Percentage Of Polymorphic Loci Research Articles

Population structure of Rhizoctonia solani inciting sheath blight of rice in Haryana, India

Rhizoctonia solani Kuhn inciting sheath blight is known to cause substantial quantitative and qualitative losses in rice. Sixty six isolates of R. solani representing different agro-ecological regions of Haryana were classified based on their cultural and morphological, pathogenic and genetic traits. R. solani isolates were found highly variable both in mycelial and sclerotial characters. The mean vertical disease spread caused by R. solani isolates on five rice cultivars viz. Tetep, IR 64, Pusa Basmati 1, Govind and HKR 127 varied between 24.67 and 57.25% and the fungal isolates formed three clusters based on their pathogenic behaviour. Inter simple sequence repeats (ISSR) and Universal rice primers (URPs) were used to study the population structure of R. solani isolates. The Nei’s diversity (h), Shannon’s diversity index (I) and percentage of polymorphic loci (P%) were observed to be 0.2761, 0.4301 and 100%, respectively at the population level. Genetic variation was maintained within the populations as reflected by the higher gene flow (Nm = 4.5997). Agro-ecological regions contributed to 6% of the total genetic variation, whereas the major proportion of genetic variation (89%) was attributed to the differences within populations and only 5% among populations.

Genetic diversity studies of apricot of trans-Himalaya based on morphological and SARP markers

Forty-seven apricot genotypes were used to assess genetic diversity (GD) based on morphological and SRAP (Sequence-related amplified polymorphism). Six qualitative and 16 quantitative characters were studied among the genotypes. Twenty combinations of SRAP markers were used, and 115 polymorphic bands out of 134 bands were observed. The overall GD estimated, as percentage polymorphic loci (85.06%), Nei’s genetic diversity (0.27±0.19), and Shannon’s information index (0.40±0.25) were high. Analysis of molecular variance (AMOVA) revealed higher GD (92%) within the groups of apricot. The unweighted pair group method (UPGMA) demonstrated that the apricot genotypes had a similarity range from 0.96 to 0.48, with a mean value of 0.72 similarity coefficient. Furthermore, UPGMA clustering and Bayesian-based STRUCTURE analysis revealed an intermixing in the clustering of apricot genotypes. There is no clear grouping between apricots according to their kernel taste and stone colour, which revealed that these genotypes have a similar genetic background. Knowledge gained from the present study has a practical utility in the management of germplasm conservation and breeding programmes.

Scot molecular markers and population differentiation in Hedera helix L.

Hedera helix L. is a specie that is used for its ornamental and medicinal properties widely. In spite of its very good biochemical characterization, the knowledge about the DNA variability is very limited and no DNA markers were used to analyses the genomic variability of the populations, up to date. In the present study, genetic diversity of 56 Hedera helix, individuals nine populations were studied using 10 Start Codon Targeted (SCoT) markers. High polymorphic bands (95.78%), polymorphic information content (0.25) and allele number (1.34) showed SCoT as a reliable marker system for genetic analysis in Hedera helix. At the species, the percentage of polymorphic loci [P] was 66.20%, Nei?s gene diversity [H] was 0.159, Shannon index [I] was 0.148 and unbiased gene diversity [UHe] was 0.56. Genetic variation within populations (70%) was higher than among populations (30%) based on analysis of molecular variance (AMOVA). We used SCoT molecular marker for our genetic investigation with the following aims: 1- Investigate genetic diversity both among and with date Hedera helix, 2-Identify genetic groups within these nine populations ivy, and 3-produce data on the genetic structure of date ivy populations. The results obtained revealed a high within-population genetic variability.

