Sequence-related Amplified Polymorphism Data Research Articles

Evaluation in Genetic Variation of Krachai by Sequence Related Amplified Polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) Techniques

Krachais are local name of Thai herb which are identified within 2 genera, namely Bosenbergia (white or red krachai) and Kaempferia (black krachai). The rhizome of Bosenbergia rotunda (L.) Mansf. contains major aromatic compounds against COVID19 but its many morphological characteristics such as leaves, stems and rhizome are like other species in same genus or family. In this study, a total of 13 accessions containing 5 samples of B. rotunda, 2 samples of Boesenbergia spp. and 3 samples of Kaempferia parviflora including 3 samples of other species in same family as outgroups were analyzed and clustered using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. The results showed that 8 SRAP primers (M1E1, M1E2, M1E7, M2E10, M3E9, M5E1, M5E2 and M6E10) could generate 79 polymorphism bands with an average of 92.15% whereas a total of 5 RAPD primers (OPY04, OPY02, OPY04, JAT11 and JAT12) could give 64 polymorphisms with 100% as a percentage of the polymorphism band. The PIC of the SRAP marker (0.470) has a higher value than the RAPD marker (0.264). The highest similarity coefficients within genus Boesenbergia of 1.000 and 0.952 were obtained from SRAP and RAPD markers, respectively. The UPGMA dendrogram of SRAP and RAPD information among krachai presented 2 and 4 groups, respectively. The cluster of Boesenbergia was separated from K. parviflora and other species in same family. Furthermore, the results also pointed that Boesenbergia sp. from Phayao is in correct genus and is B. pandurata (Roxb.) Schltr. because of having red leaf while Boesenbergia sp. from Chiang Rai showed confusion between SRAP and RAPD data. It was concluded that SRAP and RAPD have great potential for the study of genetic diversity of Boesenbergia and other species in family Zingiberaceae.

Morphological and Molecular Characterizations of Musa (ABB) 'Mali-Ong' in Thailand.

Simple SummaryThe banana cultivar Musa (ABB) ‘Mali-Ong’ is widely used in the processed food industry in Thailand, where it determines the quality of the products. However, the sub-cultivars of ‘Nam Wa Mali-Ong’ are almost indistinguishable, with few morphological differences and minimal genetic variation. This study used 77 morphological characteristics and two types of molecular markers to distinguish Nam Wa Mali-Ong from other cultivars. The study also assessed the genetic variation of nine ‘Nam Wa Mali-Ong’ clones and compared them with 10 other samples of bananas with different genomes or chromosome sets. The molecular markers grouped the ‘Nam Wa Mali-Ong’ samples. Four clones (A, B, D, and I) were superior and had higher bunch weights. This study will be useful for germplasm evaluation and future ‘Nam Wa Mali-Ong’ improvements.Musa (ABB) ‘Mali-Ong’ is an economically important banana cultivar in Thailand. We morphologically and molecularly characterized ‘Nam Wa Mali-Ong’. Leaf blade width was the only statistically different morphological character among the clones. To determine genetic variation, nine ‘Nam Wa Mali-Ong’ clones were compared with 10 samples of Musa ABB, AA, and BB cultivars by fingerprinting using seven pairs of sequence-related amplified polymorphism (SRAP) and eight inter simple sequence repeat (ISSR) markers. The SRAP and ISSR primers generated 65 and 76 amplicons, respectively, of which 57 (87.7%) and 62 (81.6%) amplicons, respectively, were polymorphic; the polymorphic information content was 0.28–0.49. The SRAP data revealed two distinct groups: Group I, comprising two subgroups (one including all ABB samples and the other containing the BB genome accessions), and Group II, comprising the AA genome accessions. The ISSR data revealed two groups: Group I, which incorporated the AA (Hom Champa) genome, and Group II, consisting of two subgroups: Subgroup A, comprising only the AA (Hom Chan) accessions, and subgroup B, comprising all the ABB accessions and wild banana M. balbisiana (BB genome). The ‘Nam Wa Mali-Ong’ samples clustered together, regardless of the markers used. SRAP and ISSR markers will be useful for germplasm evaluation and future Musa (ABB) improvements.

