Genomic Simple Sequence Repeat Research Articles

Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea

Exploitation of genetic diversity is essential for sustainable crop production. Molecular markers have potential to reach these goals in more rapid and efficient manner. Simple sequence repeats (SSRs) are one of the most popular molecular markers in breeding studies due to their co-dominant inheritance, abundance in the genome, multi-allelic and reproducible nature. Here, we developed genomic SSR markers from chickpea with the use of ddRADSeq data. 1,396 SSR regions with an average of 530 SSR/Mb in the whole genome were successfully identified. Considering different types of repeats, dinucleotides were the most frequent type accounting for 62.03% of the total SSR regions identified, followed by trinucleotides (25.50%) and tetranucleotides (4.58%). The AT/TA motif was greatly characterized among dinucleotide repeats, and it was also the most common type in the chickpea genome accounting for 36.5% of the total SSR regions identified, followed by AG/GA (139) and TC/CT (135) among dinucleotide motifs. Considering their genomic distribution and simple visualization on agarose gels, we examined SSR regions of 10 bp and longer for identification of SSR markers. A total of 10 SSR markers were successfully designed and resulted in successful polymorphic bands among chickpea genotypes. Consequently, the results show that ddRADSeq is effective for marker development and these markers might be valuable for biodiversity studies, marker-assisted selection (MAS) and linkage map construction in chickpea.

Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper

AbstractThe Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution.

Cross species transferability of G-SSR and EST-SSR markers to Neltuma affinis Spreng.

Aim of study: To examine the transferability of G-SSR (genomic simple sequence repeats) and EST-SSR (expressed sequence tag simple sequence repeats) markers developed for several Neltuma species to N. affinis, a species with no genomic data. Area of study: West-Center of Entre Ríos province, Argentina. The set of molecular markers here proposed can be used to analyze samples from the entire species’ distribution range. Material and methods: Twenty-five genomic G-SSRs and eleven EST-SSRs from multiple species were amplified in thirty N. affinis genotypes. Polymorphism, discrimination power and possible deviations from Hardy-Weinberg equilibrium were assessed. Main results: Seventeen highly polymorphic G-SSRs were successfully transferred to N. affinis, with a PIC (polymorphic information content) average value of 0.811 and a He (expected heterozygosity) average value of 0.694; thirteen were validated, showing very low frequencies of null alleles and no linkage disequilibrium. Additionally, seven polymorphic EST-SSRs were transferred. As expected, PIC and He average values were low. Six out of seven markers were validated, and very low frequencies of null alleles and no linkage disequilibrium were observed. Research highlights: This work provides information on the levels of microsatellites’ cross transferability to N. affinis, and its polymorphism degree. Two sets of polymorphic SSRs (genomic and expressed) to study the genetic status of the species are proposed.

Tolerance evaluation and genetic relationship analysis among some economically important chestnut cultivars in Türkiye using drought-associated SSR and EST-SSR markers.

The aim of this study was to evaluate drought tolerance and genetic relationships among some important chestnut cultivars for Türkiye by using drought-related genomic simple sequence repeat (SSR) markers and genic expressed sequence tag-simple sequence repeat (EST-SSR) markers. Using five SSR markers, the average number of alleles (avNa), mean heterozygosity (Havp) and polymorphism information content (PIC) were determined to be 9.22, 0.395 and 0.375, respectively. In addition, using eight EST-SSR markers, the values of avNa, Havp and PIC were determined to be 7.75, 0.309 and 0.262, respectively. All microsatellite markers used in this study showed 100% polymorphism among chestnut cultivars. In UPGMA dendrograms obtained with both SSR and EST-SSR markers, the Erfelek and Hacıömer chestnut cultivars were determined to be the most similar cultivars. Some assessments are discussed regarding drought tolerance for specific alleles obtained from the EST-SSR markers GOT045, GOT021, GOT004, FIR094 and VIT033 in chestnut cultivars. Some preliminary results regarding drought tolerance in chestnut cultivars were obtained in our study with the help of these markers. Our study also characterized the genetic relationships among chestnut cultivars of great importance using drought-related character-specific markers.

Genome-wide identification and characterization of microsatellite markers in Bactrian Camel

Simple sequence repeats (SSRs) have been widely used for parentage testing, marker-assisted selection, and evolutionary studies. The insufficient availability of SSR markers in Bactrian camels partially accounts for the lack of systematic breeding. Therefore, we aimed to establish a comprehensive SSR dataset for the Bactrian camel. Our approach involved genome searching to locate every SSR in the genome, SSR-enriched sequencing to acquire polymorphism information, and literature research to collect published data. The resulting dataset contains 213,711 SSRs and details their characteristics, including genome coordinates, motifs, lengths, annotations, PCR primers, and polymorphism information. The dataset reveals a biased distribution of SSRs in the Bactrian camel genome, reflecting the mutation mechanism and complex evolution of SSRs. In practice, we successfully demonstrated the utility of the dataset through parentage testing using 15 randomly selected SSRs. This comprehensive dataset can facilitate systematic breeding and enable QTL mapping and GWAS of the Bactrian camel.

Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes.

Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens-Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA. SSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing.

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB.

The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.

Parental Polymorphism Survey for Identifying Genes/QTLs for BPH Resistance in Assam Land Race 10-3

The current research was taken up at Institute of Biotechnology (IBT), PJTSAU, Hyderabad Telangana, India in kharif from August to November, 2021 to access the parental polymorphism between 10-3 and Telangana Sona. 10-3, an Assam landrace, is a bold grain rice variety with high BPH resistance to biotype-4. Whereas, Telangana Sona (RNR 15048) is a short and slender grain variety of rice that is popular among farmers and consumers across Telangana and other Indian states due to its high yield and low glycemic index. Despite being blast resistant, Telangana Sona is susceptible to the insect pest Brown Plant hopper (BPH) Nilaparvata lugens (Stål). The present study aimed to characterize the parental polymorphism between 10–3 and Telangana sona to facilitate mapping of genetic loci linked with BPH resistance in the 10–3 and to optimize the retention of favourable alleles from Telangana sona during marker assisted backcross breeding. Eight hundred and sixteen highly variable Simple Sequence Repeats (SSRs) including thirty-five BPH linked markers covering 12 chromosomes were used to assess DNA polymorphism between 10-3 and Telangana Sona. Out of 816 markers screened, 97 (11.89%) were found to be polymorphic between 10–3 and Telangana Sona of which, 82 were genomic SSRs and 15 were BPH linked markers. Chromosome 6 exhibited highest polymorphism percentage with a value of 30%, indicating that this chromosome is useful in studying parental variation and lowest polymorphism percentage found on chromosome 5 (3.49%). These 97 polymorphic markers will help in construction of linkage map for identifying QTLs linked with BPH resistance and for marker assisted backcrossing breeding in Telangana Sona.

Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2-4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2-4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

GenoSSRFinder: a tool for rapid, precise, and targeted simple sequence repeat detection in genomic studies.

The GenoSSRFinder is a new tool enables the research of Simple Sequence Repeats (SSRs) in DNA sequences and genomes much simpler and more precise in short time. The analysis is carried out by targeting a certain SSR in genome and gene sequences. This utility is quick, accurate, and does its function quite well. It quickly goes across the sequence, revealing all of the locations at which the selected SSR may be found. This tool will tell researchers where selected SSR begins and where it stops, how long it is, how often it repeats, and how long each repetition is. GenoSSRFinder gets the findings quickly, and they will be simple to comprehend. Therefore, when studying SSRs, researchers will have more time to use to thorough work as a result of this time savings. In addition, it provides a valuable information since it is highly precise. GenoSSRFinder is simple to use and produces high-quality findings. It is also accelerating SSRs gene research, which is a direct result of the new approach we use to analyse SSRs. Three case studies in this study demonstrated the usefulness of this program by immediately studying a particular SSR that was associated with genetic illness, biodiversity and criminal science in living organisms. This demonstration explains that GenoSSRFinder might be utilized in a wide variety of fields, such as the research of genetic illnesses, the biodiversity and genetic studies, or even in criminal investigations.

A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

Abstract The alvinocaridid shrimp Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, is an evolutionarily important deep-sea species in hydrothermal vents of north-western Pacific. A genome survey of S. leurokolos was carried out in order to provide a foundation for its whole-genome sequencing. A total of 599 Gb high-quality sequence data were obtained in the study, representing approximately 118× coverage of the S. leurokolos genome. According to the 17-mer distribution frequency, the estimated genome size was 5.08 Gb, and its heterozygosity ratio and percentage of repeated sequences were 2.85 and 87.03%, respectively, showing a complex genome. The final scaffold assembly accounted for a total size of 9.53 Gb (32,796,062 scaffolds, N50 = 597 bp). Repetitive elements nearly constituted 45% of the nuclear genome, among which the most ubiquitous were long interspersed nuclear elements, DNA transposons and long-terminal repeat elements. A total of 12,121,553 genomic simple sequence repeats were identified, with the most frequent repeat motif being di-nucleotide (70.27%), followed by tri-nucleotide and tetra-nucleotide. From the genome survey sequences, the mitochondrial genome of S. leurokolos was also constructed and 71 single nucleotide polymorphisms were identified by comparison with previous published reference. This is the first report of de novo whole-genome sequencing and assembly of S. leurokolos. These newly developed genomic data contribute to a better understanding of genomic characteristics of shrimps from deep-sea chemosynthetic ecosystems, and provides valuable resources for further molecular marker development.

