Molecular Markers in Salvia L.: Past, Present and Future

Karaca, Mehmet; İnce, Ayşe Gül

doi:10.1007/978-3-319-73900-7_9

Cited by 6 publications

(3 citation statements)

References 341 publications

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“…Among conventional DNA markers such as RAPD, AFLP and ISSR have been widely used while the application of single sequence repeats (SSRs) has been limited in Salvia (Karaca and Ince, 2017). We identified a set of high-quality markers to fill in the gap in the previous of S. splendens genetic assessment.…”

Section: Discussionmentioning

confidence: 99%

Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage

et al. 2020

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Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage's recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3-4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.

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Section: Discussionmentioning

confidence: 99%

Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage

et al. 2020

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“…In a typical graft, one plant is selected for its root to serve as the lower part, called rootstock, and a second plant is selected for its foliar part to serve as the upper part, called scion. The WGBS method is a well‐established protocol to detect single‐base resolution of methylated cytosines in the whole genome, called the methylome (Karaca & Ince, 2018). The literature has adequate data on the changes in DNA methylation levels among tissues and species and the effects of various factors, including grafting.…”

Section: Introductionmentioning

confidence: 99%

“…The WGBS method is a well-established protocol to detect singlebase resolution of methylated cytosines in the whole genome, called the methylome (Karaca & Ince, 2018). The literature has adequate data on the changes in DNA methylation levels among tissues and species and the effects of various factors, including grafting.…”

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confidence: 99%

Grafting‐induced seed gossypol levels by demethylation of (+)‐delta‐cadinene synthase genes in upland cotton

Karaca

İnce

2022

Plant Breeding

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Two-year-grafting experiments within and between Gossypium barbadense and Gossypium hirsutum accessions were conducted to study the source, transfer, and alteration of gossypol and methylation of (+)-δ-cadinene synthase (CDN) genes along with whole chromosomes of A01, A04, A11, D01, D05, and D11, harbouring the cotton CDNs, using the whole genome bisulfite sequencing (WGBS) method. The results revealed that although a glandless line used in this study had a low level of gossypol in the seeds, it did not contain any pigment glands, indicating that expression pathways of gland and gossypol were under genetic control of different loci in cotton.Grafts with glandless rootstocks produced significant amounts of total gossypol in the seeds, clearly demonstrating that the source of gossypol biosynthesis was not specific to the root. Heterografts consisting of scion GN, a glandless line, and scion TM-1 grafted on Pima 3-79 rootstocks caused increased total seed gossypol levels whereas homograft TT had decreased total seed gossypol levels. Alteration of total gossypol levels was also associated with gland density, and DNA demethylation levels of (+)-δ-cadinene synthase genes.

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Conservation of Biodiversity and Genetic Resources for Sustainable Agriculture

Karaca

İnce

2019

Innovations in Sustainable Agriculture

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Molecular Markers in Salvia L.: Past, Present and Future

Cited by 6 publications

References 341 publications

Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage

Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage

Grafting‐induced seed gossypol levels by demethylation of (+)‐delta‐cadinene synthase genes in upland cotton

Conservation of Biodiversity and Genetic Resources for Sustainable Agriculture

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