DNA-barcoding, SCoT and SRAP Based Somaclonal Variation in Micropropagated Withania somnifera Plantlets

Ashwagandha (Withania somnifera) is one of the recognized plant species that considered of most traditional natural supplements. Tissue culture is an efficient method as fast and affordable in plant propagation. Few studies have discussed the genetic impact of such method on ashwagandha plant. The aim of this research was to identify the genetic stability of micropropagated plantlets and to assess the impact of in vitro-propagation on somaclonal variability in ashwagandha using start codon-targeted (SCoT), sequence-related amplified polymorphism (SRAP) and DNA-barcoding assays. SCoT marker assay produced a total number of 132 bands with an average of 11 bands per primer, where scorable PCR fragments were generated from all primers. The phylogenetic tree constructed using SCoT binary data, revealed genetic variability among studied plant samples. SRAP primer combinations showed a total of 78 bands by an average of 11.1 bands / combination, in which all combinations produced scored PCR fragments. Over SRAP assay, one specific band was obtained that was present in different ashwagandha micropropagated plant samples compared to the control (mother plant). This PCR fragments were obtained using me1F/em1R primer combination (287 bp). The phylogenetic tree constructed using SRAP data was successful to differentiate between micro-propagated plants and the control. The DNA- barcoding analysis using chloroplast gene RNA polymerasel (rpoCl) gene was used to detect the soma- clonal variation between control and one micro-propagated plant of ashwagandha. The phylogenetic tree constructed using DNA-barcoding sequences was successful to differentiate between the two samples, where control and micropropagated plantlets were grouped in two different groups. This study suggests the valuableness of using SRAP and DNA-barcoding in detecting soma-clonal variation among micropropagated plantlest of ashwagandha.

Genetic diversity and relationships among populations of jackfruit, an underutilized nutrient-rich climate-smart fruit tree crop in Kenya and Uganda

ABSTRACT Jackfruit (Artocarpus heterophyllus Lam.) is an underutilized fruit tree crop in East Africa. Despite its importance for food and nutritional security, only limited information exists on the extent of genetic variability among Ugandan and Kenyan jackfruit populations. This study was aimed at analyzing the extent of genetic diversity in jackfruit germplasm from selected regions of Kenya and Uganda. A total of 30 mature fruit samples were collected randomly from three districts (Kampala, Wakiso and Mbale) in Uganda and five counties (Siaya, Kwale, Mombasa, Busia, and Murang’a) in Kenya. Genetic characterization was using six simple sequence repeat (SSR) and nine sequence-related amplified polymorphism (SRAP) markers. The results revealed that 62.50% of the loci for SSR and 82.14% for SRAP markers were polymorphic. The average polymorphism information contentwas 0.48 for SSR and 0.56 for SRAP markers. The Jaccard’s similarity coefficient ranged from 0.55 to 1.0 for SSR and from 0.33 to 0.93 for SRAP markers, indicating considerable genetic diversity among jackfruit germplasm. Based on combined SSR and SRAP data, analysis of molecular variance revealed greater genetic diversity within the populations (76%) than among the eight populations (24%). Dendrogram and principal coordinate analysis separated the germplasm into two clusters, with several intermediates. The germplasm distribution among the clusters and sub-clusters was not associated with the geographical region. The significant genetic variability existing in Ugandan and Kenyan jackfruit germplasm can be used to improve jackfruit through breeding. The substantial genetic diversity should enable jackfruit breeders to develop high-yielding varieties with improved quality traits.

