gene of cultures from two representative single spored isolates XC02 and XC03 were amplified and sequenced (White et al. 1990; Carbone and Kohn 1999; Li et al. 1994). The sequences were submitted to GenBank (MT579855 and OK326765 for ITS; MT597425 and OK256882 for TEF1-α; MT587799 and OK330480 for mtSSU). BLASTn analysises indicated that the nucleotide sequences of the three loci of the two isolates were 99.8% to 100% homologous to sequences of F. oxysporum in the NCBI database and Fusarium MLST database. A multilocus phylogenetic tree was drawn via UPGMA analysis of the combined ITS, TEF1-α and mtSSU partial sequence data from Fusarium MLST database (Fig. S2). Pathogenicity of each isolate was tested on ten 15-day-old healthy coriander seedlings in each treatment according to the method of Yang et al. (2020). The first wilt symptoms developed 3 days after inoculation, and 7 to 10 days after inoculation 90% to 100% of the plants were dead. Control plants remained healthy. To fulfill the Koch's postulates, F. oxysporum were reisolated from the diseased tissues and verified based on morphology and sequencing as described above. The experiments were repeated twice with similar results. F. oxysporum has been reported to cause coriander wilt disease in India, Argentina, California (Koike and Gordon 2005), and Italy (Gilardi et al. 2019). To our knowledge, this is the first report of F. oxysporum causing coriander wilt disease in north China. Compared with F. equiseti in the previous report (Yang et al. 2020), F. oxysporum isolates possessed higher separation frequence and stronger pathogenicity to coriander seedlings. Thus attentions should be taken on F. oxysporum causing coriander wilt diseases when developing effective management strategies in north China.

Assessment of agro-morphological and molecular diversity among Indian mustard (Brasssica juncea) genotypes

An experiment was conducted in randomized block design with three replications during winter (rabi) season2015–16 at Instructional farm, RCA, MPUAT, Udaipur. Genetic diversity of the 10 Indian mustard [Brassica juncea(L.) Czern. &amp; Coss] varieties was evaluated by Random Amplified Polymorphic DNA markers and morphologicalcharacters. Fifteen RAPD primers were used out of which three were amplified. These three amplified primers produced total 148 amplicons, of which 128 amplicons (86.48%) were polymorphic. The polymorphic information content value ranged from 87.50% (OPA-2) to 100% (OPA-11) with an average of 93.33%. A dendrogram based on UPGMA analysis separated 10 Indian mustard varieties in four clusters at 0.58 similarity coefficient. Genetic divergence using Mahalanobis D2 statistics was worked out and based on D2 values, the varieties were grouped into four different clusters. Cluster 1 included maximum (seven) genotypes and cluster 2, 3 and 4 had only one genotype. Maximum divergence was observed between clusters 1 and 4 followed by cluster 1 and 2. Number of siliquae per plant was the main trait contributing to this divergence followed by test weight, seed yield per plant, number of seeds per siliqua, days to 50% flowering and number of secondary branches per plant. The genotypes PM-27 and Pusa Vijay were the most diverse on the basis of UPGMA clustering analysis and genotypes PM-27 and Bio-902 were most divergent on the basis of D2 value clustering. The results obtained can be utilized in hybridization and selection for breeding programmes.

Assessment of weed invasion at bait sites in a Central European lower montane zone

The effects of wild game feeding on the local environment have been widely investigated in northern European countries but have received little consideration in Central Europe. Bait sites, that is, places where food is set out to entice wild boar for hunting are becoming ever more widespread, and they are having an increasing impact on surrounding vegetation. The aim of the present study was to assess the extent of weed invasion at different bait types. 3 bait sites located in forests, 3 baits in clearings and 3 baits on unpaved forest roads in the Central European lower montane zone, in Hungary. The field work was conducted in May and August. Four transects were laid out (at right angles to each other) from the centre of each bait, and consisted of 22 one meter square quadrats, in which vegetation survey were conducted. The application of multivariate statistical methods (PCA) and UPGMA analysis to the data collected revealed substantial differences between the bait types. The baits in the forest were the least degraded, with a sparse understory cover in both surveys. Road baits displayed a notable difference, as they varied depending on canopy closure, accessibility and exposure. Sites in clearings proved to be the most infected. Furthermore, there was a significant difference between the vegetation of the periods examined, arable weeds dominated in August. A stress gradient was detected along the transects, with the proportion of weeds decreasing from the centre, while the natural components of the vegetation increased. The effect was more noticeable in clearings, probably due to their greater openness. Invasion is typically limited to the immediate environment of the bait sites, but valuable patches of habitat can also be destroyed, and bait sites may serve as bridgeheads for biological invasions.

Dimensional and genetic characterization of the last oriental plane trees (Platanus orientalis L.) of historical sites in Lazio (central Italy)

In central Italy, Platanus orientalis L. specimens characterize many gardens in urban and suburban villas. In this research, centuries-old oriental plane trees were studied in different historical sites of Lazio according to the COVE (COnservation of VEteran trees) multidisciplinary model. Historical sources, morphological and dendrometric aspects, crown quality, genetic traits of each specimen, as well as their susceptibility to the canker stain disease, were investigated. Platanus orientalis was clearly distinguished from P. occidentalis and their hybrid P. acerifolia through molecular tools. UPGMA analysis based on SSR and ISSR molecular markers clustered the plane trees in different sub-groups, probably according to the different sites of sampling. These findings, supported by historical and morphological data collected in the considered sites, showed that almost all the trees studied are a small remnant of those planted in the period running from the second half of XVI century to the first decades of XVII century. Plant health conditions diverge within and among the sites inspected. Past-prolonged severe pruning treatments of trees located near the main monuments affected their growth, causing faster and premature senescence. However, the management of historical gardens has so far led to an efficient prevention of Ceratocystis platani introduction, spread and establishment. This study highlights the importance of a multidisciplinary approach to interpret the present status of the ancient tree asset within historical sites and let the past become a lesson for the future in a broader scenario of conservation and management of cultural heritage.

