Transferability Of SSR Markers Research Articles

Transferability of SSR markers from Eugenia uniflora L. to Myrtaceae species of the Atlantic Forest

Transferability of SSR markers from Eugenia uniflora L. to Myrtaceae species of the Atlantic Forest

An assessment on intraspecific transferability of SSR markers on fennel (Foeniculum vulgare Mill.) varieties.

The amplification potential of 27 SSR primer pairs originally reported on exotic fennel (Foeniculum vulgare Mill.) was studied on Indian fennel. Only 13 primer pairs developed amplicons (only one amplicon per primer pair) of sizes ranging from 100 to 450 bp. To determine their polymorphic potential, a set of 20 diverse fennel germplasm lines was used. Four primers exhibiting polymorphism, did segregate the 20 diverse lines in 9 clusters. However, these primer pairs did not differentiate between 17 improved varieties of fennel.

Short Communication: Cross-species amplification of microsatellite markers developed for Jatropha curcas within five species of Jatropha

Abstract. Saptadi D, Heliyanto B, Sudarsono. 2020. Short Communication: Cross-species amplification of microsatellite markers developed for Jatropha curcas within five species of Jatropha. Biodiversitas 21: 5072-5076. The transferability of SSR markers can be used to access the genetic diversity of related species. There are four close relatives of Jatropha curcas L in Indonesia, which can be utilized as a new diversity source through the interspecific crossing. This research was conducted to determine the ability of cross-species amplification of SSR markers developed from J. curcas to other Jatropha species (J. integerrima, J. multifida, J. gossypifolia, J. podagrica). It also investigated the relationship between these species. Out of 28 primers checked,11 primers showed cross-species amplification in all the species tested. Primer pairs EU099519, EU099528, and EU099525 have no transferability to other species. The overall percentage of polymorphism (PP) among all species tested was 95%, with the mean genetic similarity (GS) was 0.34. Least PP (17.35%) and highest GS (0.60) was found between pairs of J. podagrica and J. multifida. The correlation between the PP with GS was relatively high (0.75). The farthest and closest genetic distance was found between J. curcas/J. gossypifolia and J. podagrica/J. multifida, respectively. Further, selected primers from this study can be utilized in species differentiation, molecular identification of interspecific hybrids, and exploiting the genetic resource.

Cross genera transferability of microsatellite markers from other members of family Bignoniaceae to Tecomella undulata (Sm.) Seem

Transferability of SSR markers from related species/genera is a rapid and cost-effective method to enhance genomic database of genetically neglected crops. Monotypic genus Tecomella undulata, a pharmacologically important endangered timber tree, found in hyper arid regions is one such genetic resource limited species, wherein neither SSR identification nor cross transferability studies have been initiated. Transferability of 69 cross-genera SSR primers selected from other members of family bignoniaceae (Incarvillea sinensis, I. mairei, Jacaranda copaia, Tabebuia aurea and Arrabidaea chica) showed 40.58% (28 primers) transferability amplifying 1–10 amplicons ranging in the size from 80to 600 bp in 24 accessions of T. undulata. Per cent marker transferability varied from 66.67% (A. chica) to 38.89% (J. copaia) among the genera tested while no transferable markers could be identified from I. sinensis. Transferability of simple di-/tri-nucleotide repeat (34.2–37.5%) and complex nucleotide sequence (60.0%) based SSR motifs were higher as compared to penta-/hexa-nucleotide based repeat motifs. Within the 28 transferable markers, 26 (92.86%) were polymorphic while 2 (7.14%) were monomorphic. Average number of alleles per primer was 5.39 while average polymorphic alleles per locus were 5.11. The PIC values of SSR markers ranged from 0.23 to 0.85 with an average of 0.59. Efficiency of the identified cross species SSR markers was tested for diversity analysis using a set of 24 trees (8 each of yellow, orange and red flower colour morphotypes). The 24 samples clustered into six groups with similarity coefficient ranging from 0.29 to 0.67, while six accessions formed distinct out groups. Distribution of accessions in the SSR dendrogram showed no correlation with flower colour. More diversity (99%) was observed within populations compared to that existing between populations (1%). The present study can enrich the genomic background of T. undulata by identifying suitable polymorphic markers from confamiliar species that can be applied for genetic diversity studies, mapping of QTLs and cultivar identification as well.