Molecular Characterization of Okra Genotypes Through RAPD and SSR Markers

Okra (Abelmoschus esculentus L.) is an important nutritious vegetable. Despite its high economic and industrial value, very little attention has been paid to assess genetic diversity of okra at molecular level. For effective conservation and proper deployment of germplasm, a study on genetic diversity analysis for fiber quality traits of okra germplasm was conducted with Random Amplified Polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Random Amplified Polymorphic DNA as well as simple sequence repeat markers were utilized to evaluate the genetic diversity among ten genotypes viz., GAO 5, AOL 12–55, AOL 10–22, AOL 13–73, AOL 13–75, AOL 13–88, AOL 13–90, Parbhanikranti, Pusasawani and wild type. A set of 15 RAPD primers were tested, total of 153 RAPD scorable fragments were produced of which all alleles were observed to be polymorphic. PIC values ranged from 0.77 to 0.92 with an average value of 0.84. The genotypes were broadly divided into two clusters. Cluster II included only wild type genotype. Sub cluster A1 comprised of genotype GAO 5. For SSR all 15 primers showed amplification and produced a total of 31 bands. The genetic distance (GD) among the okra genotypes ranged from 0.18 to 0.60. The highest GD (0.60) was detected between GAO 5 and Wild type, while the lowest GD (0.18) was observed between AOL 13–73 and AOL 13–88. The average observed mean heterozygosity was 0.60 and observed mean percentage of polymorphic loci was 67%. The diversity obtained could be exploited in the program of selection and varietal improvement of okra.

Cross-amplification and characterization of microsatellite markers in species of Manihot Mill. (Euphorbiaceae) endemic to the Brazilian Cerrado

ABSTRACT The genus Manihot Mill. contains about 120 species of which about 104 occur in Brazil. We tested the cross-amplification of ten microsatellite markers developed for Manihot esculenta in 15 species of Manihot endemic to the Brazilian Cerrado. We also evaluated the genetic diversity of Manihot irwinii, M. orbicularis, and M. purpureocostata. Ten pairs of primers were amplified among 14 species of Manihot. The percentage of polymorphic loci per species varied from 70 to 100 %. Nine markers showed amplification and polymorphism when evaluated on polyacrylamide gel. The markers were combined to form three sets for multiplex genotyping for genetic diversity analysis, and showed 51, 75, and 75 alleles in M. irwinii, M. orbicularis, and M. purpureocostata, respectively. The levels of genetic diversity for the transferred markers were high for the three species and proved to be useful for population genetics studies of species of Manihot endemic to the Cerrado. The results of this study will help to better understand the genetic diversity, taxonomy and relationships among species Manihot, and to develop conservation programs for the genus.

Growth rate and genetic structure of Sinapis arvensis susceptible and herbicide resistant populations originating from Greece

Weed resistance to herbicides is a serious agricultural issue that threatens the sustainability of world food production, as its widespread appearance has reduced the diversity of weed control practices and posed economic and environmental risks. Wild mustard (Sinapis arvensis), a very competitive weed in winter cereals, has evolved resistance to ALS-inhibiting herbicides used in Greece. As growth rate and genetic structure of weeds affect their competitive ability against crops, the purpose of this work was to study the effect of geographical origin and resistance profile on growth rate and genetic structure of five S. arvensis populations. In particular, the cross-resistant to tribenuron and imazamox P2, P3 and P4 populations originating from the counties of Larissa, Phthiotida, and Pieria, respectively, the resistant to tribenuron P1 originating from Chalkidiki and the susceptible PS originating from Thessaloniki were evaluated. The growth rate was studied by determining fresh weight, number of leaves, height, and seed weight of plants, whereas the genetic structure by using six inter simple sequence repeat (ISSR) molecular markers. Regarding growth rate, the b slope values of the linear equation fitted on fresh weight regression against sampling time were 10.87, 9.94 and 11.41 for P2, P3 and P4 populations, respectively, which were higher than those of P1 (8.03) and PS (6.79) populations, while the b slopes of leaf number were 3.8 and 4.63 for P3 and P1 populations, which were higher than those of PS (2.1), P2 (2.79) and P4 (2.84). The use of ISSR markers showed also differences between populations in their genetic structure parameters [genetic diversity (h), Shannon index (I), number of alleles (Na), percentage of polymorphic loci for each population (P%), variance among and within populations, and FST value, that is a measure of differentiation among populations due to genetic structure], which attributed to origin and herbicide resistance profile. The ISSR bands indicated that 80% of the molecular variation was within populations and 20% among populations. In addition, the dendrogram produced by the combination of GenALEx and MEGA7 statistical software, along with the corresponding PCoA graphical output indicated similar groups of the individuals belonging in these populations.