Polymorphisms in the hypervariable control region of the mitochondrial DNA differentiate BPH populations.

The brown planthopper (BPH; Nilaparvata lugens) is one of India's most destructive pests of rice. BPH, a monophagous migratory insect, reported from all major rice-growing ecosystems of the country, is capable of traversing large distances and causing massive crop loss. A crucial step for developing viable management strategies is understanding its population dynamics. Very few reliable markers are currently available to screen BPH populations for their diversity. In the current investigation, we developed a combinatorial approach using the polymorphism present within the mitochondrial Control Region of BPH and in the nuclear genome (genomic simple sequence repeats; gSSRs) to unravel the diversity present in BPH populations collected from various rice-growing regions of India. Using two specific primer pairs, the complete Control Region (1112 to 2612 bp) was PCR amplified as two overlapping fragments, cloned and sequenced from BPH individuals representing nine different populations. Results revealed extensive polymorphism within this region due to a variable number of tandem repeats. The three selected gSSR markers also exhibited population-specific amplification patterns. Overall genetic diversity between the nine populations was high (>5%). Further, in silico double-digestion of the consensus sequences of the Control Region, with HpyCH4IV and Tsp45I restriction enzymes, revealed unique restriction fragment length polymorphisms (digital-RFLPs; dRFLPs) that differentiated all the nine BPH populations. To the best of our knowledge, this is the first report of markers developed from the Control Region of the BPH mitogenome that can differentiate populations. Eventually, such reliable and rapid marker-based identification of BPH populations will pave the way for an efficient pest management strategy.

Evaluation of Perfect Microsatellites in Nile Tilapia (Oreochromis niloticus) Genome

Microsatellites or simple sequence repeats (SSRs) consist of a sizable part of genomes and play a crucial role in the function of genes and the organization of the genome. The complete availability of a genome sequence for Nile tilapia (Oreochromis niloticus) provides the possibility of accomplishing a genome-wide analysis of SSRs in this species. I analyzed the abundance and density of perfect SSRs in the Nile tilapia genome and observed a sum of 252,047 microsatellites with 1–6 bp nucleotide motifs. This indicates that about 2.7 % of the Nile tilapia whole genome sequence (927.77Mb) is made up of perfect SSRs, with an average length of 135.68bp/Mb. The average density and frequency of perfect SSRs were 271.69 loci/Mb and 5834.46 bp/Mb, respectively. The six classes of perfect SSRs proportional distribution within the Nile tilapia genome were not even. Dinucleotide repeats (40.13 %) with a total count of 101145 of an average length of 26.11 bp happen to be the most abundant class of SSRs, while the percentages of mononucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats was 31.88 %, 11.98 %, 11.52 %, 4.22 %, and 0.26 %, accordingly. The various classes of SSRs repeat differ in their number of repeats with the highest being 95. My results indicate that 21 motifs contain the prevalent categories with a frequency above 1 locus/Mb: A, AAC, AAG, AATAG, AATTC, AC, AG, AGAT, AT, ATCT, ATG, ATGG, ATT, ATTT, C, CCT, CTG, CTTT, GT, GTTT.

Genome-Wide Analysis and Polymorphism Evaluation of Microsatellites Involved in Photoperiodic Flowering-time Genes in Kenaf (Hibiscus Cannabinus L.)

ABSTRACT Kenaf (Hibiscus cannabinus L.) is one of the most important crops, which is grown for natural fiber production. However, the deficiency of SSR markers limits the genetic improvement of kenaf. In this study, SSRs (simple sequence repeats) were identified from the reference genome and coding sequence (CDS) of Fuhong952, a sequenced variety of kenaf. SSR loci were mined using the Seiners 2.0 software and the characteristics of SSR loci were analyzed. A total of 301, 505 and 14, 269 SSRs with an overall density of 279.70 SSRs/Mb and 182.70 SSRs/Mb were identified from whole-genome and CDS, respectively. 12bp was the predominant repeat in the entire genome and CDS, trinucleotide repeats were the most abundant among both types of sequences. For different SSR repeat types, the SSR frequency decreased dramatically as repeat times increased. AT was the most frequent single motif across the entire genome, while AG was the most abundant motif in CDS. The homologous genes in kenaf were obtained from the 71 genes associated with photoperiodic flowering-time. As such, 115 primer pairs were designed and synthesized using these homologous genes in kenaf. The amplification of 108 pairs revealed stable and clear bands, and two pair of primers located in HcFCA and HcVIN3 were significantly associated with photoperiodic flowering-time using one-way ANOVA and regression analysis. The detailed results of the SSR markers in this study provides valuable information about the frequency distribution of SSRs in the whole genome and will expedite genomic research for improvement in kenaf.

