High-throughput simple sequence repeat (SSR) mining saturates the carrot (<i>Daucus carota</i> L.) genome with chromosome-anchored markers

Uncu, Ayşe Özgür; Uncu, Ali Tevfik

doi:10.1080/13102818.2019.1701551

Cited by 16 publications

(10 citation statements)

References 41 publications

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“…The majority of the polymorphic SSRs reported here were positioned in the intergenic regions, with 36.54% distributed in the gene regions (Supplementary Table S3 ) even though a lower proportion of SSRs are known to reside in the gene region, as reported in other organisms 55 , 56 . Comparable to our report, 29–30% of the SSR markers developed from the genome sequences in carrot and hazelnut belong to the transcribed regions 12 , 57 . Also, the tri and hexa repeat loci have been more prevalent in the transcribed regions, and those two motifs comprise 49% of total SSRs in this study, apparently leading to high genic SSRs.…”

Section: Discussionsupporting

confidence: 66%

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Bhattarai

Shi

Kandel³

et al. 2021

Sci Rep

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The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.

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Section: Discussionsupporting

confidence: 66%

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Bhattarai

Shi

Kandel³

et al. 2021

Sci Rep

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“…Therefore, we believe that 63 highly polymorphic miRNA-SSRs identified in this study would be a valuable genomic tool for understanding the genetic makeup of seed type trait of pomegranate. Recently, Uncu and Uncu (2020) ) developed chromosome anchored SSR markers for carrot genome assembly, and identified 51,160 single-locus markers through e-PCR. Further, they experimentally evaluated 50 markers across 17 carrot accessions and found 46 markers produced expected product sizes suggesting accuracy rate of 90% in predicting the amplification profiles by e-mapping.…”

Section: Discussionmentioning

confidence: 99%

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

et al. 2022

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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.

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“…Subsequently, we selected 906 high variable class (> 40 nt) markers for validation and identified 289 primer pairs producing expected product size with single amplicon. The ePCR technique has been applied to validate in silico -discovered DNA markers in different plant species including wheat ( Han et al, 2015 ), sesame ( Dossa et al, 2017 ), carrot ( Uncu and Uncu, 2020 ), cucumber ( Liu et al, 2015 ), bitter melon ( Cui et al, 2017 ), and tobacco ( Wang et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…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 ( Zhang et al, 2007 ), 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 ( Wang et al, 2015 ), Nicotiana ( Wang et al, 2018 ), peanut ( Zhao et al, 2017 ; Lu et al, 2019 ), eggplant ( Portis et al, 2018 ), carrot ( Uncu and Uncu, 2020 ), and more recently in pomegranate ( Patil et al, 2020c ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

et al. 2021

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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.

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High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

Abstract: View related articles View Crossmark data Citing articles: 1 View citing articles High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

Cited by 16 publications

References 41 publications

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

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