Determination of Sex-Linked by Fluorescent Amplified Fragment Length Polymorphism Molecular Marker in Oreochromis niloticus L. Fish

Nile tilapia (Oreochromis niloticus L.) is a worldwide significant aquaculture species rapidly gaining rank as a farmed commodity. Six fish specimens (three males and three females) of Nile tilapiawere collected from Kafr El-Sheikh Egypt (31.3oN and 30.93oE). Fluorescent Amplified Fragment Length Polymorphism (AFLP) analysis was applied to qualitatively discriminate sex-dependent genomes, was successfully able to determine sex-linked marker. Principal Coordinate Analysis (PCA) identified sex-linked marker easily. PCR amplification was obtained using three pairs of primers. Total number of scored bands detected the specimens was 1243 as 129, 154, 291, 148, 165 and 356 bands for the three primer pairs, respectively. All bands ranged between 50 to 542 bp including 919 polymorphic. Percentage of polymorphic loci was 73.93%. The PCA test revealed different distribution of male and female samples according to the degree of similarity. The difference in PCA revealed genetic variation among the studied samples. Such observations reflect the success of the F- AFLP markers. A PCA variable showed clustering in four quadrants variables for female and male samples in different quadrants.

Different landscape effects on the genetic structure of two broadly distributed woody legumes, Acacia salicina and A. stenophylla (Fabaceae).

Restoring degraded landscapes has primarily focused on re‐establishing native plant communities. However, little is known with respect to the diversity and distribution of most key revegetation species or the environmental and anthropogenic factors that may affect their demography and genetic structure. In this study, we investigated the genetic structure of two widespread Australian legume species (Acacia salicina and Acacia stenophylla) in the Murray–Darling Basin (MDB), a large agriculturally utilized region in Australia, and assessed the impact of landscape structure on genetic differentiation. We used AFLP genetic data and sampled a total of 28 A. salicina and 30 A. stenophylla sampling locations across southeastern Australia. We specifically evaluated the importance of four landscape features: forest cover, land cover, water stream cover, and elevation. We found that both species had high genetic diversity (mean percentage of polymorphic loci, 55.1% for A. salicina versus. 64.3% for A. stenophylla) and differentiation among local sampling locations (A. salicina: ΦPT = 0.301, 30%; A. stenophylla: ΦPT = 0.235, 23%). Population structure analysis showed that both species had high levels of structure (6 clusters each) and admixture in some sampling locations, particularly A. stenophylla. Although both species have a similar geographic range, the drivers of genetic connectivity for each species were very different. Genetic variation in A. salicina seems to be mainly driven by geographic distance, while for A. stenophylla, land cover appears to be the most important factor. This suggests that for the latter species, gene flow among populations is affected by habitat fragmentation. We conclude that these largely co‐occurring species require different management actions to maintain population connectivity. We recommend active management of A. stenophylla in the MDB to improve gene flow in the adversity of increasing disturbances (e.g., droughts) driven by climate change and anthropogenic factors.

Genetic polymorphism in Siberian stone pine (Pinus sibirica Du Tour) populations from Ural and Altai-Sayan mountains

The article presents the results of analysis of the variability of 23 allozyme loci in 10 populations of Siberian Stone pine. Populations from South Siberia mountain regions had higher percentage of polymorphic loci in averageand mean number of alleles per loci (P99% = 44,57 %, NA = 1,543 ± 0,014) compared to Ural populations (P99%=29,57%,NA = 1,348 ± 0,015). The average values of the observed and expected heterozygosity in the populations of the Altai-Sayan (HO = 0,087 ±0,007 and HE = 0,090 ± 0,004) and the Ural mountain region (HO = 0,083 ± 0,008 и HE = 0,082 ± 0,005)were close. About 8.4% of the total genetic diversity is due to differences between the studied populations. The results ofmultidimensional data analysis confirm the existence of the Altai-Sayan and Ural refugia in the post-glacial period andthe dispersal of Siberian stone pine to the North from the Ural glacier refugium.