Genetic Differentiation of an Endangered Megalobrama terminalis Population in the Heilong River within the Genus Megalobrama

Megalobrama terminalis, which inhabits the Sino-Russian Heilong-Amur River Basin, has decreased critically since the 1960s. It has been listed in the Red Book of Endangered Fish Species by the Russian Federation in 2004. To guide the utilization and conservation programs of M. terminalis in the Heilong River (MTH), 3.1 kb of mitochondrial DNA (mtDNA) concatenated sequences and sequence-related amplified polymorphism (SRAP) markers (15 primer combinations) were applied to explore the genetic divergence and population differentiation of MTH within the genus Megalobrama. Clear genetic divergence between MTH and six other populations of the genus Megalobrama was found by haplotype network (mtDNA) and principal component (SRAP) analyses. Moreover, the STRUCTURE analysis based on SRAP data showed that MTH could be assigned to a particular cluster, whereas conspecific M. terminalis in the Qiantang River and Jinsha River Reservoir belonged to the same cluster. Analysis of molecular variance (AMOVA) and Fst statistics for the mtDNA and SRAP data revealed significant genetic variance and differentiation among all detected populations. Taken together, the results suggest that MTH has a strong genetic differentiation from other populations within the genus Megalobrama, which contributes to effective utilization in artificial cultivation and breeding of MTH. Furthermore, these results also provide a scientific basis for the management of MTH as a separate conservation unit.

SRAP markers for genetic diversity assessment of lavender (Lavandula angustifolia mill.) varieties and breeding lines

Lavender (Lavandula angustifolia Mill.) is an essential oil-bearing and medicinal plant of great economic and social importance to Bulgaria, which is the world largest producer of lavender oil nowadays. Currently, the industrial cultivation of lavender in Bulgaria employs up to seven varieties established during the last century. Despite the growing industrial lavender cultivation, few molecular markers have been applied for characterization of lavender genetic resources and breeding. The present study employed sequence-related amplified polymorphism (SRAP) markers to characterize the genetic resources and genetic diversity within and between two groups of ten Bulgarian and five foreign lavender varieties and breeding lines. The data generated following analysis with 51 SRAP primer pairs showed amplification of a high number (4697) and ratio (77.2%) of polymorphic SRAP fragments resulting in relatively high value of the polymorphism information content, with an average of 0.27 ± 0.03 for the used primer pairs. Analysis of molecular variance of the SRAP data further revealed high level of genetic diversity (96.6% of the total variations) within the analyzed groups of Bulgarian and foreign varieties and rather low diversity (3.4% of total variations) between the two groups. The possibilities for further applications of SRAP markers in lavender breeding and cultivation are discussed.

Farklı konukçulardan elde edilen Botrytis cinerea populasyon yapısının moleküler tanılanması

Botrytis cinerea (teleomorph: Botryotinia fuckeliana) causes gray mold disease on vegetable crops in greenhouses. Profound knowledge on pathogen diversity is necessary for efficiently disease management. In this study, forty-two B. cinerea isolates collected from 36 different greenhouses in Antalya province of Turkey were investigated. Twelve SRAP (sequence-related amplified polymorphism) and 18 ISSR (inter simple sequence repeat) primers producing high polymorphic fragments were used to genetic diversity of B. cinerea isolates infecting dill, basil, lettuce, bean, cucumber, tomato, pepper and eggplant. The unweighted pair-group method with arithmetic average analysis (UPGMA) was used to evaluate of combined ISSR and SRAP data showing a similarity range 0.15-0.90 among the isolates. Cophenetic correlation of the tree was high level (r=0.93). Interestingly, cluster analysis showed a divergent group consisting of lettuce isolates which were genetically different from the other isolates. On the other hand, transposable elements (Flipper and Boty) were detected among isolates from all the hosts. Isolates containing only the Fliper element were detected. The results showed that genetically characterized B. cinerea populations by a high level of genetic diversity were associated with genotype flow and the evolutionary potential of B. cinerea. In further studies, the newly tested molecular markers are useful and can be suggested for analyzing of genetic diversity and population structure of this pathogen on different hosts.

