REMAP Markers Research Articles

Genetic fingerprinting ofZiziphus jujubaby using SCoT and REMAP molecular markers

AbstractJujube is both consumed as a food source and medicinal plant in local markets. It is expected that different geographical populations ofZiziphus jujuba, differ in their genetic content as they grow in different ecological conditions. It is important to have detailed information on population genetic structure and the available genetic variability to make a proper germplasm collection of jujube. We have no data on jujube populations of Iran based on SCoT and REMAP molecular markers, and therefore we planned a population genetic study of these trees in 10 geographical areas. We used SCoT and REMAP molecular markers for our genetic investigation. We found the loci with a high value of Gst (1.00) in SCoT and REMAP markers that can be used in fingerprinting of jujube.

Molecular insights into the genetic diversity and population structure of Artemisia annua L. as revealed by insertional polymorphisms.

The online version contains supplementary material available at 10.1007/s40415-022-00860-x.

Biosystematics, fingerprinting and DNA barcoding study of the genus Lallemantia based on SCoT and REMAP markers

Lallemantia is a medicinally important plant in the world. Due to interspecific hybridization and horizontal gene transfer, spices relationship and delimitation on the genus Lallemantia is difficult based on different molecular markers. Therefore, selecting the appropriate marker can be important. Fingerprinting techniques continue to be used for genomic profiling for the characterization of germplasm and the establishment of the identity of varieties/hybrids/parental sources of aromatic and medicinal plants. For this, we need to produce detailed information on genetic diversity available in Lallemantia as well as investigate spices relationship and delimitation. Therefore, the present study was performed on Lallemantia species in Iran. We used the start codon targeted and retrotransposon-microsatellite amplified polymorphism molecular marker for our genetic investigation with the following aims: 1- To reveal the species delimitation and species relationship in Lallemantia, and 2- To investigate discriminating power of the start codon targeted and retrotransposon-microsatellite amplified polymorphism markers by Gst and NM analysis. The results obtained revealed that the start codon targeted marker is the best to show the relationships between species while the retrotransposon-microsatellite amplified polymorphism marker is the best for species delimitation. we found the loci with the high value of Gst (1.00) in start codon targeted and retrotransposon-microsatellite amplified polymorphism markers that can be used in barcoding and fingerprinting of L. royleana.

Genetic diversity and inter-relationship of henbane populations of North-West of Iran based on IRAP and REMAP markers | JBES @zenodo

Genetic diversity and inter-relationship of henbane populations of North-West of Iran based on IRAP and REMAP markers | JBES @zenodo

Genetic diversity of Aegilops tauschii accessions and its relationship with tetraploid and hexaploid wheat using retrotransposon-based molecular markers

Aegilops is known as the ancestor species of wheat and has a major role in the evolution of wheat. Considering the importance of this species and the fact that Iran is the center of the distribution, fifteen IRAP and REMAP markers were used to evaluate the genetic diversity of Ae. tauschii accessions from different regions of Iran and its relationship with Triticum durum and Triticum aestivum. A high level of polymorphism (99%) was observed for both retrotransposon markers. Polymorphism information content, the effective number of alleles (Ne), Nei’s genetic diversity (H), and Shannon’s information index (I) for IRAP markers were more than REMAP markers. The most genetic diversity was detected in Ae. tauschii accessions. The cluster analysis separated the accessions into three distinct groups. Ae. tauschii accessions from Golestan province grouped in the same cluster with T. aestivum genotypes, indicating that these accessions are probably more like to the progenitor of the bread wheat D genome. Our results revealed that retrotransposon-based molecular markers could be used as the appropriate and reliable marker system to evaluate genetic diversity and relationship in Triticum and Aegilops accessions.

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.

Development, evaluation and characterization of browning-resistant hybrids of white button mushroom (Agaricus bisporus)

Postharvest browning in white button mushroom is a major limiting factor determining the quality and marketability of mushrooms. In the present study, 361 hybrids were developed using non-fertile isolates from eleven button mushroom strains. A total of forty one browning tolerant hybrids were selected and evaluated for the yield. Five of these were evaluated on large scale in commercial units and two have been finally selected on the basis of higher yield than the strains used by the commercial units. The selected five hybrids showed very low level of enzymes responsible for browning i.e., laccase, polyphenol oxidases and tyrosinase.The hybrids were characterized using SSR, IRAP and ReMAP markers and distinguishing bands for hybrids could be identified. The developed hybrids will address post harvest browning problems of button mushroom industry.