Transferability of SSR Markers used for Genetic Relationship to Five Species/Genera in Cucurbitaceae

THIS STUDY assessed the genetic diversity and relationships among 24 local accessions across five genera of the Cucurbitaceae family including Lagenaria siceraria (gourd), Citrullus lanatus (‘’Egusi’’melon), Cucurbita pepo (pumpkin), Telfairia occidentalis (fluted pumpkin) and Trichosanthes cucumerina (snake tomato) based on the transferability of six L. siceraria (bottle gourd) and six C. pepo (pumpkin) derived SSR markers. The study revealed a high level of transferability of C. pepo markers, ranged from 83-100% across the genera/species. The transferability rate of the L. siceraria SSR markers was 66% within T. occidentalis and 83% in T. cucumerina. An average of 33% transferability of L. siceraria SSR markers amplified in C. pepo. The 12 SSR markers were polymorphic and a total of 109 alleles were obtained, ranging from 3 to 19 with an average of 9.08 per marker. The polymorphism information content (PIC) values ranged from 0.45 to 0.89 with an average of 0.79, indicating a high level of informativeness. Using un-weighted pair group method with arithmetic average cluster analysis (UPGMA), two groups of 15 and 9 accessions were identified, which comprised C. lanatus, Lagenaria siceraria and C. pepo, T. occidentalis and T. cucumerina accessions, respectively. The present study has shown the transferability of L. siceraria and C. pepo SSR markers across other genera in the Cucurbitaceae. The results also indicated the existence of a considerable level of inter/intraspecific genetic diversity and relationship among cucurbit species of the five genera under study.

Genetic diversity of Aegilops L. species from Azerbaijan and Georgia using SSR markers

Five microsatellite (SSR) markers were used to evaluate the genetic diversity of six Aegilops species from Azerbaijan and Georgia. A total of 39 alleles were generated with an average of 7.8 alleles per primer. Twenty markers were species-specific and 6 were accession-specific. The transferability of SSR markers across six species was 100%, with exception of gwm210. The mean polymorphism information content (PIC) and expected heterozygosity (He) values for the entire collection were 0.688 and 0.725, respectively. The average PIC value was the highest in Ae. biuncialis accessions (0.55). The genetic distance (GD) indices, based on five SSR markers, ranged from 0 to 0.83, with a mean value of 0.47. The highest genetic similarity was noted between Ae. neglecta and Ae. triuncialis (GD = 0.26), and the lowest between Ae. neglecta and Ae. tauschii (GD = 0.66). The dendrogram created based on SSR data grouped 72 Aegilops accessions into six clusters according to their taxonomic classification. The accessions from the same province were often placed in the same subclusters, indicating that grouping based on genetic parameters was closely related to the geographic region within countries. The PCoA analysis could differentiate Aegilops accessions according to their species and confirmed subgrouping obtained by cluster analysis.

Potential use of SSR and ISSR markers in estimation of DNA polymorphism within genus Vicia

The development of novel markers usually requires high costs and is time consuming. Instead of developing new markers, their transfer within a genus is an alternative particularly suitable in less studied species. Hence the goal of this study was to evaluate the ability of SSR markers, previously developed from Vicia faba, and ISSR markers to estimate DNA polymorphism within the genus Vicia. Eight Vicia species were used for cross-species amplification. Transferability of SSR markers in the studied species ranged from 25% to 100%, with an average of 56.25%. Although three SSR primers were polymorphic, the nature of the amplification products indicated that their further usefulness is questionable. ISSR primers generated polymorphic products of amplification in all tested Vicia species. The average polymorphism of ISSR primers was 93.75%, which implies that these primers can be used within the genus Vicia.

Cross transferability of SSR markers to endangered Cedrela species that grow in Argentinean subtropical forests, as a valuable tool for population genetic studies