Genetic Fingerprinting of Two Species of Averrhoa Using RAPD and SRAP Markers

Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) marker analyses were conducted in two underutilized fruit trees of the family, Oxalidaceae, namely Averrhoa bilimbi and A. carambola, commonly known as cucumber tree and starfruit tree respectively. The current study focused on the utility of 23 RAPD primers and 31 SRAP primers. The RAPD primer, OPD-07 produced the greater number of amplified fragments, exhibited higher level of polymorphism and could differentiate between almost all the collections on the basis of the efficiency of different primer parameters. The most competent SRAP primer combination for the characterization of Averrhoa collections was ME2/EM6. Cluster and PCA analyses on both RAPD and SRAP data differentiated the A. bilimbi and A. carambola collections. Both markers showed that A. bilimbi collections, Ab2, Ab3 and Ab4 were distinct from the rest. Both SRAP and integrated data were capable of distinguishing sour and sweet collections of A. carambola. The present study provides the first in-depth report on the molecular diversity between the two species of the genus Averrhoa with regard to RAPD and SRAP markers. Both RAPD and SRAP could discriminate the species, and collections of Averrhoa. SRAP are the preferred choice because it differentiates various collections and possess good amplification, stability and polymorphism.

Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

Analysis of Genetic Diversity in Chrysopogon aciculatus Using Intersimple Sequence Repeat and Sequence-related Amplified Polymorphism Markers

Molecular genetic diversity and relationships among 86 Chrysopogon aciculatus (Retz.) Trin. accessions were assessed using intersimple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Twenty-five ISSR markers generated 283 amplification bands, of which 266 were polymorphic. In addition, 576 polymorphic bands were detected from 627 bands amplified using 30 SRAP primers. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher proportion of polymorphic loci (PPL; 94%) than SRAP markers (91.87%). The ISSR and SRAP data were significantly correlated (r = 0.8023). Cluster analysis of the separate ISSR and SRAP data sets clustered the accessions into three groups, which generally were consistent with geographic provenance. Cluster analysis of the combined ISSR and SRAP data set revealed four major groups similar to those based solely on ISSR or SRAP markers. The findings demonstrate that ISSR and SRAP markers are reliable and effective tools for analysis of genetic diversity in C. aciculatus.

Genetic diversity within Turkish watermelon [Citrullus lanatus (Thunb.)Matsumura & Nakai] accessions revealed by SSR and SRAP markers

The genetic diversity of Turkish watermelon genotypes selected from the watermelon genetic resource collection was evaluated by simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers. Most of the accessions were collected from various geographical regions of Turkey. Different Citrullus species, wild relatives, foreign landraces, open pollinated (OP), and commercial hybrid cultivars were also assessed for genetic relatedness. Fourteen SSR primers and 31 SRAP primer combinations were used in the experiment. Both SSR markers (100%) and SRAP markers (97.3%) generated high polymorphisms. Based on the SSR and SRAP data, the genetic similarity coefficients were calculated, and dendrograms were constructed using the unweighted pair-group method with arithmetic average (UPGMA). Cluster and principle coordinate analyses indicated that Citrullus lanatus var. Lanatus subspecies genotypes collected from the different regions of Turkey were closely genetically related. Overall, our results displayed low genetic variability within the Turkish watermelon germplasm in contrast with their high morphological diversity.

Fingerprinting a Number of Prunus Persica Varieties Cultivated In Duhok Province Using Srap Markers

In order to evaluate the genetic relationship among the germplasms of Prunus persica, sequence related amplified polymorphism (SRAP) marker was used to analyze genetic diversity of nine genotypes of peach cultivated in Duhok Governorate/ Kurdistan Region- Iraq. Twelve primer pairs generated 658 bands，379 bands were polymorphism; level of polymorphism observed in the present study with 12 primers pairs was 60.89 %. Revealed by NTSYS software the SM coefficient of genetic similarity ranged from 0.056 to 0.35. A dendrogram was constructed based on SRAP data using UPGMA cluster method. The nine genotypes of peach were classified into three groups and five sub-groups which were basically corresponded with the genetic relationships based on SRAP marker data.

