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The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. A...
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Background:
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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]. ...
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/.
... The genomic sequence of vegetable crops aids breeders in developing additional molecular markers for improvement of commercially important vegetable crops. Several vegetable crops, including tomato (Tomato Genome Consortium 2012), cherry tomato (Wang et al. 2020), brinjal , capsicum (Qin et al. 2014), potato (Diambra 2011), carrot (Iorizzo et al. 2016), radish (Kitashiba et al. 2014), cucumber, musk melon (Garcia-Mas et al. 2012), watermelon (Guo et al. 2013), bitter gourd (Urasaki et al. 2017), sponge gourd (Wu et al. 2020), Chinese cabbage (Wang et al. 2011), lettuce (Reyes-Chin-Wo et al. 2017, globe artichoke (Portis et al. 2016) and cassava (Prochnik et al. 2012) have had their whole genomes sequenced, paving the way for a new genomics era for research in vegetable crops ( Table 1). ...
... The increasing knowledge of genome sequence in vegetable crops has opened new avenues for gene functional research, by determination of genetic function for a trait and the phenotype being examined using a traditional forward genetic technique. The fundamental goal of an inverse genetic process is to change the gene or its level of expression to investigate the phenotype that results (Portis et al. 2016). ...
Main conclusion
The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops.
Abstract
Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.
... Mb) and each chromosome is very long (ranged from 235.67 Mb to 307.45 Mb), which may lead to low-density. However, some studies showed that the SSR density was not related to genome size [44,45]. Further, there may be differences in identification criteria between different studies. ...
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.
... Total genomic DNA was extracted from young leaves (three plants per accession) and characterized using 26 genomic-SSR (gSSR) markers targeting loci distributed through all of the 17 chromosomes of globe artichoke (Supplementary Table 2A). The markers were selected according to their good resolution power and reliability (Scaglione et al., 2009(Scaglione et al., , 2016Portis et al., 2012Portis et al., , 2016. ...
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
... Information on start positions of markers had allowed successful anchoring of the new SSR markers to the physical map of groundnut (Lu et al., 2019). Portis et al. (2016) also reported genomic distribution of SSRs and their relations with annotated genomic components (gene space) based on the information on assembled pseudomolecules of globe artichoke genome. The information on chromosome wise location of miRNA-SSR markers could help in precise validation and introgression of genes/QTLs for seed type in pomegranate. ...
Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate.
... 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.
... Several reports showed that species that possessed larger genomes typically display a lower SSR density (SSRs/Mb; Morgante et al., 2002;Portis et al., 2018). Nonetheless, the different genomic sizes will result in different microsatellite repetition levels, but SSR density is not associated with genome size (Behura and Severson, 2014;Portis et al., 2016). In this study, the three species B. rapa, C. bursa-pastoris and B. vulgaris were found to have larger genomes and exhibit a lower density of SSR. ...
... Similar patterns of motif distribution have been found in other species. For example, several studies reported that AT/AT repeats appear to be typical in non-transcribed regions, and AG/CT prevail in gene sequences, while AC/GT and CG/GC repeats are the least frequent dinucleotides in both genomic and gene sequences (Cavagnaro et al., 2010;Portis et al., 2016). GC-rich motifs showed a strong bias in their distribution in cabbage gene sequences, most notably for mono-, di-and tri. ...
... Overrepresentation was found in several subcategories, such as BP and MF, but no enrichment was observed. In previous studies, SSRs are reported to occur in certain gene functions within eggplants, globe artichoke and Medicago truncatula, while transcription factors (TFs) constitute a distinct gene class containing SSRs (Portis et al., 2016(Portis et al., , 2018Min et al., 2017). In addition, TFs carrying SSRs have also been suggested to have critical functions, and their association with species diversity in Brassicaceae family should be clarified. ...
Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage ‘TO1000.’ Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14–0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
... However, there was no link found between the SSR density and genome size among the SSRs discovered in our analysis of 13 legume species. This is consistent with some of the recent findings that found no relation between the genome size and SSR density, and that the genome size differences may influence the degree of microsatellite repeats in the genome [15][16][17][18]. ...
... followed by Lupinus albus and Cicer arietinum (0.3%), whereas Glycine max, Medicago tranctula, Trifolium pratense, Phaseolus vulagaris, and Vigna anguaris has the lowest percentage (0.1%). In all SSR classes, it was observed that longer repeats were less abundant; a decreased trend in SSR frequency with an increased trend in their repeat number has been observed in other species [18,21]. ...