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

Gene flow between cultivated and wild gene pools is common in the contact zone between agricultural lands and natural habitats and can be used to study the development of adaptations and selection of novel varieties. This is likely the case in the northern Adriatic region, where centuries-old cultivated orchards of sweet chestnut (Castanea sativa Mill.) are planted within the natural distribution area of the species. Thus, we investigated the population structure of several orchards of sweet chestnuts. Furthermore, the genetic background of three toponymous clonal varieties was explored. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this research, and both grafted and non-grafted individuals were included in this study. Five closely related clones were identified, which represent a singular, polyclonal marron variety, found in all three cultivation areas. Furthermore, many hybrids, a result of breeding between cultivated and wild chestnuts, have been found. Analyzed semi-wild orchards defined by a diverse genetic structure, represent a hotspot for further selection and could result in creation of locally adapted, high-yielding varieties.

Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops.

Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.

Genetic diversity and structure of a core collection of Huangqi (Astragalus ssp.) developed using genomic simple sequence repeat markers

Genetic diversity and structure of a core collection of Huangqi (Astragalus ssp.) developed using genomic simple sequence repeat markers

Development and characterisation of SSR markers in the potato rot nematode Ditylenchus destructor

Summary The potato rot nematode, Ditylenchus destructor, causes serious disease limiting the production of many crops. This disease usually decreases sweet potato yield by 20-50%, and in heavily infested fields the crop may be completely lost. Although the nematode has economic importance in China, its transmission route and genetic diversity are unknown. In this study, a collection of 1761 contigs of the D. destructor genome was mined for simple sequence repeat (SSR) markers, which resulted in the identification of 9745 SSRs. A total of 150 pairs of SSR primers were further developed and used for validation of the amplification rate and assessment of the polymorphism. Nine SSR markers were finally identified and analysed using 96 individual specimens of D. destructor sampled from four provinces in China. These loci were found to be moderately polymorphic with 2-8 alleles per locus. The observed and expected heterozygosity across the four populations ranged from 0.000 to 0.833 and from 0.000 to 0.666, respectively. This is the first report of the development and characterisation of genomic SSR markers in D. destructor. Our study demonstrated the obvious gene differentiation among different populations of D. destructor in China. This suggests that D. destructor in China may have been introduced from multiple origins. Much more work is needed on this species to identify patterns of spread, and the microsatellite loci we develop here should be useful in many regions for modelling range expansion, studying the evolution of resistance, and increasing the effectiveness of pest management strategies.

Development and Characterization of 20 Genomic SSR Markers for Ornamental Cultivars of Weigela.

Weigela (Caprifoliaceae) is a genus of ornamental plants popular for its phenotypic variation and hardiness, that includes species hybridized to produce the commercially available cultivars. Despite its popularity, limited genetic resources exist for the genus. Twenty genomic simple sequence repeat (gSSR) markers distributed across the genome were developed using low coverage whole-genome sequencing data of Weigela Spilled Wine®. A cross-amplification evaluation with these 20 gSSR markers on a collection of 18 Weigela cultivars revealed a total of 111 unique alleles, including 36 private alleles. A diagrammatic key was constructed to identify cultivars using only six of the gSSR markers, demonstrating the newly developed gSSR markers are immediately useful for cultivar identification. Future uses could include breeding with marker-assisted selection, determining the history of hybridization of the current cultivated lines, aiding in the construction of genetic maps, and assessing the patterns of population genetic structure of Weigela spp.

Cross-species transferability of genomic SSR markers and genetic diversity among Asparagus racemosus Willd. Accessions

Asparagus racemosus Willd. is an important multipurpose plant, recognized as queen of herbs due to its important medicinal properties. The objective of this study was to contribute to the understanding of A. racemosus genetic diversity by genotyping 20 accessions from ten different agro-ecological zones of Kerala state, India using simple sequence repeat (SSR) markers. A set of 22 SSR markers previously developed for A. officinalis were evaluated for polymorphism in A. racemosus accessions and 18 primer pairs were useful and revealed 46 alleles. Transferability from A. officinalis to A. racemosus varied from 60 to 100% and 15 primers were successfully amplified in all the accessions. Thus, the transferability of SSR primers across the species increased the value of such markers as information about Expressed Sequence Tag (EST) derived markers as well as genomic SSR markers for A. racemosus are not currently available. Comprehensive and systematic surveys on A. racemosus diversity revealed 82.81% polymorphism among accessions. The polymorphic information content values of the transferred SSR markers were between 0.05 and 0.48. A set of six unique alleles detected in five accessions may be useful in genotype identification procedures. Cluster analysis placed the accessions into three main clusters. SSRs derived from garden asparagus were a good resource for genetic studies in A. racemosus.