Determination of salt tolerance levels and genetic relationships of Vicia sativa cultivars using gene targeted functional markers

The objectives of the present study were to determine salt tolerance levels of 12 different common vetch (Vicia sativa L.) cultivars at germination stage in the presence of 250 mM NaCl and to reveal genetic relationships based on gene targeted functional markers (GTFMs) associated with salt tolerance. The results revealed the presence of a significant genetic variation among the cultivars although s alt stress significantly reduced all germination parameters tested. The cultivar Ozveren was the most salt tolerant with 20.1% reduction in final germination percentage compared to control seeds while cultivars Alınoglu, Ayaz and Bakir did not germinate. The maximum delays in germination rate (G50 = 3.78 days) and synchrony (G10-90 = 3.45 days) were obtained from the cultivars Urkmez and Ozveren, respectively. The GTFMs provided a total of 53.1% polymorphism. The primers of MtSOS2 gene gave the highest numbers of alleles per primer pair while the highest polymorphism rate (77.8%) was obtained from the MtP5CS gene. The first three components of principal component analysis explained 57.63% of total variation. This study concluded that the cultivars determined to be salt tolerant and sensitive at germination stage distributed into three main clades determined by UPGMA analysis while the GTFMs associated with salt tolerance successfully determined the genetic relationships of common vetch cultivars.

Use of scanning electron microscopy to analyze sculpturing pattern and internal features of pollen grain wall in some members of Astragaleae (subfamily: Papilionoidae).

Palynological features of tribe Astagaleae L. have been observed with scanning electron microscopy (SEM), to assess features that can be used to re-examine the placement and taxonomic position of tribe. The palynomorph attributes of 10 species included in three genera of Astragaleae (Astragalus L., Glycyrrhiza L., and Oxytropis DC.) are investigated. The assignment of genus Oxytropis in tribe Astragaleae was also reevaluated based on pollen characters. Pollen appear to be prolate, prolate-spheroidal, and subprolate. Polar axis size (P) varies from 31.3μm ±1 to 17.5μm ±1.4 and equatorial axis size (E) varies from 22.2μm ±1.8 to 13.1μm ±0.9. Prominent apertures found consistently dispersed along the surface of pollen. Three kinds of ornamentation pattern were recorded, that is, reticulate or reticulate-perforate and perforate. The studied species display variation in equatorial and polar diameter, aperturation and sculpturing pattern, exine thickness, and pollen shape. On the basis of descriptive pollen features, a dichotomous taxonomic key and UPGMA analysis has been made for effortless and quick identification. The study concluded that disparities of the entire features are typically unrelenting and concerned with the species and shows potential systematic significance. The combination of palynological attributes in association with additional traits has prospective for systematic identification at species and genus level.

Morphological and molecular characterization of Croatian carob tree (Ceratonia siliqua L.) germplasm

The results of morphological and AFLP variability of 120 plants of carob tree (Ceratonia siliqua L.), collected from 12 different locations (10 biological replicates for each location) on the coast and islands of the southern Croatian Adriatic, indicate high molecular and morphological variability among these carob populations. Analysis of molecular variance revealed significant differences among populations (26.07%; p < 0.001; a = 0.05). Out of the total variability, 22.49% refers to the variability among, and 77.51% within populations. UPGMA and STRUCTURE analysis based on AFLP genetic data clustered carob populations into three main groups representing three real genetic populations. UPGMA analysis based on morphological traits of leaves, pods, and seeds clustered carob populations into five groups. Mantel test showed significant correlation between morphological and genetic data (r = 0.58, p < 0.001; a = 0.05). According to the high genetic and morphological variability, the germplasm collection in the analysis could represent an important genetic pool for future breeding programmes. The goal of future research should be the conservation of C. siliqua in its natural habitats, and the establishment of gene banks of genetic resources with the purpose of creating new carob cultivars in breeding programmes.

Assessment of molecular diversity among mungbean [Vigna radiata (L.) Wilczek] genotypes using EST-SSR marker

Genetic diversity can be assessed through molecular markers at the DNA level because of their abundance as compared to morphological characters and independence of environmental influences. By using expressed sequence tag-simple sequence repeat (EST-SSR) markers molecular diversity of thirty mungbean genotypes was analysed at S.D.A.U., Sardarkrushinagar (Gujarat) during 2019. DNA was extracted using CTAB method. Total 21 EST-SSR primers were screened across all the genotypes. Amplification of eleven alleles were done and high polymorphism (100.00%) was found from 5 EST-SSRs primers (MB21347, MB11596, MB34120, MB24478 and MB15212). Each locus has 2 to 3 alleles, with 2.2 average alleles per locus. The range pf PIC (Polymorphic Information Content) was 0.204 to 0.580, with 0.348 average. Similarity indices derived from Jaccard’s similarity co-efficient were estimated on the basis of five EST-SSR primers ranged from 0.091 to 1.00. Genotype, LM-584 and PIMS 1 showed minimum similarity. Two main clusters and six sub-clusters were formed in a dendrogram prepared using UPGMA analysis. PCA and PCoA plot based on EST-SSR primer study was constructed and genotypes have been distributed into four major groups in each method. Overall results suggested that EST-SSR can be a great tool to explore genetic diversity in mungbean.

Construction of a core collection of native Perilla germplasm collected from South Korea based on SSR markers and morphological characteristics

The leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and eight morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon–Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by eight morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modification of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.