Single nucleotide polymorphism (SNP) discovery through genotyping-by-sequencing (GBS) and genetic characterization of Dendrobium mutants and cultivars

Ryu, Jaihyunk; Kim, Woon Ji; Im, Juhyun; Kang, Kyung‐Won; Kim, Sang Hoon; Jo, Yeong Deuk; Kang, Si-Yong; Lee, Jeong-Hee; Ha, Bo‐Keun

doi:10.1016/j.scienta.2018.09.053

Cited by 16 publications

(8 citation statements)

References 31 publications

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“…Understanding the frequency and spectrum of mutations resulting from a certain irradiation condition is very important for designing an efficient strategy, and determining an adequate population size, for mutation breeding. Although various irradiation conditions, such as the type of radiation, irradiation dose, dose rate, target tissue, and sample pretreatment, have been applied in mutation breeding, sequencing analyses to obtain genome-scale views of DNA mutations have only been performed recently [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. We first carried out a genomic analysis of DNA mutations and recombination events in gamma-irradiated reproductive organs to examine the feasibility of using them for crop improvement.…”

Section: Discussionmentioning

confidence: 99%

“…For example, gamma-rays, which are classified as a low-LET radiation and have been most widely used in mutation breeding, induce SBSs predominantly while high-LET radiation such as heavy ion beams and fast neutrons generate higher proportion of large deletions and translocations compared to low-LET radiation [ 9 , 10 , 11 , 12 ]. Recently, DNA mutations caused by proton beam irradiation were characterized using a genotype-by-sequencing (GBS) analysis, in which short sequences near DNA regions cut by a specific restriction enzyme are analyzed to investigate SBSs and small InDels in a cost-effective way [ 13 , 14 ]. Regarding irradiated plant tissues, Hase et al [ 15 ] showed, using a whole-genome sequencing analysis, that the irradiation of dry seeds resulted in a significantly higher frequency of DNA mutations, especially InDels, compared with the irradiation of seedlings.…”

Section: Introductionmentioning

confidence: 99%

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Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes

Kang

Choi

et al. 2021

Plants

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The irradiation of dry seeds is the most widely-used irradiation method for improving seed-propagated crops; however, the irradiation of other tissues also has useful effects. The irradiation of plant reproductive organs, rather than seeds, for mutation breeding has advantages, such as producing non-chimeric progeny. However, the mutation frequency and spectrum produced using this method have not been analyzed on a genome-wide level. We performed a genotype-by-sequencing analysis to determine the frequencies of single-base substitutions and small (1–2 bp) insertions and deletions in hot pepper (Capsicum annuum L.) plants derived from crosses using gamma-irradiated female or male gametophytes. The progeny of irradiated gametophytes showed similar or higher DNA mutation frequencies, which were dependent on the irradiation dose and irradiated tissue, and less biased single base substitutions than progeny of irradiated seeds. These characteristics were expected to be beneficial for development of mutation population with a high frequency of small DNA mutations and performing reverse-genetics-based mutation screening. We also examined the possible use of this irradiation method in manipulating the meiotic recombination frequency; however, no statistically significant increase was detected. Our results provide useful information for further research and breeding using irradiated gametophytes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes

Kang

Choi

et al. 2021

Plants

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“…Amplifluor (Rickert et al, 2004 ; Fuhrman et al, 2008 ) and, particularly, KASP markers (Wang et al, 2015 ; Ryu et al, 2018 , 2019 ; Udoh et al, 2020 ; Brusa et al, 2021 ) are very successful commercial products and currently popular over a range of research areas. However, KASP technology is relatively expensive, especially for small experiments (reviewed in Kaur et al, 2020b ).…”

Section: Introductionmentioning

confidence: 99%

Modified “Allele-Specific qPCR” Method for SNP Genotyping Based on FRET

et al. 2022

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The proposed method is a modified and improved version of the existing “Allele-specific q-PCR” (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.

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“…The KASP has a wide range of usage on different livings and it can be used easily for genotyping with cost advantage [22]. Cacao [25], apple [26,27], soybean [28,29], grain amaranth [30] ash tree [31], robus [32], dentrobium [33], watermelon [34], peanut [35; 36], maize [23], rice [37] and wheat [20,38,39,40,41] are some of the plants species which KASP assay has successfully applied for different purposes like Whole Genome Sequencing (WGS), GBS, breeding or identify to genetic diversity up to the present.…”

Section: Introductionmentioning

confidence: 99%

Molecular sexual determinants in Pistacia genus by KASP assay

Şahin

Aydın

et al. 2022

Mol Biol Rep

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I. Background: Pistacia is kind of unisexual plant species that can take 4-5 years to initiate bearing stage of trees in terms of economic value. The fruits of species have an extreme importance in food, health and baking industry as a raw material. So, identify the individual in early juvenile period for pollination and position of trees is very crucial for growers. The objective of this study is developing markers for each Pistacia species which helps the screening the sex of plant seedling quickly before they reach reproduction stage without waiting morphological data. II. Methods and Results:Within the context, by using the power of KASP (Kompetitive Allele Speci c PCR) assay technology as a marker screening system, we successfully discriminate 7 Pistacia species out of 8 which are P. atlantica, P. integerrima, P. khinjuk, P. mutica, P. terebinthus, P. vera and P. lentiscus. We have used a highthroughput DNA sequence read archive (SRA) to assemble a reference genome to use in our studies as de novo bioinformatics method. 4 genomic regions were sequenced with collected plant material from Antepfıstıgı Research Institute Collection Garden predominantly and 8 species were aligned intraspeci cally for Single Nucleotide Polymorphism (SNP) mining. 12 SNP markers are converted to KASP markers and 5 of them (SNP-PIS-133396, SNP-PIS-167992, P-ATL-91951-565, P-INT-91951-256, P-KHI-91951-115) showed obvious allelic discrimination between male and female species. SNP-PIS-167992 and P-ATL-91951-565 were identi ed as best marker assays due to the allelic frequency differences in graphs which are apparent for all individuals and homozygosis/heterozygosis observed clearly. These markers could be most comprehensive for whole genus because the discriminability power of several species in once. III. Conclusions:As a conclusion, this study is reported rst Pistacia gender discrimination by KASP, besides the precursor study for sex discrimination by KASP in plants.In this study 12 SNP markers were converted to KASP markers (Table 1) to use in the assays.

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Single nucleotide polymorphism (SNP) discovery through genotyping-by-sequencing (GBS) and genetic characterization of Dendrobium mutants and cultivars

Cited by 16 publications

References 31 publications

Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes

Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes

Modified “Allele-Specific qPCR” Method for SNP Genotyping Based on FRET

Molecular sexual determinants in Pistacia genus by KASP assay

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