Genetic structure and diversity of upland rice germplasm using diversity array technology (DArT)-based single nucleotide polymorphism (SNP) markers

AbstractInvestigating genetic structure and diversity is crucial for rice improvement strategies, including mapping quantitative trait loci with the potential for improved productivity and adaptation to the upland ecology. The present study elucidated the population structure and genetic diversity of 176 rice germplasm adapted to the upland ecology using 7063 genome-wide single nucleotide polymorphism (SNP) markers from the Diversity Array Technology (DArT)-based sequencing platform (DArTseq). The SNPs were reasonably distributed across the rice genome, ranging from 432 SNPs on chromosome 9 to 989 SNPs on chromosome 1. The minimum minor allele frequency was 0.05, while the average polymorphism information content and heterozygosity were 0.25 and 0.03, respectively. The model-based (Bayesian) population structure analysis identified two major groups for the studied rice germplasm. Analysis of molecular variance revealed that all (100%) of the genetic variance was attributable to differences within the population, and none was attributable to the population structure. The estimates of genetic differentiation (PhiPT = 0.001;P= 0.197) further showed a negligible difference among the population structures. The results indicated a high genetic exchange or gene flow (number of migrants, Nm = 622.65) and a substantial level of diversity (number of private alleles, Pa = 1.52 number of different alleles, Na = 2.67; Shannon's information index,I= 0.084; and percentage of polymorphic loci, %PPL = 55.9%) within the population, representing a valuable resource for rice improvement. The findings in this study provide a critical analysis of the genetic diversity of upland rice germplasm that would be useful for rice yield improvement. We suggested further breeding and genetic analyses.

Primer development and functional classification of EST-SSR markers in Ulmus species

At present, the available SSR markers of elm (Ulmus) have been seriously deficient, which can not meet the needs of molecular marker-assisted breeding and evaluation of germplasm resources. In this study, transcriptome data of Ulmus pumila were used as materials to develop EST-SSR markers of elms. EST-SSR markers were also classified according to gene function for the first time. In this study, 8288 perfect and 569 compound SSR loci were detected from 17,624 EST sequences (36,609,384 bp). Most of the perfect SSR sequences were based on short sequence lengths of 10–22 bp. The most common SSR repeat units were A/T (3330, 40.18%), AG/CT (1211, 14.61%), and AAG/CTT (568, 6.85%). All EST-SSR loci were function classified based on the Cluster of Orthologous Groups (COG) database. There were substantial differences in the type and proportion of SSR repeat units among the functional classes. Most EST-SSR loci were located in gene-coding regions. Ninety pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-nine primers were verified with clear bands. The number of alleles per locus (Na) ranged from 2 to 6; the number of effective alleles (Ne) ranged from 1.061 to 3.261; the observational heterozygosity (Ho) and expected heterozygosity (He) ranged from 0 to 0.968 and 0.112 to 0.651, respectively. The clustering pattern is consistent with traditional taxonomy that provides a molecular basis for the classification of elm. There were differences in the effective amplification and percentage of polymorphic loci among different functional SSR loci. The analysis of 880 primer combinations showed that markers within a single COG group were less effective than across groups. This study clarified the importance of SSR primer selection for clustering results. This study developed a large number of SSR markers in elm, providing effective markers for molecular marker-assisted breeding, genetic mapping, and other related research.

Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

BackgroundAmorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei.ResultsThe population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23 to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon’s Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions.ConclusionsOur results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

Using two retrotransposon-based marker systems (SRAP and REMAP) for genetic diversity analysis of Moroccan Argan tree.

