Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes

Ryu, Jaihyunk; Kim, Woon Ji; Im, Juhyun; Kim, Sang Hun; Lee, Kang-Seop; Jo, Han-Jig; Kim, Ee-Youb; Kang, Si-Yong; Lee, Jeong-Hee; Ha, Bo‐Keun

doi:10.1016/j.ejbt.2018.08.001

Cited by 16 publications

(13 citation statements)

References 26 publications

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“…This was probably due to the relatively large differences between A . victoriali s and the other Allium species, the presence of duplicated loci, unsuccessful primer design near the SNP regions, or the need to optimize PCR conditions (Ryu et al 2018 ; Ma et al 2021 ). Two successful markers (A_SNP5A1 and A_SNP6A1) could be used to discriminate the two Dongfeng samples and the other four A .…”

Section: Discussionmentioning

confidence: 99%

“…KASP technology is an effective and widely used genotyping method that determines the alleles at a specific locus within genomic DNA (Han et al 2019;Li et al 2019). This method has facilitated plant genetic diversity studies, for example, in the genotyping of Rubus (Ryu et al 2018), non-heading Chinese cabbage (Li et al 2019), and persimmon (Ma et al 2021). However, it has not been previously applied in the analysis of A. victorialis germplasms.…”

Section: Identification Of a Victorialis Germplasms By Kasp Assaysmentioning

confidence: 99%

“…SNPs have become the preferred markers for numerous genetics and genomics applications (Li et al 2019 ). In particular, the revolutionary advances in genome sequencing (Ryu et al 2018 ; Han et al 2020 ) have made the SNP-based genotyping technology an effective method for large-scale genotyping, genetic diversity analyses, and genetic map construction in many plant species (Li et al 2019 ). Kompetitive allele-specific PCR (KASP) is a novel and extensively used genotyping technology that enables bi-allelic scoring of SNPs (Han et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

Feng

Wang²,

Chen

et al. 2021

Mitochondrial DNA Part B

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The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum , Allium fistulosum , and Allium cepa , but genetically close to Allium tuberosum . The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera . In addition, two KASP markers for discriminating the Dongfeng samples from the other four A . victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.

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Section: Discussionmentioning

confidence: 99%

Section: Identification Of a Victorialis Germplasms By Kasp Assaysmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

Feng

Wang²,

Chen

et al. 2021

Mitochondrial DNA Part B

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“…Rubus sachalinensis L evl belongs to the genus Rubus in the Rosaceae family. There are more than 900 species worldwide (Ryu et al 2018), and there are about 194 species in China. They are mainly distributed in forest margins and grasslands at an altitude of 1000-2500 m in the northern region (Editorial Committee of Flora of China, Chinese Academy of Sciences 1985).…”

Section: Rubus Sachalinensis L Evl; Chloroplast Genome; Phylogenetic Analysismentioning

confidence: 99%

The complete chloroplast genome sequence of Rubus sachalinensis Lévl

Liu

Song

Kang

et al. 2021

Mitochondrial DNA Part B

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Rubus is a medicinal plant distributed in northern China and has high economic and social value. In this study, we reported the complete chloroplast genome sequence of the plant. We determined that the length of the chloroplast genome of Rubus sachalinensis L evl is found to be 155,787 bp and the GC content is 37.24%. The cp genome sequences contains 132 genes, including 37 tRNA genes, eight rRNA genes, and 87 mRNA genes, respectively. The genomic data can help the classification and evolution of Rubus plants, and provide a theoretical basis for the study of Rubus sachalinensis L evl.

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“…В работе J. Ryu et al (2018) SNP-маркеры были использованы и для регистрации мутационных изменений, индуцированных воздействием гамма-лучей, у растений 14 образцов ежевик и гибридов Boysenberry.…”

Section: Aflp (Amplified Fragment Length Polymorphism -по лиморфизм длины амплифицированных фрагментов)unclassified

Molecular markers in the genetic diversity studies of representatives of the genus <i>Rubus</i> L. and prospects of their application in breeding

et al. 2020

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Род Rubus L. (семейство Rosaceae Juss.), по оценкам разных систематиков, состоит из 12–16 подродов, объединяющих ~750 видов. Самые крупные по числу видов подроды – Idaeobatus (Focke) Focke, к которому относятся малины, и типовой подрод Rubus (=Eubatus Focke), включающий виды ежевик. Представители рода Rubus обладают высокой пищевой и хозяйственной ценностью, а также лекарственными свойствами. Селекционные исследования направлены на расширение генетического разнообразия и создание новых сортов малин и ежевик, устойчивых к биотическим и абиотическим стрессорам и отличающихся высоким качеством плодов. Современные селекционно-генетические программы все шире включают достижения молекулярной генетики и геномики. В данной статье представлен обзор фундаментальных и прикладных исследований генетического разнообразия культивируемых и дикорастущих видов рода Rubus, выполненных на основе методов молекулярного маркирования. Рассмотрены основные типы молекулярных маркеров (RFLP, RAPD, SSR, ISSR, AFLP, SCAR, SSCP, ретротранспозонные маркеры и т. д.) и области их применения в изучении представителей рода Rubus. Приведены результаты работ по использованию методов ДНК-маркирования для решения самых разных задач, включая: исследование межвидового и внутривидового генетического разнообразия, филогенетических связей видов и надвидовых таксонов, выяснение спорных вопросов систематики, генотипирование и уточнение родословных сортов малин и ежевик, изучение сомаклональной изменчивости и др. Наиболее важным результатом в практическом плане является создание насыщенных молекулярно-генетических карт для разных видов малин и ежевик, на которых локализованы многочисленные гены и QTL, детерминирующие различные хозяйственно ценные признаки. В то же время необходимо отметить, что число маркеров, перспективных для проведения эффективного молекулярного скрининга, пока еще недостаточно.

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Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes

Cited by 16 publications

References 26 publications

Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains

The complete chloroplast genome sequence of Rubus sachalinensis Lévl

Molecular markers in the genetic diversity studies of representatives of the genus <i>Rubus</i> L. and prospects of their application in breeding

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