Species composition and genetic structure of Fusarium graminearum species complex populations affecting the main barley growing regions of South America

Members of the Fusarium graminearum species complex (FGSC), such as F. graminearum and F. asiaticum, are the main cause of fusarium head blight (FHB) of wheat and barley worldwide. In this study, 117 FGSC isolates obtained from commercial barley grain produced in Argentina (n = 43 isolates), Brazil (n = 35), and Uruguay (n = 39) were identified to species and trichothecene genotypes, and analysed using amplified fragment length polymorphism (AFLP) and sequence‐related amplified polymorphism (SRAP) markers. In addition, reductase (RED) and trichothecene 3‐O‐acetyltransferase (Tri101) were sequenced for a subset of 24 isolates. The majority of the isolates (n = 103) were identified as F. graminearum, which was the only species found in Argentina. In Uruguay, only one F. cortaderiae isolate was found among F. graminearum isolates. In Brazil, F. graminearum also dominated the collection (22/35), followed by F. meridionale (8/35), F. asiaticum (2/35), F. cortaderiae (2/35) and F. austroamericanum (1/35). Species were structured by trichothecene genotype: all F. graminearum were of the 15‐acetyldeoxynivalenol (ADON), F. meridionale, F. asiaticum and F. cortaderiae were of the nivalenol (NIV), and F. austroamericanum was of the 3‐ADON genotype. Both AFLP and SRAP data showed high levels of genetic variability, which was higher within than among countries. Isolates were not structured by country of origin. SRAP analysis grouped F. graminearum in a separate cluster from the other species within the complex. However, AFLP analysis failed to resolve the species into distinct clades with partial clustering of F. meridionale, F. austroamericanum, F. asiaticum and F. graminearum isolates.

MOLECULAR ANALYSIS OF ZIZIPHUS SPP. CULTIVARS IN EGYPT

Ziziphus spinia-christi and Z. mauritiana are known as ‘Balady’ and ‘Hendi’ cultivars, respectively, in Egypt. They were used in this study to analyze the genetic diversity of Egyptian Ziziphus and to authenticate a new superior cultivar namely ‘Hozaien’. This cultivar arose more than fifty years ago and has been reported as a bud sport mutation of ‘Balady’ cultivar despite its extremely morphological and biochemical variations. The sequence related amplified polymorphism (SRAP) and the randomly amplified polymorphic DNA (RAPD) molecular markers were utilized to analyze the genetic relationships amongst the three cultivars. A total of 141 SRAP and 75 RAPD amplicons were generated by 10 SRAP and 6 RAPD primer combinations; of which 87 (61.70%) and 32 (42.67%) bands were polymorphic, respectively. SRAP was more informative and showed more shared and specific unique bands than RAPD. Both cluster analysis and principal coordinate analysis based on SRAP and RAPD data clearly showed that ‘Hozaien’ cultivar has low genetic relationship with Z. spina-christi and should not be classified as a mutant of it. This result encourage us to detach this cultivar from which and subject it for more study, using more species from neighbor countries, to voucher its identity either a cultivar of another species or a new species.

