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We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an...
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... comparison purposes, the draft genome sequence of the Asian eggplant cultivars 'Nakate-Shinkuro' (Hirakawa et al., 2014), together with the full genome sequences of 12 other plant species from the Solanaceae family (Solanum lycopersicum, S. pimpinellifolium, S. pennellii, S. tuberosum, Capsicum annuum, C. chinense, C. baccatum, Nicotiana tabacum, N. attenuata, N. benthamiana, Petunia axillaris, P. inflata) and their closely related species Coffea canephora, were collected from the related public database and scanned for the presence of perfect SSRs, using the same procedures described above. The source of each of the above full genome sequences is given in Supplementary Table S1. ...
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... the ∼1.06 Gb of the gap-free eggplant genomic sequence, we identified 132,831 perfect SSR motifs (125.5 SSR/Mb), which included 20,670 compound SSRs ( Table 1). The number of imperfect SSR motifs was 178,407 ( Table 2). ...
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... number of imperfect SSR motifs was 178,407 ( Table 2). The content and distribution of SSRs in the genome sequence of the eggplant 8 https://sourceforge.net/projects/primer3 breeding line "67/3" were compared with those of 14 other plant genomes, related to different degrees (25.3 Gb of sequence in total, about 2.2 million SSRs) and retrieved from databases (Supplementary Table S1). The number of perfect SSRs found in the "67/3" genome was more than one-third higher than the number detectable in another eggplant cultivar, "Nakate- Shinkuro" ( Table 1). ...
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... content and distribution of SSRs in the genome sequence of the eggplant 8 https://sourceforge.net/projects/primer3 breeding line "67/3" were compared with those of 14 other plant genomes, related to different degrees (25.3 Gb of sequence in total, about 2.2 million SSRs) and retrieved from databases (Supplementary Table S1). The number of perfect SSRs found in the "67/3" genome was more than one-third higher than the number detectable in another eggplant cultivar, "Nakate- Shinkuro" ( Table 1). This indicates that the high quality of the recently released eggplant genome sequence markedly influenced the number of detectable microsatellites. ...
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... cumulative length of the full collection of eggplant SSRs was 3.4 Mbp, which is 0.32% of the assembled genome, a percentage analogous to those of tomato (0.31%) and potato (0.28%), but considerably higher than found in C. chinense and C. annuum (0.15 and 0.12%, respectively). Compound SSRs represented 15.6% of the eggplant perfect SSRs, a proportion exceeded only in S. lycopersicum (27.7%) and S. pennellii (37.6%) ( Table 1). ...
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... although differences in genome size may contribute to the level of repetition of microsatellites, density of SSRs has been found not to be related to genome size ( Zhao et al., 2012;Behura and Severson, 2014;Portis et al., 2016). The density of perfect microsatellites in the genome of the eggplant breeding line "67/3" is the highest observed within the Solanaceae family, although similar to those detected in S. pennellii and P. axillaris, and, in the context of this study, inferior only to that found in Coffea canephora (139.1 SSRs/Mb) ( Table 1). ...
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Citations
... This is consistent with prior findings that there is no link between SSR density and genome size, and that changes in genome size may have an influence on the number of microsatellite repeats in the genome [14,20,21]. Because of their genetic codominance, abundance, hypervariability, genome dispersion, multiallelic variation, high repeatability, mendelian inheritance, and high degree of polymorphism, SSRs are employed for numerous applications in many animal species, e.g., cattle, pigs, sheep, dogs, and horses [12,15,[22][23][24][25][26][27][28]. ...
... Almost all genomes have a significant abundance of monomeric repeats, which may be related to the inherent limits of next-generation sequencing (NGS) technologies used for data creation [29]. Similarly, dimeric repeats also recorded a higher abundance in animal genomes [27,[30][31][32]. For trimeric repeat, B. taurus had the highest percentage and F. catus had the lowest percentage. ...
Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website's database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/.
... Applicability of these markers and their efficiency for genetic mapping, genetic diversity, and population structure were investigated in additional citrus species. Additionally, Biswas et al. 24 reported a success rate of 56.21%, Biswas et al. 9 65.0%, and Barkley et al. 37 26 . Regarding to intra-chromosomal distribution of SSR motifs in C. sinensis and C. maxima mononucleotide was found to be abundant SSR type thereafter dinucleotides, which is the best conformation with the prior findings 24 . ...