The Argania is an endemic genetic resource in Morocco holding an important ecological and socio-economical benefit. However, overgrazing and overharvesting lead to a serious downturn in the number of trees. To characterize genetic diversity within and among 24 populations, represented by 240 argan trees, four combinations of SRAP primers and eight combinations of REMAP primers were used. A total of 338 REMAP and 146 SRAP markers were amplified with a polymorphism of 100%. The average polymorphism information content value was 0.20 and 0.17 for SRAP and REMAP markers, respectively. The analysis of molecular variance showed that 26% of the genetic variation was partitioned among populations. The coefficient of gene differentiation was 0.2875 and gene flow was 1.2391. The average parameter diversity was: observed number of alleles (Na)=0.729, effective number of alleles (Ne)=1.131, Shannon’s information index (I)=1.143; Nei’s gene diversity (H)=0.093 and Percentage of Polymorphic Loci=35.68. The STRUCTURE and principal coordinate analysis revealed that the Argania spinosa L. populations were aggregated into 2 genetic groups. To detect outlier, baysecan software was used and 21 were detected (7 under selection, 14 under balancing selection) presenting posterior probability higher than 0.79. The current results can be explored in the design of management programs and to comprehend the adaptation mechanism of Argan tree.

Genetic diversity and population structure of the endangered plant Salix taishanensis based on CDDP markers

Salix taishanensis, belonging to family Salicaceae, is a rare tree species endemic to China. This species is at risk of extinction because of continued habitat disturbance. However, the genetic diversity of the natural populations has not been assessed to date. By using conserved DNA-derived polymorphism marker techniques, we studied the genetic diversity and population structure of four populations of Salix taishanensis. A total of 128 discernible loci were obtained from 115 individuals using 13 primers, and 73.44% of the loci were polymorphic. Nei’s genetic diversity index (H) was 0.2227, and the Shannon diversity index (I) was 0.3505, indicating that the genetic diversity in Salix taishanensis is low. At the population level, the percentage of polymorphic loci (PPL) averaged 53.71%, H averaged 0.1932, and I averaged 0.2864. The highest level of genetic diversity was observed in the Pangquan Valley (PQG) population (PPL = 58.59%, H = 0.2040, I = 0.3044); the lowest was observed in the Mount Tai (MT) population (PPL = 49.22%, H = 0.1808, I = 0.2680). Analysis of molecular variation (AMOVA) revealed significant genetic differentiation within and between populations (P < 0.001), with 79.71% of the variation occurring among populations and 20.29% occurring within populations. Genetic variation analysis showed a coefficient of gene differentiation of 0.1723 and a gene flow value of 2.4014 among populations. A Mantel test and cluster analysis revealed no significant correlation between genetic distance and geographic distance among populations (r = −0.3189, P = 0.7083). The 115 individuals were divided into four genetic clusters according to Bayesian structure and principal coordinate analysis (PCoA), correlating significantly with geographic distribution. The low-level genetic diversity and obvious population differentiation of the S. taishanensis populations may be related to their evolutionary histories and geographical isolation. If protective measures are not taken in time, their genetic diversity will continue to decrease due to inbreeding effects. These results will assist with the formulation of conservation strategies based, such as genetic rescue and in situ and ex situ conservation.

SPAR methods reveal high genetic diversity within populations and moderate gene flow of pointed gourd (Trichosanthes dioica Roxb.) germplasm

Abstract Pointed gourd (Trichosanthes dioica Roxb.) is one of the most nutritive cucurbitaceous vegetable crops cultivated in tropical and subtropical regions around the world. Poor characterization of the available germplasm, vegetative means of propagation and dioecy are the main constraints in developing a systematic breeding programme in pointed gourd. In this investigation, genetic variability of pointed gourd accessions belonging to four agro-climatic zones of Bengal region of India was evaluated by employing polymerase chain reaction (PCR) based single primer amplification reaction (SPAR) methods, viz., random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR) and directed amplification of minisatellite DNA (DAMD). Percentage of polymorphic loci, Nei’s gene diversity index (h) and Shannon’s Information index (I) indicated a moderate level of genetic heterogeneity in studied germplasm. The mean coefficient of genetic differentiation (Gst) between populations for RAPD, ISSR and DAMD were 0.419, 0.305 and 0.315 respectively, indicating that 58.1%, 69.5% and 68.5% of genetic variability prevailed within the population. Similarly, analysis of molecular variance (AMOVA) revealed that majority of the genetic variation were partitioned among the individuals within a population. Gene flow estimate (Nm) calculated for RAPD, ISSR and DAMD marker were 0.692, 1.139 and 1.086 respectively indicating a moderate gene flow among the populations. The clustering pattern based on the combined marker systems was primarily related to the geographical distribution of the accessions. This study clearly demonstrates the efficiency of single primer based amplification reactions (SPARs) in duplicate identification, core collection and improvement of pointed gourd germplasm.