Species of Cedrela with a high economic value from Northwest and Northeastern Argentina are severely exploited. This work evaluates whether 51 nuclear SSRs, developed to study phylogenetically close species in the Meliaceae family (Cedrela odorata, Cedrela fissilis, Swietenia humilis and Swietenia macrophylla), can be used to study C. fissilis, Cedrela balansae, Cedrela saltensis and Cedrela angustifolia. A 62.8% of the total of 194 SSRs/species combinations showed a successful, homologous and cross-species amplification. As expected, a great success in SSRs transferability among Cedrela species was observed. Twenty-one screened SSRs showed a successful amplification pattern in all target species and many of them were polymorphic (9, 13, 13 and 7 SSRs for C. fissilis, C. balansae, C. saltensis and C. angustifolia, respectively). The high number of evaluated SSRs from the Cedrela genus and Meliaceae family, allowed us to obtain a suitable set of validated markers that are highly variable and easily scored, and also identify those which were less sturdy. We were able to retain a useful set of markers for three of the target species, but not for C. angustifolia. This could be due to its greater phylogenetic and morphological distances to the other three species. The lack of SSRs developed for our target species, transforms the transferred SSRs reported here in a valuable tool to monitor the genetic consequences of forest overexploitation on Cedrela species.

Development of genomic simple sequence repeat markers from an enriched genomic library of grass pea (Lathyrus sativus L.)

AbstractSimple sequence repeat (SSR) or microsatellite markers are a valuable tool for several purposes such as evaluation of genetic diversity, fingerprinting, marker‐assisted selection and breeding. In this study, a SSR genomic enriched library was developed in Lathyrus sativus (grass pea) by affinity capture of restriction fragments to biotinylated microsatellite oligonucleotides. About 400 randomly selected clones were sequenced, and SSRs were present in approximately 30% of them. Clones contained 75%, 9% and 16% of simple, interrupted and compound SSRs, respectively. Of the 10 SSRs tested, 7 primer pairs produced clearly distinguishable DNA banding patterns. Successively, SSR primer pairs were successfully tested to reveal polymorphism in a set of four different grass pea germplasm accessions. The transferability of SSR markers was high among three related species of Lathyrus, namely Lathyrus cicera, Lathyrus ochrus and Lathyrus tingitanus, and the legume crop, Pisum sativum. These results indicate that the novel SSR markers are informative and will be useful and convenient for genetic analysis in grass pea and related species.

Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis inJatropha curcas

Castor bean and Jatropha contain seed oil of industrial importance, share taxonomical and biochemical similarities, which can be explored for identifying SSRs in the whole genome sequence of castor bean and utilized in Jatropha curcas. Whole genome analysis of castor bean identified 5,80,986 SSRs with a frequency of 1 per 680 bp. Genomic distribution of SSRs revealed that 27% were present in the non-genic region whereas 73% were also present in the putative genic regions with 26% in 5′UTRs, 25% in introns, 16% in 3′UTRs and 6% in the exons. Dinucleotide repeats were more frequent in introns, 5′UTRs and 3′UTRs whereas trinucleotide repeats were predominant in the exons. The transferability of randomly selected 302 SSRs, from castor bean to 49 J. curcas genotypes and 8 Jatropha species other than J. curcas, showed that 211 (∼70%) amplified on Jatropha out of which 7.58% showed polymorphisms in J. curcas genotypes and 12.32% in Jatropha species. The higher rate of transferability of SSR markers from castor bean to Jatropha coupled with a good level of PIC (polymorphic information content) value (0.2 in J. curcas genotypes and 0.6 in Jatropha species) suggested that SSRs would be useful in germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships, and so forth, in J. curcas as well as other Jatropha species.

Transferability of SSR markers derived from cowpea (Vigna unguiculata L. Walp.) in variety identification

Transferability of SSR markers derived from cowpea (Vigna unguiculata L. Walp.) in variety identification

Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat

The growing availability of EST sequences from a range of crop plantsprovides a potentially valuable source of new DNA markers. We have examined theInternational Triticeae EST Cooperative database for the presence ofdinucleotide and trinucleotide simple sequence repeats. Analysis of 24,344 ESTsidentified 388 dinucleotide repeats and 978 trinucleotide repeats in ESTs,representing 1.6% and 4.0% of the total number of ESTs, respectively. To testthe utility and cross-species transferability of EST-derived SSR markers,primers were designed to the flanking regions of 41 barley SSRs and used toscreen 11 barley and 15 wheat varieties. Sixteen of the barley SSR markers werepolymorphic in barley and five were polymorphic in wheat. This represents arelatively high level of transferability of SSR markers between barley andwheat, which has important implications for the development of new markers andcomparative mapping of barley, wheat and other cereals. An additional 56 SSRsfrom wheat ESTs were tested in the same barley and wheat varieties. Four wheatEST SSR markers were polymorphic in wheat and one in barley. Chromosomallocations in barley and wheat were determined for the majority of polymorphicmarkers.