... Class III SSRs were found to be the most prevalent, thereafter class II and I, when the distribution of SSR types across chromosomes were examined. The frequency of SSRs and the number of repeats on each chromosome were correlated, and these results were consistent with observations from other plant species, i.e., pepper 59 , globe artichoke 55 , eggplant 26 and pomegranate 17 . Additionally, class I SSRs in each chromosome in both citrus species had mononucleotide dominance followed by dinucleotide repetitions. ...
... were used to generate primers in C. sinensis and C. maxima, 2004 and 3492 primers were specific to Chr-5 (257) and Chr-5 (558), while Chr-6 (113) add Chr-8 (217) had lower number of primers, respectively. The number of SSRs and chromosomal length in eggplant and pomegranate, respectively, were shown to be correlated, according to Portis et al. 26 and Patil et al. 17 . In our study same results were observed in C. sinensis and contrast results in C. maxima were observed, there is no correlation in C. maxima between chromosome length and number of SSR markers. ...
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
... After performing the analysis, we discovered that the frequency of SSRs in S. aralocaspica's entire genome was 393.37 SSRs/Mb. This amount was significantly higher when compared to Anemone coronaria (65.52 SSRs/Mb), Solanum melongena (120 SSRs/Mb), and Triticum aestivum (36.68 SSRs/Mb) [27][28][29]. Therefore, it can be inferred that SSRs were abundant in the whole genome of S. aralocaspica. ...
Suaeda aralocaspica, which is an annual halophyte, grows in saline deserts in Central Asia with potential use in saline soil reclamation and salt tolerance breeding. Studying its genetic diversity is critical for effective conservation and breeding programs. In this study, we aimed to develop a set of polymorphic microsatellite markers to analyze the genetic diversity of S. aralocaspica. We identified 177,805 SSRs from the S. aralocaspica genome, with an average length of 19.49 bp, which were present at a density of 393.37 SSR/Mb. Trinucleotide repeats dominated (75.74%) different types of motifs, and the main motif was CAA/TTG (44.25%). We successfully developed 38 SSR markers that exhibited substantial polymorphism, displaying an average of 6.18 alleles with accompanying average polymorphism information content (PIC) value of 0.516. The markers were used to evaluate the genetic diversity of 52 individuals collected from three populations of S. aralocaspica in Xinjiang, China. The results showed that the genetic diversity was moderate to high, with a mean expected heterozygosity (He) of 0.614, a mean Shannon’s information index (I) of 1.23, and a mean genetic differentiation index (Fst) of 0.263. The SSR markers developed in this study provide a valuable resource for future genetic studies and breeding programs of S. aralocaspica, and even other species in Suaeda.
... Numerically accurate SSR loci, based on NGS techniques, can be developed quickly and cost-effectively. Thousands of SSR markers have been developed and applied in genetic studies in many species [17,18,29,30]. ...
... The number of SSR loci was similar to some species in the Brassicaceae family, such as B. oleracea (64,546) [17]. For this reason, including differences in genome structure among different species, studies have shown that species with larger genomes usually show lower SSR densities [29,43]. For the Brassicaceae species, Xu et al. (2021) also found that the species of B. rapa, C. bursa-pastoris, and B. vulgaris, had larger genomes and a lower density of SSR. ...
... Further, there may be differences in identification criteria between different studies. Some studies carried out the SSR motif length which was restrained to 1-6, which was in consistence with mono-nucleotides, di-nucleotides, tri-nucleotides, tetra-nucleotides, penta-nucleotides, and hexa-nucleotides, respectively [17,29], while other studies restrained the SSR motif length to 2-6 bp [30], 2-8 bp [46]. This study identified motifs from di-to hexa-nucleotides, so that numerous mono-nucleotide types were not identified or counted. ...
Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.
... While the nutritional value of eggplant is lower than that of other vegetables in this family, it is a fairly good source of fiber, fat, carbohydrates, vitamins (A and C) and minerals (potassium, phosphorus, calcium, and iron) [1][2][3]. Due to the importance of creating new cultivars in breeding programs, there is an increasing interest to collect and preserve the genetic resources of eggplants from different regions [4]. Due to the great diversity of eggplants, it is possible to identify and detect different sources of diversity in eggplants [5]. ...