Genetic diversity and structure of Prunus padus populations in South Korea based on AFLP markers

We applied seven pairs of primer-restriction enzyme combinations to investigate the genetic diversity, genetic differentiation, and genetic structure of Prunus padus populations with AFLP markers. The values obtained for average of effective alleles (A e), percentage of polymorphic loci (%P), Shannon’s diversity index (I), and expected heterozygosity (H e) were 1.38, 81.4, 0.357, and 0.223%, respectively. The expected heterozygosity (Hj) obtained by using a Bayesian method was 0.256. The level of genetic diversity obtained for P. padus was low compared to that of Prunus species and other species with a similar life history. The inbreeding coefficient (F IS) from the approximated Bayesian method was 0.767. This value was lower than that obtained for Ulmus davidiana, which undergoes both sexual and asexual reproduction. However, the value obtained was larger than that for other species that undergo sexual reproduction, such as, Carpinus laxiflora, Phellodendron amurense, and Acer pseudosieboldianum. The value of genetic differentiation was 0.245 from AMOVA (ΦST) and 0.278 from Bayesian method (θII). The obtained level of genetic differentiation was large compared to that of other Prunus species plants and other species with a similar life history. According to UPGMA and Bayesian clustering, 11 populations were divided into two genetic groups. However, some populations were detected as weak genetic structures according to the geographical distribution. It was occurred by forest succession, asexual propagation strategies to adapt local environmental change, and gene flow being gradually decreased due to population fragmentation by demographic disturbances.

Phenotypic characterization of chili pepper (Capsicum annuum L.) under Phytophthora capsici infection and analysis of genetic diversity among identified resistance accessions using SSR markers

Chili pepper (Capsicum annuum L.) is one of the most important vegetable crops, largely suffers from various biotic stresses, including Phytophthora capsici L., imposing huge yield loss. Due to the lack of agronomically superior traits in available resistant accessions, chili breeders are constantly searching for new sources of resistance with genetically diverse traits. In the present study, a total of 233 chili pepper accessions from Ethiopia and India were screened under P. capsici infection. A total of 22 highly resistant and 17 moderately resistant accessions were identified. Among these, only 32 chili pepper accessions with mean disease index ranging from 1.4 to 2.0 and 2.20–3.8, were selected for genetic diversity analysis. From a total of 19 SSR primers analyzed, only 14 SSR primers were shown to be polymorphic. The result showed that a total of 31 alleles with an average of 2.214 alleles per primer were amplified across the selected accessions. A maximum of 3 alleles were observed in only 3 SSR primers. The analysis of 14 SSR primers resulted in PIC values ranging from 0.12 to 0.98 with an average of 0.64, the percentage of polymorphic loci of 11.45–96.87% with an average of 57.69% and effective number of alleles (Ne) of 1.058–2.174 with a mean of 2.213. This indicated that the 14 SSR primers detected variation among 32 chili pepper accessions. The genetic dissimilarity index (GDI) value ranged from 0.05 to 0.51, with the highest GDI (0.51) in Gutowayu_80039 and IC_537646 accessions. The population structure and cluster analysis grouped the chili pepper accessions into three genetic resistance groups. In addition, the UPGMA cluster analysis of the 14 SSR primers clearly distinguished between one resistance group and the other. As per AMOVA analysis, a total of 42% and 58% of variation among and within populations were detected in the nine populations of C. annuum, respectively. The resistance/moderate resistance accessions greatly showed both phenotypic and genotypic variation. The accessions GojamMecha_9082, Mareko_233636, GojamMecha_9086, IC_526851, and IC_537587 showed high level of resistance with diversified resistance loci, which could be used as a source of resistance for chili pepper breeders.

