Development of SNP markers for marker-assisted breeding in Chinese cabbage using Fluidigm genotyping assays

Choi, Su Ryun; Oh, Sang Heon; Dhandapani, Vignesh; Jang, Chang Soon; Ahn, Chun-Hee; Rameneni, Jana Jeevan; Kim, Hyuna; Jeon, In-Bae; Lim, Yong Pyo

doi:10.1007/s13580-019-00211-y

Cited by 8 publications

(6 citation statements)

References 26 publications

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“…Penanda biomolekuler untuk penanda yang berharga di kelapa sawit dan tanaman lainnya berkembang biak. Meskipun teknologi molekuler telah mengarah pada penggunaan sekuensing generasi berikutnya (Choi et al, 2020), analisis asosiasi genom (Xia et al, 2019), data transkriptomik (Dhillon et al, 2021;Ma et al, 2021), dan pengeditan genom (Budiani et al, 2019;Yarra et al, 2020;Yeap et al, 2021), namun penanda genetik 3 Linkage map construction SPET markers SNP markers…”

Section: Kajian Terkini Marka Molekuler Untuk Karakter Unggul Kelapa ...unclassified

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Faizah

2022

war

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Penyakit busuk pangkal batang (BPB) yang disebabkan patogen Ganoderma boninense menjadi penyakit utama pada kelapa sawit yang menurunkan produktivitas secara signifikan. Pengembangan varietas kelapa sawit tahan penyakit BPB melalui beberapa tahapan dan evaluasi di setiap prosesnya. Tulisan ini akan menjelaskan hal-hal yang berkaitan dengan respon ketahanan dan tahapan pengembangan biomarka berbasis nukleotida untuk mendapatkan varietas kelapa sawit tahan Ganoderma. Evaluasi fenotipe dan genotipe plasma nutfah sebagai sumber material genetik, metode pemuliaan dan seleksi tanaman tahan, respon ketahanan tanaman, dan gen-gen yang terlibat dalam ketahanan penyakit menjadi komponen yang berkaitan dengan efektif dan efisien biomarka pada program pemuliaan kelapa sawit tahan penyakit BPB. Pengembangan biomarka untuk seleksi karakter unggul pada kelapa sawit dan tanaman lain juga dijelaskan pada artikel ini.

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Section: Kajian Terkini Marka Molekuler Untuk Karakter Unggul Kelapa ...unclassified

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Faizah

2022

war

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“…We used previously reported single nucleotide polymorphic (SNP) markers that were used in map construction between "Chiifu" and "Kenshin" [49,50], and 106 newly developed primers targeting insertion and deletion (InDel) variations to construct a genetic map using the 09CR-DH population (Table S7). Additionally, some simple sequence repeat (SSRs) markers reported in Kim et al [51] were used in this study to construct the genetic map frame.…”

Section: Marker Development and Genotypingmentioning

confidence: 99%

“…The genotyping of SNPs was performed using two methods: the LightScanner System (Idaho Technologies, Salt Lake City, UT, USA), based on a high-resolution melting (HRM) analysis, performed in accordance with Pang et al [49] and Li et al [57]; and the Fluidigm ® EP1™ system using 96.96 Dynamic Array™ IFC (Fluidigm, South San Francisco, CA, USA), performed in accordance with Choi et al [50], in which markers were named as <F-two digit code representing chromosome number>_<two digit code representing order of markers beginning to end on chromosome>. The PCR amplification was followed as an initial denaturation of 94 • C for 4 min, 35 cycles of 94 • C for 30 s, 55 • C for 30 s, and 72 • C for 30~60 s, followed by a final extension of 72 • C for 5 min.…”

Section: Marker Development and Genotypingmentioning

confidence: 99%

Quantitative Trait Locus Mapping of Clubroot Resistance and Plasmodiophora brassicae Pathotype Banglim-Specific Marker Development in Brassica rapa

Choi

Chhapekar

et al. 2020

IJMS

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Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quantitative trait loci (QTLs) for clubroot resistance have been identified in Brassica, disease-related damage continues to occur owing to differences in host variety and constant pathogen variation. Here, we investigated the inheritance of clubroot resistance in a double haploid population developed by crossing clubroot resistant and susceptible lines “09CR500” and “09CR501”, respectively. The resistance of “09CR500” to Plasmodiophora brassicae pathotype “Banglim” was controlled as a single dominant gene, with the segregation of resistance and susceptibility being nearly 1:1. PbBrA08Banglim was identified as having a logarithm of odds value of 7.9–74.8, and a phenotypic variance of 26.0–97.1% with flanking marker “09CR.11390652” in A08. After aligning QTL regions to the B. rapa reference genome, 11 genes were selected as candidates. PbBrA08Banglim was located near Crr1, CRs, and Rcr9 loci, but differences were validated by marker analysis, gene structural variations, and gene expression levels, as well as phenotypic responses to the pathotype. Genotyping using the “09CR.11390652” marker accurately distinguished the Banglim-resistance phenotypes in the double haploid population. Thus, the developed marker will be useful in Brassica breeding programs, marker-assisted selection, and gene pyramiding to identify and develop resistant cultivars.

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“…Alternatively, when prior information is available on sequence variation in the populations of interest and a reduced number of markers is sufficient, other genotyping methods are available that may be simpler to analyse, have less missing data, increased reliability, and may reduce costs. High-throughput platforms including Illumina Infinium iSelect HD (Illumina, San Diego, CA), the Sequenom MassARRAY platform (Agena Bioscience, San Diego, CA), and Standard Biotools Dynamic Arrays (San Francisco, CA, USA) offer a range of genotyping approaches suitable for large numbers of samples that are cost and time-effective (Choi et al 2020; Davey et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenileThuja plicatain UK Woodlands

Guillardín,

Glover,

Kerr

et al. 2024

Preprint

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Thuja plicata is a conifer tree that is appreciated for its cultural, ecological and wood quality features in its natural range in western North America. It is also used in Europe and the UK for timber production. Some T. Plicata plantations in the UK are converted to Continuous Cover Forestry (CCF) management which uses natural regeneration and concerns have been raised about the genetic diversity in both the adult trees and the offspring. We studied species diversity, stand structure, and genetic diversity in four UK woodlands planted with T. plicata which contained both adults and naturally regenerated individuals. We discovered 61,104 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 504 SNPs for analysis. We selected 67 SNPs for PCR-based genotyping of 163 adults and 176 juveniles. We found a large number of monomorphic sites (40.3%) most of which were restricted to adults in a single woodland, indicative of a high genetic differentiation among woodlands. The effective population size (Ne) was very low across all sites (Ne < 100), varied between adults and juveniles, and was lowest in the most diverse woodland in terms of species and structure. In contrast, heterozygosity was high overall (Ho = 0.38), except in the divergent woodland (Ho = 0.26), and did not vary between adults and juveniles. Our findings and genotyping methods provide insights into the ability of CCF-managed woodlands, including instances of low genetic diversity in T. plicata, to face environmental shifts and disease threats.

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Development of SNP markers for marker-assisted breeding in Chinese cabbage using Fluidigm genotyping assays

Cited by 8 publications

References 26 publications

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

Quantitative Trait Locus Mapping of Clubroot Resistance and Plasmodiophora brassicae Pathotype Banglim-Specific Marker Development in Brassica rapa

Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenileThuja plicatain UK Woodlands

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