Background
Eggplant is an important vegetable that has long been cultivated in different parts of Iran. The major objectives of the eggplant breeding program are to improve fruit quality, increase yield performance through heterosis breeding, and introduce abilities of pest and disease resistance from wild relatives. In order to select suitable parents for breeding purposes, with respect to the genetic and morphological diversity of eggplant cultivars, it is necessary to have sufficient knowledge of genetic diversity and classification of germplasms.
Methods
This experiment was conducted in a randomized block design at the Seed and Plant Improvement Institute (SPII) in Karaj, Iran. Here, morphological diversity was assessed among a collection of eggplants which comprised four Iranian lines and 13 non-Iranian genotypes. For this purpose, 16 morphological traits were analyzed in the plants. Given the weakness of morphological analysis in providing precise characterizations of genetic divergence, a molecular study was also carried out by using five Simple Sequence Repeat (SSR) markers. In addition to the univariate analysis, the multi-descriptor variation was studied among the genotypes using two methods of multivariate analyses.
Results
The genotypes differed significantly in terms of the morphological traits. The multivariate analyses of morphological data indicated that eggplants from two different origins were clearly differentiated. Three main clusters were distinguished by a morphological UPGMA dendrogram in which non-Iranian genotypes, with the exception of 11,212, constituted cluster I and required the maximum number of days to flower, days to fruit set, and days to first harvest. Cluster II was identified with two Iranian lines BJ30, Y60, and one non-Iranian genotype (11,212) which showed the highest values of stem diameter, fruit diameter, fruit length, fruit length-to-width ratio, number of fruits per plant, and yield. Cluster III comprised two Iranian lines, D1 and D7, and showed the maximum plant height, number of internodes, number of nodes, number of leaves, number of stems, fruit weight, and fruits weight per plant. The highest and lowest intra-cluster genetic distances were observed in cluster I and cluster II, respectively. Based on SSR analysis, high levels of similarity were detected between several genotypes, namely, Y60 and 13,411; BJ30 and 1111; D7 and 13,521; 21,881 and 13,421.
Conclusions
High levels of heterozygosity and polymorphism information content (PIC) were observed in this study. This not only indicated high levels of polymorphism and an equal distribution of the evaluated loci but also suggested that these genotypes can be considered for the development of diverse parental lines which are of interest in breeding programs.
... A total of 638,316 SSRs were identified from 5737.8 Mb sequences in five bamboo genomes. The results seemed to be consistent with the previous study that species possessing larger genomes showed a larger number of SSRs, but lower SSR density [49,50]. Nonetheless, P. edulis possessing the largest genome size did not display the lowest density of SSR, and R. guianensis with the smallest genome size did not show the minimum number of SSR as well (Table 1). ...
Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection.
... An availability of gap free genome sequence of eggplant (Barchi et al., 2019) and Eggplant Microsatellite Data Base (EgMiDB; http://www. eggplantmicrosatellite.org/) (Portis et al., 2018) opens the ways to utilise this data for identification of more SSRs linked to BW resistance through BSA approach. ...
Wilt caused by the bacteria Ralstonia solanacearum, Enterobacter cloacae and Burkholderia glumae, independently or in complex, in Solanaceous vegetables is leading to enormous crop losses. The resistance mechanisms in tomato, chilli peppers, eggplant and potato are polygenically governed and the molecular level analyses have been successful to understand the key genes and pathways involved. QTL and candidate gene mapping, development of molecular markers explaining significant level of phenotypic variation, transcriptome analysis, expression analysis for the putative candidate genes and metabolome analyses which have been successful to reveal the genes and pathways in resistance are discussed in this paper. Genetic transformations using the key genes thus identified have been successful to generate the resistant lines. In addition to a systematic discussion on these topics, the major QTLs for bacterial wilt resistance in tomato and chilli peppers have been analyzed, contributing genes identified and annotated and the mechanisms conserved between these crops are discussed.
... Six classes of perfect SSRs were evaluated (from mono-to hexanucleotide) for their abundance in the assembled genome. Dinucleotides were the most abundant, in accordance with what has been previously reported in literature [30][31][32][33][34][35][36][37][38][39], representing 60.2% of the identified SSRs. Trinucleotides were the second most abundant class (23.7%), followed by tetranucleotides (6.8%). ...
