Development of SNP markers using genotyping-by-sequencing for cultivar identification in rose (Rosa hybrida)

Heo, Moon-Sun; Han, Koeun; Kwon, Jae-Hoon; Kang, Byoung-Cheorl

doi:10.1007/s13580-017-0268-0

Cited by 10 publications

(8 citation statements)

References 25 publications

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“…Because of this challenge, at the end of last century, developing DNA markers for DUS testing, variety profiling or origin tracing was proposed, and case studies in crop, vegetables and fruit trees have been introduced in BMT sessions 65 or reported in scientific journals [66][67][68] . For rose, codominant markers from the nuclear genome have been developed and used in genetic studies of diploid and tetraploid rose or DNA profiles [69][70][71][72][73] . Few studies have focused on the genetic variation rose chloroplast genome 74,75 .…”

Section: Discussionmentioning

confidence: 99%

“…In addition to SSR markers, SNPs are a powerful tool for genetic studies in plants, and these markers have been used to evaluate the genetic differentiation among accessions as well as population structure and diversity in crops 86 . A large number of SNP markers have been mined from the nuclear genome of roses 72 , 87 , 88 , and an SNP array (WagRhSNP68k) was developed for genetic mapping in tetraploid cut roses 73 , 89 . Based on the comparative analysis of nucleotide diversity among regions in these Rosa species, a set of 20 regions with high divergence have been found and these regions could be used as a starting point for candidate molecular markers for phylogenetic and phylogeographic studies in the Rosa genus.…”

Section: Discussionmentioning

confidence: 99%

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Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Zheng

Huang

2020

Sci Rep

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the rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. the chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. comparative genome analysis showed that the iR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. the phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species. Chloroplasts are vital and unique components of photosynthetic cells in plants and algae. They are responsible for multiple functions, e.g., assimilation of carbon and nitrogen, synthesis of amino acids and fatty acids, etc., and play important roles in plant growth and development 1. Chloroplasts may have originated from cyanobacteria through endosymbiosis 2,3 , and chloroplasts possess their own deoxyribonucleic acid (DNA). In the majority of plant species, the chloroplast genome (cp genome) is inherited maternally, with the exception of certain gymnosperms, in which the cp genome is paternally inherited 4. In recent years, knowledge about the organization and evolution of the cp genome has rapidly improved because of the development of DNA sequencing technology and bioinformatics methods. The cp genome is relatively conserved in angiosperms, and its size ranges from 107 to 218 kb, including 100-200 encoding genes 5. A typical angiosperm cp genome has circular DNA, including two small inverted repeats (IRa and IRb), a large single copy (LSC) region and a small single copy (SSC) region 6. Compared to nuclear DNA, the cp genome is small, single-stranded, relatively conserved and has uniparental inheritance, and its nucleotide m...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Zheng

Huang

2020

Sci Rep

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“…Re-sequencing for diversity analysis avoids possible ascertainment bias while offering allele dosage estimates from read proportions 23–25 , although various steps in the actual protocol used may negatively affect the reliability of dosage estimation in polyploids. Re-sequencing at very low coverage per individual (skim sequencing) or the use of a complexity reduction step 26 , such as restriction-site-associated DNA sequencing or genotyping by sequencing (GBS), has been proposed to reduce cost, and indeed have already been applied in rose 5,27,28 . Population genetics analysis that do not require individual genotype information (Pool-seq) reduces the number of libraries, while protocols for reducing the costs of libraries have also been developed 29 .…”

Section: Genome Sequence and Genomic Tools In Rosementioning

confidence: 99%

In the name of the rose: a roadmap for rose research in the genome era

et al. 2019

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The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.

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“…Recently, SNP-based consensus-maps were constructed by RAD-seq for diploid roses 10,40 . Though genotyping by sequencing has been proved to be successful in detection of bi-allelic SNP markers in both diploid and tetraploid roses, a high-density genetic map for founder species of modern roses remains necessary to facilitate QTL positioning, map based cloning and comparative genomics studies 10,40,41 .…”

Section: Introductionmentioning

confidence: 99%

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Li¹,

Yang²,

Yang³

et al. 2019

Sci Rep

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Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis ‘Old Blush’ (OB) and R. wichuraiana ‘Basyes’ Thornless’ (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.

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Development of SNP markers using genotyping-by-sequencing for cultivar identification in rose (Rosa hybrida)

Cited by 10 publications

References 25 publications

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

In the name of the rose: a roadmap for rose research in the genome era

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

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