Development of a SCAR Marker for Rapid Identification of New Kentucky Bluegrass Breeding Lines

As a commonly used turfgrass, Kentucky bluegrass (Poa pratensis L.) (KBG) has many commercially available cultivars for production. After several years of screening, two new lines were obtained (‘KBG03’ and ‘KBG04’), which have high tolerance to summer. The study showed that the two lines revealed similar morphological characteristics, with light green leaf color, narrow leaf blade, high plant height and light 1,000-grain weight. A total of 400 random amplified polymorphic DNA (RAPD) primers and 256 sequence-related amplified polymorphism (SRAP) primer combinations were screened among the two lines and other 4 imported commercial cultivars. The percentages of polymorphic sites were 65.5% (RAPD) and 22.6% (SRAP) respectively. By cluster analysis of RAPD and SRAP data, the dendrogram at a similarity of 0.29 gave two main clusters, of which one group had 4 commercial cultivars, and the other had the two new breeding lines. Furthermore, one specific band of ‘KBG04’ was successfully converted into a dominant sequence characterized amplified region marker (SCAR196). Then the SCAR marker was verified by 39 KBG DNA samples, including imported varieties, domestic varieties and self-breeding lines of our laboratory, and it exhibited high consistency with the original RAPD polymorphic amplification. The results showed that the SCAR marker can be used to distinguish the new line ‘KBG04’ from numerous KBG germplasms, which would be useful for cultivar identification and property rights protection in the future.

Development of a SCAR Marker for Rapid Identification of New Kentucky Bluegrass Breeding Lines

As a commonly used turfgrass, Kentucky bluegrass (Poa pratensis L.) (KBG) has many commercially available cultivars for production. After several years of screening, two new lines were obtained (‘KBG03’ and ‘KBG04’), which have high tolerance to summer. The study showed that the two lines revealed similar morphological characteristics, with light green leaf color, narrow leaf blade, high plant height and light 1,000-grain weight. A total of 400 random amplified polymorphic DNA (RAPD) primers and 256 sequence-related amplified polymorphism (SRAP) primer combinations were screened among the two lines and other 4 imported commercial cultivars. The percentages of polymorphic sites were 65.5% (RAPD) and 22.6% (SRAP) respectively. By cluster analysis of RAPD and SRAP data, the dendrogram at a similarity of 0.29 gave two main clusters, of which one group had 4 commercial cultivars, and the other had the two new breeding lines. Furthermore, one specific band of ‘KBG04’ was successfully converted into a dominant sequence characterized amplified region marker (SCAR196). Then the SCAR marker was verified by 39 KBG DNA samples, including imported varieties, domestic varieties and self-breeding lines of our laboratory, and it exhibited high consistency with the original RAPD polymorphic amplification. The results showed that the SCAR marker can be used to distinguish the new line ‘KBG04’ from numerous KBG germplasms, which would be useful for cultivar identification and property rights protection in the future.

Genetic diversity in populations of the endangered medicinal plant Tetrastigma hemsleyanum revealed by ISSR and SRAP markers: implications for conservation

Genetic diversity of 27 Tetrastigma hemsleyanum accessions from wild or cultivated populations was evaluated using SRAP (sequence-related amplified polymorphism) and ISSR (inter-simple sequence repeat) markers. ISSR and SRAP analysis yielded 112 and 66 scorable amplified bands, respectively, of which 85.71 and 77.27 % were polymorphic. ISSR revealed efficiency over SRAP due to high Shannon’s Information Index (I), Nei’s gene diversity (H), and total genetic diversity (Ht). The dendrograms showed clear clustering pattern of geographically distribution. The correlation between the coefficient matrices for the SRAP and ISSR data was high (r = 0.869, P < 0.01). Higher level of genetic similarity was observed in intra-population than in inter-population. The average genetic similarity among cultivated populations were far above that among wild populations, the low level of gene flow, distance isolation, and asexual reproduction were likely related to the low level of differentiation among populations. The promotion of genes exchange will be very beneficial to conserve and utilize the enormous genetic variability contained in the T. hemsleyanum.

Evaluating genetic diversity and constructing core collections of Chinese Lentinula edodes cultivars using ISSR and SRAP markers.