Microsatellites, or simple sequence repeats (SSRs), are polymorphic loci that play a major role as molecular markers for genome analysis and plant breeding. The legume SSR database is a webserver which contains simple sequence repeats (SSRs) from genomes of 13 legume species. A total of 3,706,276 SSRs are present in the database, 698,509 of which are genic SSRs, and 3,007,772 are non-genic. This webserver is an integrated tool to perform end-to-end marker selection right from generating SSRs to designing and validating primers, visualizing the results and blasting the genomic sequences at one place without juggling between several resources. The user-friendly web interface allows users to browse SSRs based on the genomic region, chromosome, motif type, repeat motif sequence, frequency of motif, and advanced searches allow users to search based on chromosome location range and length of SSR. Users can give their desired flanking region around repeat and obtain the sequence, they can explore the genes in which the SSRs are present or the genes between which the SSRs are bound design custom primers, and perform in silico validation using PCR. An SSR prediction pipeline is implemented where the user can submit their genomic sequence to generate SSRs. This webserver will be frequently updated with more species, in time. We believe that legumeSSRdb would be a useful resource for marker-assisted selection and mapping quantitative trait loci (QTLs) to practice genomic selection and improve crop health. The database can be freely accessed at http://bioinfo.usu.edu/legumeSSRdb/.
... The reference genome and all data information are available in the public domain database (http://www.artichokegenome.unito.it/cymsatdb/) (Portis et al. 2016). The information on the genome sequences provides the possibility of new genetic assays, assessment of the genetic diversity, gene isolation and marker-assisted breeding. ...
Globe artichoke (Cynara cardunculus var. scolymus L.; Asteraceae) is a diploid (2n = 2× = 34), perennial, mostly cross-pollinated species native to the Mediterranean Basin. It represents an important component of the agricultural economy of southern Europe, and is grown for its large immature inflorescences, called capitula or heads. Artichokes have recognized nutraceutical properties for human health. Its commercial production is based mainly on perennial vegetatively-propagated clones. Recently its cultivation has been shifted toward seed-propagation of hybrids. Italy holds the richest biodiversity of cultivated Cynara, which has resulted in the culture of varieties and landraces adapted to specific local climatic conditions and markets. Cultivar-groups comprise early and late types, but also spiny, violet, Romanesco and Catanese types. Traditionally selections have been made within a given clone, removing off-types. Due to its heterozygous nature, a great variability is seen after crossing or selfings, promoting the selection of new cloned varieties. Seed-propagated hybrids are feasible upon the use of genic male sterility. In the past 20 years new technologies have been applied to broaden the knowledge of the molecular basis inherent, from the first genetic linkage map, the identifications of QTL for yield and related traits, up to the recent whole-genome sequence.
... The present study aimed to offer highly informative chromosome-wise SSR markers in pomegranate. The genomic sequences containing perfect SSRs accounted for 1.74% (5.18 Mb) of total assembled genome, which is slightly higher than observed in the grapevine (0.67%) genome (Portis et al., 2016). The 'Tunisia' genome revealed 55,836 (15.28%) ...
... SSRs/Mb) in 'Tunisia' genome slightly deviated from a previous report that established a negative relationship between genome size and SSR density (Morgante et al., 2002). Such trends were also witnessed through comparing various plant genomes (Portis et al., 2016). By conducting SSR survey in genome sequences of 16 tree species, Xia et al. (2017) found that SSR densities with the tree species may be greater than > 1,200, as in Theobroma cacao (1,446) and others. ...
... 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 . ...
The simple sequence repeat (SSR) survey of ‘Tunisia’ genome (296.85 Mb) identified a total of 365,279 perfect SSRs spanning eight chromosomes, with a mean marker density of 1,230.6 SSRs/Mb. We found a positive trend in chromosome length and the SSR abundance as marker density enhanced with a shorter chromosome length. The highest number of SSRs (60,708) was mined from chromosome 1 (55.56 Mb), whereas the highest marker density (1,294.62 SSRs/Mb) was recorded for the shortest chromosome 8 (27.99 Mb). Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. Across the eight chromosomes, the class III had maximum number of SSR motifs (301,684, 82.59%), followed by the class II (31,056, 8.50%) and the class I (5,003, 1.37%). Examination of the distribution of SSR motif types within a chromosome suggested the abundance of hexanucleotide repeats in each chromosome followed by dinucleotides, and these results are consistent with ‘Tunisia’ genome features as a whole. Concerning major repeat types, AT/AG was the most frequent (14.16%), followed by AAAAAT/AAAAAG (7.89%), A/C (7.54%), AAT/AAG (5.23%), AAAT/AAAG (4.37%), and AAAAT/AAAAG (1.2%) types. We designed and validated a total of 3,839 class I SSRs in the ‘Tunisia’ genome through electronic polymerase chain reaction (ePCR) and found 1,165 (30.34%) SSRs producing a single amplicon. Then, we selected 906 highly variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across multiple draft genomes of pomegranate, which provided us a subset of 265 highly polymorphic SSRs. Of these, 235 primers were validated on six pomegranate genotypes through wet-lab experiment. We found 221 (94%) polymorphic SSRs on six genotypes, and 187 of these SSRs had ≥ 0.5 PIC values. The utility of the developed SSRs was demonstrated by analyzing genetic diversity of 30 pomegranate genotypes using 16 HvSSRs spanning eight pomegranate chromosomes. In summary, we developed a comprehensive set of highly polymorphic genome-wide SSRs. These chromosome-specific SSRs will serve as a powerful genomic tool to leverage future genetic studies, germplasm management, and genomics-assisted breeding in pomegranate.