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

BackgroundStenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions.ResultsBased on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h = 0.47, I = 0.66) and ISSR markers (h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers.ConclusionsPhenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.

Hermaphroditism in Marijuana (Cannabis sativa L.) Inflorescences - Impact on Floral Morphology, Seed Formation, Progeny Sex Ratios, and Genetic Variation.

Cannabis sativa L. (hemp, marijuana) produces male and female inflorescences on different plants (dioecious) and therefore the plants are obligatory out-crossers. In commercial production, marijuana plants are all genetically female; male plants are destroyed as seed formation reduces flower quality. Spontaneously occurring hermaphroditic inflorescences, in which pistillate flowers are accompanied by formation of anthers, leads to undesired seed formation; the mechanism for this is poorly understood. We studied hermaphroditism in several marijuana strains with three objectives: (i) to compare the morphological features of this unique phenotype with normal male flowers; (ii) to assess pollen and seed viability from hermaphroditic flowers; and (iii) to assess the effect of hermaphroditism on progeny male:female (sex) ratios and on genetic variation using molecular methods. The morphological features of anthers, pollen production and germination in hermaphroditic flowers and in staminate inflorescences on male plants were compared using light and scanning electron microscopy. Seeds produced on hermaphroditic plants and seeds derived from cross-fertilization were germinated and seedlings were compared for gender ratios using a PCR-based assay as well as for the extent of genetic variation using six ISSR primers. Nei’s index of gene diversity and Shannon’s Information index were compared for these two populations. The morphology of anthers and pollen formation in hermaphroditic inflorescences was similar to that in staminate flowers. Seedlings from hermaphroditic seeds, and anther tissues, showed a female genetic composition while seedlings derived from cross-fertilized seeds showed a 1:1 male:female sex expression ratio. Uniquely, hermaphroditic inflorescences produced seeds which gave rise only to genetically female plants. In PCR assays, a 540 bp size fragment was present in male and female plants, while a 390 bp band was uniquely associated with male plants. Sequence analysis of these fragments revealed the presence of Copia-like retrotransposons within the C. sativa genome which may be associated with the expression of male or female phenotype. In ISSR analysis, the percentage of polymorphic loci ranged from 44 to 72% in hermaphroditic and cross-fertilized populations. Nei’s index of gene diversity and Shannon’s Information index were not statistically different for both populations. The extent of genetic variation after one generation of selfing in the progeny from hermaphroditic seed is similar to that in progeny from cross-fertilized seeds.

Genetic Diversity of Ectomyelois ceratoniae (Zeller 1881) (Lepidoptera: Pyralidae) Collected from Three Different Host-Plants in Tunisia by Using RAPD-PCR

The carob moth, Ectomyelois ceratoniae Zeller (Lepidoptera: Pyralidae), is an insect pest that causes damage to various crops and fruit trees throughout the world. In Tunisia, this pest attacks date, pomegranate and citrus by seriously affecting the fruit quality. Therefore, the objective of this work is to investigate genetic variation in the carob moth among and within three host-plants by three RAPD markers. The results showed high genetic diversity in the pest. The mean percentage of polymorphic loci was 78.38 %. The total variance percentage of 5 % among populations and 95 % within the populations is suggestive of the role of sexual reproduction for generating high genetic diversity. The average genetic distances among populations ranged from 0.028 to 0.043. The date population is more related to the pomegranate population compared to citrus specimens. The UPGMA dendrogram and the two-dimensional principal component analysis (PCA) showed that there is no correlation between E. ceratoniae genotypes and their host plants and geographic localisation suggesting that gene flow between populations is independent of geographic distance and appears to be unrestricted.