Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

Gramazio, Pietro; Prohens, Jaime; Borràs, Dionís; Plazas, Mariola; Herraiz, Francisco Javier; Vilanova, Santiago

doi:10.1007/s10681-017-2057-3

Cited by 26 publications

(21 citation statements)

References 79 publications

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“…The interest in this species lies in its drought tolerance [19,20], high content of bioactive phenolic compounds [21][22][23][24], and resistance to some diseases [25,26]. As a result, S. incanum has been used for a plethora of breeding and genetic studies [6,24,[27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs

et al. 2020

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Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments.

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Section: Introductionmentioning

confidence: 99%

Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs

et al. 2020

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“…Additional informative SSR markers were also developed from S. melongena genomic libraries enriched for AG/CT motif ( Vilanova et al, 2012 ) and, more recently, from transcriptome analysis of S. incanum and S. aethiopicum , two close relatives of the common eggplant ( Gramazio et al, 2016 ). In eggplant SSR markers have been applied in diversity, phylogenetic as well as linkage mapping studies ( Barchi et al, 2010 , 2012 ; Munoz-Falcon et al, 2011 ; Fukuoka et al, 2012 ; Hurtado et al, 2012 ; Prohens et al, 2012 ; Cericola et al, 2013 ; Gramazio et al, 2017 ). Recently a high quality genome draft of eggplant, covering 1.06 Gb of gap-free sequence with an N50 of 2.9 Mb, was produced by a combination of Illumina sequencing and optical mapping and was anchored to 12 pseudomolecules 2 ( The Eggplant Genome Consortium, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource

et al. 2018

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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 intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an “Eggplant Microsatellite DataBase” (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.

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“…Crop variety right protection has gained more and more attention in China, and a statistically reliable and efficient DNA fingerprinting system is in urgent need for red bayberry. SSRs have been the most used molecular marker type in DNA fingerprinting technology, for their convenience of usage and the high polymorphic information content (PIC) per marker (Gramazio et al, 2017). However, even though SNPs usually have lower polymorphic information content (PIC) per marker than SSRs, the usage of SNPs has been increasing dramatically in recent years due to several advantages (Fernandes et al, 2020;Hadizadeh et al, 2020;Wu and Alexander, 2020;Xin et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…In cucumber (Cucumis sativus L.), multiplex PCR amplification and GBS were applied for genotyping multiple genomic segments in the variety fingerprinting (Zhang et al, 2020). SNP-based fingerprinting systems have also been constructed recently in oolong tea (Camellia sinensis L.) (Lin et al, 2020), cacao (Theobroma cacao L.) (Mahabir et al, 2020), eggplants (Solanum L.) (Gramazio et al, 2017), and pineapple (Ananas comosus L.) (Zhou et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

Zhong

et al. 2020

Front. Plant Sci.

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High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.

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Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

Abstract: Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

Cited by 26 publications

References 79 publications

Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs

Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs

Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

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