Assessment of genetic diversity and relationships among Triticum urartu and Triticum boeoticum populations from Iran using IRAP and REMAP markers

Einkorn wheat is known as the donor of ‘A’ genome to cultivated wheat and source of many important genes. Therefore, genetic erosion in cultivated wheat provides a good reason to investigate genetic diversity in these species. In the present study, genetic diversity of 14 populations of Triticum urartu and Triticum boeoticum collected from west and north-west of Iran was examined by IRAP and REMAP markers. In total, 26 out of 36 IRAP and 41 out of 88 REMAP combinations amplified polymorphic and scorable banding patterns. IRAP and REMAP combinations produced 6.53 and 5.21 polymorphic bands per assay, respectively. Mean of polymorphism information content for IRAPs and REMAPs were 0.38 and 0.40 and marker index values for them were 2.60 and 2.09, respectively. Analysis of molecular variance based on IRAP and REMAP data revealed significant within and among population variances, although within population variance was higher than that of among population. Primer combinations based on Sukkula and Nikita retrotransposons produced the highest number of markers in the whole population. Cluster and principal coordinate analyses using REMAP data grouped the populations based on the species and geographical origin, but grouping based on IRAP could not separate the two species. However, based on both marker systems considerable diversity was observed among and within the studied populations.

Genetic finger printing of salt- and drought-tolerant cotton cultivars (Gossypium hirsutum) by IRAP-REMAP and SRAP molecular markers

With growth in size of human population, production of salt and drought-tolerant cotton cultivars with good agronomic and yield characteristics is an important task. Inter-specific and intra-specific hybridization is one of the main approaches to produce elite cultivars in cotton. Therefore, to choose proper parental genotypes for hybridization, it is necessary to study the genetic and agronomic variability within the cultivars with high salt and drought-tolerance. Therefore, the present study used IRAP, REMAP and SRAP molecular markers to illustrate genetic variability in cotton genotypes (Gossypium hirsutum) and to group the genotypes based on genetic affinity. The results revealed that some of the genotypes had private bands, which can be correlated with their salt- or drought-tolerant characteristics. Network and STRUCTURE analyses of molecular data grouped the genotypes with genetic affinity, while some genotypes differed from the others. Therefore, we suggest different crossing combinations between these groups based on genetic distance and desirable agronomic characteristics within salt- and drought- tolerant cottons. In general, IRAP, REMAP and SRAP molecular screening of the cotton genotypes seems to be an efficient, low-cost and rapid method for genetic fingerprinting purposes in large germplasm.

Preliminary evidence for associations between molecular markers and quantitative traits in a set of bread wheat (Triticum aestivum L.) cultivars and breeding lines

The identification of polymorphic markers associated with various quantitative traits allows us to test their performance for the exploitation of the extensive quantitative variation maintained in gene banks. In the current study, a set of 97 wheat germplasm accessions including 48 cultivars and 49 breeding lines were evaluated for 18 agronomic traits. The accessions were also genotyped with 23 ISSR, nine IRAP and 20 REMAP markers, generating a total of 658 clear and scorable bands, 86% of which were polymorphic. Both neighbor-joining dendrogram and Bayesian analysis of clustering of individuals revealed that the accessions could be divided into four genetically distinct groups, indicating the presence of a population structure in current wheat germplasm. Associations between molecular markers and 18 agronomic traits were analyzed using the mixed linear model (MLM) approach. A total of 94 loci were found to be significantly associated with agronomic traits (P≤0.01). The highest number of bands significantly associated with the 18 traits varied from 11 for number of spikelets spike−1 (NSS) to two for grain yield in row (GRY). Loci ISSR16-9 and REMAP13-10 were associated with three different traits. The results of the current study provide useful information about the performance of retrotransposon-based and ISSR molecular markers that could be helpful in selecting potentially elite gene bank samples for wheat-breeding programs.

Comparison of ISSR, IRAP and REMAP markers for assessing genetic diversity in different species of Brassica sp.