... The variation of perfect microsatellites repeats was investigated in all SRR classes (Supplementary Materials). As previously reported, longer repeats (>25) tend to be less abundant in the genome [37,38,40,41]. As can be observed in Figure 2, the tri-, tetra-, penta-, and hexanucleotides relative distribution was higher between one and 10 motif repeats, while mononucleotides distribution increased from 14 motif repeats onward and dinucleotides showed higher abundance between 8 and 19 motif repeats. ...
... Compared with our previously published data [37,38], in which SSR classification was based on microsatellite length (nt), the present classification reports a lower number of SSRs belonging to class I and II. The choice of shifting from a microsatellite length (nt) classification to a repeat number-based one was performed in order to maximize the polymorphism discrimination power and informativeness of the Class I and Class II markers (Figure 3b). ...
Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.
... Among the various marker techniques, microsatellites or simple sequence repeat (SSR) markers represent one of the most informative, abundant, and easy-to-use marker systems for genetic studies and plant breeding programs (Bohra et al., 2011(Bohra et al., , 2012Ravishankar et al., 2013;Xu et al., 2013;Abd Ei-Moghny et al., 2017). Recently, three major classes of SSRs were reported in eggplant genome based on the SSR motifs length and repeats, which included class I (hypervariable: > 30 nt), class II (potentially variable: 20-30 nt), and class III (variable: < 20 nt) types (Portis et al., 2018). Earlier, Temnykh et al. (2001) also highlighted the significance of SSR tract lengths for marker development and breeding in rice. ...
... Discovery and characterization of the DNA markers spanning entire genome such as SSRs provides the foundation for trait discovery studies and molecular breeding. Following genome sequencing, genome-wide SSRs were designed for several plant species, including rice , soybean (Song et al., 2010), Brachypodium (Sonah et al., 2011), maize (Xu et al., 2013), foxtail millet (Pandey et al., 2013), Brassica (Shi et al., 2014), cotton , Nicotiana , peanut Lu et al., 2019), eggplant (Portis et al., 2018), carrot (Uncu and Uncu, 2020), and more recently in pomegranate (Patil et al., 2020c). ...
... In this study, we found that the number of SSRs and SSR densities vary according to the length of the chromosomes. Consistent with our finding, Portis et al. (2016) (Ott et al., 2011) and eggplant (Portis et al., 2018). Concerning the intra-chromosomal distribution of motif types in 'Tunisia, ' hexanucleotide was the most common SSR type followed by dinucleotides, which is in best agreement with earlier report, where hexamers accounted for 55.16% of all motifs, and pentamers were the least abundant type (2.33%) in tree genomes . ...
... To date, simple sequence repeat (SSR), conserved ortholog set II (COSII), characterized amplified region (SCAR), amplified fragment length polymorphism (AFLP), restriction site−associated DNA sequencing (RADseq), internal transcribed spacer (ITS), sequence-related amplified polymorphism (SRAP), intersimple sequence repeat (ISSR), and random amplified, microsatellite polymorphism (RAMP)-PCR markers have been applied in genetic diversity, population structure, morphological variation, phylogenetic inference, traceability, and cultivar/species identification and discrimination (Zhang et al., 2001Yin et al., 2005;Sze et al., 2008;Chung et al., 2009;Kwon et al., 2009;Levin et al., 2009;Zhao et al., 2010;Balasubramani et al., 2011;Liu et al., 2012Liu et al., , 2020bTripathi, 2013;Xin et al., 2013;Chen and Zhong, 2014;Wang et al., 2015a;Chen J. et al., 2017;McCulloch et al., 2020;Jung et al., 2021). SSR markers can be used for the detection of genetic polymorphisms of species, calculation of genetic relationships (genetic distance) between varieties, identification of cultivars, and even construction of genetic maps and QTL mapping with sufficient SSR markers Essid et al., 2015;Ibrahim et al., 2016;Thammina et al., 2017;Portis et al., 2018b). One hundred fifteen SSR and 12 ILP markers were applied to construct a genetic map with the F1 population (Hu, 2015). ...
Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.