Genetic diversity among 89 Chinese Lentinula edodes cultivars was analyzed by inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A 123 out of 126 ISSR loci (97.62%) and 108 out of 129 SRAP loci (83.73%) were polymorphic between two or more strains. A dendrogram constructed by cluster analysis based on the ISSR and SRAP markers separated the L. edodes strains into two major groups, of which group B was further divided into five subgroups. Clustering results also showed a positive correlation with the main agronomic traits of the strains, and that strains with similar traits clustered together into the same groups or subgroups in most cases. The average coefficient of pairwise genetic similarity was 0.820 (range: 0.576-0.988). Compared to the wild strains, Chinese L. edodes cultivars indicated a lower level of genetic diversity. Two preliminary core collections of L. edodes, Core1 and Core2, were established based on the ISSR and SRAP data, respectively. Core1 was constructed by the advanced M (maximization) strategy using the PowerCore version 1.0 software and contained 21 strains, whereas Core2 was created by the allele preferred sampling strategy using the cluster method and contained 18 strains. Both core collections were highly representative of the genetic diversity of the original germplasm, as confirmed by the values of Na (observed number of alleles), Ne (effective number of alleles), H (Nei's gene diversity) and I (Shannon's information index), as well as results of principal coordinate analysis. The loci retention ratio of Core1 (99.61%) was higher than that of Core2 (97.65%). Moreover, Core1 contained strains with more types of agronomic traits than those in Core2. This study builds the basis for further effective protection, management and use of L. edodes germplasm resource.

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, of which 163 were polymorphic, while SSR assay detected 101 alleles with 87 polymorphic alleles and 114 genotypes. A comparative analysis of the diversity index, effective multiplex ratio, and marker index of the 2 markers showed higher efficiency of SRAP markers in watermelon germplasm fingerprinting. The Mantel test resulted in a high correlation between SRAP and SSR data with a value of $\gamma$ = 0.863, revealing a good fit between the 2 marker systems. Genetic diversity among the accession set was estimated by a construction of dendrograms using SRAP, SSR, or SRAP-SSR combined data. There was clear consistency between the 3 dendrograms on the positioning of most accessions. The study demonstrated that most Chinese cultivated germplasms (CCGs) were clustered independently of their geographical distribution and horticultural classification, and had a narrow genetic base; most CCGs and foreign cultivars had a high genetic closeness and showed similar lineages; and the 4 wild accessions were the most genetically diverse, followed by the small-fruited accessions from northern China and edible-seeded accessions. We concluded that CCGs lacked genetic variation, and we offer a means of introducing new genetic diversity into the watermelon germplasm pool in China, which is essential to maximizing productivity in watermelon.

DNA typing and genetic relations among populations of Kelussia odoratissima using ISSR and SRAP markers

Kelussia odoratissima is well known for its medicinal importance. It has been announced as an endangered species. Thus, examining the genetic variation and conservation of this plant is necessary. In the present study, inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) molecular markers were employed for the first time to access the genetic diversity and relationships of 77 wild individual plants of K. odoratissima collected from seven populations in Central Zagros region of Iran. A total of 146 bands were amplified by 12 ISSR primers, of which 129 (87.80 %) were polymorphic, while 69 polymorphic bands (83.30 %) were observed among 86 bands amplified by 11 SRAP primers. Polymorphic information content (PIC = 0.32), resolving power (Rp = 7.80), and marker informativeness (MI = 3.48) generated by ISSR primers were higher than that of SRAP analysis (PIC = 0.30, Rp = 5.61, and MI = 1.88). The study indicated that ISSR were more effective than SRAP markers for assessing the degree of genetic variation of K. odoratissima. In both UPGMA dendrograms of ISSR and SRAP, in most cases, individuals from each population were clustered in various groups without clear separation, which demonstrates the high variability of this germplasm in Iran. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the Mantel’s test between the dendrograms for ISSR and SRAP data indicated a poor fit for the ISSR and SRAP data types (r = 0.10). Besides, principal coordinate analysis results showed that the first three principal coordinates account for 65.57 % of the total variation and studied seven populations were separated from each other and placed into five groups. These results have an important implication for K. odoratissima germplasm characterization, improvement, and conservation.