Molecular markers provide facilities in order to study genetic diversity and relationship among genotypes. In this study, genetic diversity among 35 genotype of Brassica sp. (belonging B. napus, B. juncea, B. rapa, B. nigra) were determined using 13 ISSR, 3 IRAP markers and 18 REMAP (primer combinations of ISSR and retrotransposon primer). The percentage of polymorphism for ISSR, IRAP and REMAP was 96.38, 94 and 96%, respectively. By comparison between markers, ISSRs indicated the highest expected heterozygosity (He) and Shannon’s information index (I) with value of 0.34 and 0.51, respectively, while REMAP marker had by far the highest number of polymorphic bands (340) and marker index (7.1) among all fragments scored over all markers. In pattern of clustering based on Bayesian methods, K = 8 was resulted for combined data clustering that was more organized clustering for genotypes compared to others. This research suggests the combined data of ISSR, IRAP and REMAP markers are most reliable than each solely marker whilst have been clustered genotypes in their taxonomic classification of Brassica without any mixture. Principle coordinate analysis (PCoA) separated 35 genotypes in four groups which all of genotypes were clustered correctly based on their taxonomic classification. The findings of this study provide the valuable insight into the Brassica species relationships in terms of similarity among genotypes which can be helpful in breeding programs, and also demonstrate that retrotransposon markers are legible for genetic diversity and next genetic analysis in Brassica genus.

Assessment of genetic diversity in Nordic timothy (Phleum pratense L.).

BackgroundTimothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers.ResultsUsing four primer combinations, 533 REMAP markers were analyzed, compared with 464 polymorphic alleles in the 13 SSR loci previously. The average marker index, which describes information obtained per experiment (per primer combination or locus) was over six times higher with REMAPs. Most of the variation found was within accessions, with somewhat less, 89 %, for REMAPs, than for SSR, with 93 %.ConclusionsSSRs revealed differences in the level of diversity slightly better than REMAPs but neither marker type could reveal any clear clustering of accessions based on countries, vegetation zones, or different cultivar types. In our study, reliable evaluation of SSR allele dosages was not possible, so each allele had to be handled as a dominant marker. SSR and REMAP, which report from different mechanisms of generating genetic diversity and from different genomic regions, together indicate a lack of population structure. Taken together, this likely reflects the outcrossing and hexaploid nature of timothy rather than failures of either marker system.

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

BackgroundIn Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome.ResultsWe characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values.ConclusionOur strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0550-1) contains supplementary material, which is available to authorized users.

Genetic Variation in Three Closely Related Minuartia (Caryophyllaceae) Species Endemic to Greece: Implications for Conservation Management

The genus Minuartia is highly diverse in the Mediterranean region and includes several endemic and locally restricted species. The genetic variation of three Minuartia species (M. dirphya, M. parnonia, M. wettsteinii) which are endemic to Greece was investigated, aiming to also develop effective conservation plans for their protection. Minuartia dirphya and M. wettsteinii are known to occur only at their type localities, each forming a small population, while M. parnonia is more widespread with seven populations located in the south-east Peloponnese. Genetic diversity was estimated using ten chloroplast microsatellite and five REMAP markers. The chloroplast microsatellite markers exhibited limited polymorphism among species only, while REMAP revealed a significant amount of genetic variation at the population and species level. All the analyses performed (dendrograms, PCoA, STRUCTURE) showed clear differentiation among species, highlighting M. wettsteinii as the most genetically distant. As shown by AMOVA, a degree of differentiation was detected within M. parnonia, where 41 % of the total variation was partitioned among populations and 59 % to the individuals within them. At the species level, the highest genetic diversity (PPB = 75.86 %, Hj = 0.2728, I = 0.3509) was observed in M. parnonia, followed by M. dirphya (PPB = 55.17 %, Hj = 0.2350, I = 0.2767), while the lowest was observed in M. wettsteinii (PPB = 28.74 %, Hj = 0.1449, I = 0.1498). Scarce gene flow (N m = 0.5451) was observed among M. parnonia populations. The current study is important for developing conservation management plans for the three threatened Minuartia species.

INTRAVARIETAL VARIABILITY OF 'CRLJENAK KASTELANSKI' AND ITS RELATIONSHIP WITH 'ZINFANDEL' AND 'PRIMITIVO' SELECTIONS

Six ?Crljenak kastelanski? (CK), two ?Primitivo? and one selection of ?Zinfandel? were evaluated in Split, southern Croatia. Vine yield components and fruit composition were measured over two growing seasons, 2008 and 2009. Significant differences were obtained among nine selections for all viticultural traits, with the exception of the number of clusters per vine and Ravaz index. CK selections seem to be not uniform and perform some unique characters in comparison to ?Zinfandel? and ?Primitivo? selections. The certified selection of ?Zinfandel? (ZIN01) showed better vegetative growth having higher yield, cluster length, width and weight, berries per cluster and berry weight than other selections. The ?Primitivo? and CK selections had similar fruit composition and had advanced fruit maturity compared to ?Zinfandel?. The genetic differences were investigated using SSR, IRAP, REMAP and AFLP markers. SSR, IRAP and REMAP markers were not polymorphic, while the level of AFLP polymorphism was comparable with similar studies, however, not sufficient to discriminate clones according to geographical origin or basic viticultural characters. The obtained results indicate a significant genetic variability between the investigated selections and they justify further efforts in clonal selection for CK.

Analysis of genetic diversity in Japanese apricot (Prunus mume Sieb. et Zucc.) based on REMAP and IRAP molecular markers

Japanese apricot (mei) originated in China, and was divided into two types: fruiting mei and flowering mei, and fruiting mei can be divided by their pericarp into green mei, red mei and white mei. 84 cultivars (43 fruiting mei and 41 flowering mei) were used in this study. To identify their genetic relationships, genetic diversity analysis using REMAP with IRAP techniques was performed. The results showed that the observed number of alleles was 1.9955 in Japanese apricot populations, the effective number of alleles was 1.4887, Nei's gene diversity was 0.2910, and Shannon's information index was 0.4465. Eighty-four Japanese apricot varieties could be divided into 18 groups at the similarity coefficient of 0.743, and 4 groups at the similarity coefficient of 0.705 with the UPGMA cluster method. Fruiting mei and flowering mei clustered into different groups which showed that the complexity of inheritance and the extent of evolution were different. PopGen32 analysis suggested that Japanese fruiting mei would be introduced from Zhejiang province in China and Japanese flowering mei from Jiangsu province in China.

Stability of micropropagated Musa acuminata cv. Grand Naine over clonal generations: A molecular assessment

The present work was undertaken to investigate clonal fidelity of banana ( Musa acuminata cv. Grand Naine) regenerants from six different in vitro subculture generations and in the explant suckers by using ISSR and REMAP molecular markers. Both types of markers revealed high degree of monomorphism. Very low variation was observed up to the eighth subculture generation with polymorphic bands being low in both ISSR (0.96%) and REMAP (0.95%) markers. Epigenetic stability was studied by DNA methylation analysis of the eighth subculture generation samples. Single 570 bp methylation sensitive band was absent in two of the fifteen MspI predigested samples, while it was present in HpaII predigested and undigested samples. The results of the investigation confirmed that the micropropagation of banana up to the eighth subculture generation show low variation.

Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp.

The application and informativeness of RAPD, ISSR, IRAP and REMAP markers to study the genetic diversity and relationship among the Citrus and its relative genotypes were investigated. High levels of polymorphism were observed for all four marker systems. The RAPD technique generated the highest number of polymorphic bands and average number of polymorphic band per assay unit. Average limit of the discriminating power was very close to its actual discriminating power of each marker. The highest and the lowest values of effective number of patterns were obtained from the marker REMAP (5.94) and RAPD (4.48), respectively. Correlation between the genetic similarities matrices were estimated from all four markers using the Mantel matrix correspondence test, and results showed significant correlations among the RAPD, ISSR, IRAP and REMAP similarity matrices. The highest correlations were found comparing RAPD and ISSR markers, whereas RAPD and REMAP ( r = 0.143) markers were poorly correlated. To assess the usefulness of the overall information provided by these marker data for establishing phylogenetic relationships and Citrus germplasm classification, cluster analysis was performed. All four techniques, solely or in combination, discriminated the genotypes very efficiently and generated a high similarity in dendrogram topologies, although some differences were observed. The linkage analysis was conducted based on the segregation of 38 RAPD, 13 ISSR, 19 IRAP and 9 REMAP loci in 96 progeny of an intergeneric cross Citrus sinensis and Poncirus trifoliata. Among the 81 studied loci 65 loci distributed on five linkage groups. Comparing the result obtained with RAPD, ISSR, IRAP and REMAP markers in this study, IRAP and REMAP proved to be as a reliable molecular marker for fingerprinting, mapping and diversity study of Citrus and its relatives.