• Plant Biotechnology Reports
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• v.3 no.4
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• pp.309-315
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• 2009

Molecular markers developed from the flanking sequences of two cytoplasmic male sterility (CMS)-associated genes, orf456 and ${\Psi}atp6-2$, have been used for marker-assisted selection of CMS in pepper. However, in practice, the presence of orf456 and ${\Psi}atp6-2$ at substoichiometric levels even in maintainer lines hampers reliable selection of plants containing the CMS gene. In this study, we developed a novel CMS-specific molecular marker, accD-U, for reliable determination of CMS lines in pepper, and used the newly and previously developed markers to determine the cytoplasm types of pepper breeding lines and germplasms. This marker was developed from a deletion in a chloroplast-derived sequence in the mitochondrial genome of a CMS pepper line. CMS pepper lines could be unambiguously determined by presence or absence of the accD-U marker band. Application of orf456, ${\Psi}atp6-2$and accD-U to various pepper breeding lines and germplasms revealed that accD-U is the most reliable CMS selection marker. A wide distribution of orf456, but not ${\Psi}atp6-2$, in germplasms suggests that the pepper cytoplasm containing both orf456 and ${\Psi}atp6-2$ has been selected as CMS cytoplasm from cytoplasm containing only orf456. Furthermore, factors other than orf456 may be required for the regulation of male sterility in pepper.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.730-736
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• 2015

Tomato spotted wilt virus (TSWV) causes one of the most destructive viral diseases that threatens global tomato production. Sw-5b was reported as the resistance gene effective against TSWV. The objective of this research was to develop a single-nucleotide polymorphism (SNP) marker to distinguish tomato cultivars resistant to TSWV from susceptible cultivars for marker-assisted breeding. First, we determined genotypes for TSWV resistance in 32 commercial tomato cultivars using the previously reported Sw-5b gene-based marker. Then, DNA sequences of Sw-5b alleles in tomato cultivars showing resistant or susceptible genotypes were analyzed; a single SNP was found to distinguish tomato cultivars resistant to TSWV from susceptible cultivars. Based on the confirmed SNP, a SNP primer pair was designed. Using this new SNP sequence and high-resolution melting analysis, the same 32 tomato cultivars were screened. The results were perfectly correlated with those from screening with the Sw-5b gene-based marker. These results indicate that the SNP maker developed in this study will be useful for better tracking of resistance to TSWV in tomato breeding.

• Molecules and Cells
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• v.26 no.6
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• pp.548-553
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• 2008

The erect habit of fruit setting is a unique characteristic of ornamental peppers and wild pepper species. The erect habit is known to be controlled by the up locus on pepper (Capsicum annuum L.) chromosome 12. The result of a genetic analysis using Saengryeog 211 (pendant), Saengryeog 213 (erect), and their $F_1$ and $BC_1$ progeny demonstrated that up is a recessive gene. To develop an up-linked marker, bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) were employed using 108 $F_{2:3}$ individuals. The closest AFLP marker, $A2C7_{469}$, was located at a genetic distance of 1.7 cM from the up locus and was converted into a cleaved amplified polymorphic sequence (CAPS) marker. This marker was mapped at a genetic distance of 4.3 cM from the up locus. When the CAPS was applied to seven ornamental lines and 27 breeding lines with erect fruit, these genotypes of 28 lines were correctly predicted. Thus, the CAPS marker will be useful for marker-assisted selection (MAS) of pepper breeding lines with the up allele at the early seedling stage.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Journal of Plant Biotechnology
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• v.46 no.3
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• pp.165-171
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• 2019

Marker-assisted backcrossing (MABC) is useful for selecting an offspring with a highly recovered genetic background for a recurrent parent at early generation to various crops. Moreover, marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and it accelerates recurrent parent genome (RPG) recovery. In this study, we were employed to incorporate rin gene(s) from the donor parent T13-1084, into the genetic background of HK13-1151, a popular high-yielding tomato elite inbred line that is a pink color fruit, in order to develop a rin HK13-1084 improved line. The recurrent parent genome recovery was analyzed in early generations of backcrossing using SNP markers obtained from genotyping-by-sequencing analysis. From the $BC_1F_1$ and $BC_2F_1$ plants, 3,086 and 4868 polymorphic SNP markers were obtained via GBS analysis, respectively. These markers were present in all twelve chromosomes. The background analysis revealed that the extent of RPG recovery ranged from 56.7% to 84.5% and from 87.8% to 97.8% in $BC_1F_1$ and $BC_2F_1$ generations, respectively. In this study, No 5-1 with 97.8% RPG recovery rate among $BC_2F_1$ plants was similar to HK13-1151 strain in the fruit shape. Therefore, the selected plants were fixed in $BC_2F_2$ generation through selfing. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in the backcross generations. MABC can greatly reduce breeding time as compared to the conventional backcross breeding. For instance, MABC approach greatly shortened breeding time in tomato.

• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.139-143
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• 2010

Late blight caused by Phytophthora infestans is historically a serious epidemic disease in potato and tomato cultivations. Accession L3708 (Solanum pimpinellifolium), a new source for late blight resistance was identified in AVRDC, and carries the resistance gene, Ph-3, incompatible to P. infestans race 3. The AFLP markers linked to Ph-3 were previously developed from the L3708 accession (Chunwongse et al. 2002). To facilitate tomato breeding with the Ph-3 gene, an attempt was made to convert AFLP markers to sequence-characterized amplified region (SCAR) markers. Among 6 AFLP markers, only one AFLP marker, L87, was successfully converted to SCAR marker. The resistance-specific 230 bp AFLP fragment was cloned and sequenced, and the PCR primer amplifying a 123 bp fragment was designed. This SCAR marker could discriminate resistant and susceptible individuals with high stringency. The developed SCAR marker could be used for the marker assisted-selection in tomato breeding programs.

• Journal of Life Science
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• v.19 no.1
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• pp.152-155
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• 2009

The old-gold-crimson ($og^c$) fruit color mutation produces deep red tomato fruit with high lycopene content. age is a null mutation allele of lycopene-${\beta}$-cyclase (Crt-b) gene (B locus) that converts lycopene to ${\beta}$-carotene in the cartenoid biosynthesis pathway in tomato. Breeding of high lycopene tomato cultivars can be accelerated by marker-assisted selection (MAS) for introgression of $og^c$ allele by using a gene-based DNA marker. In order to develop a marker, single nucleotide deletion of adenine(A) with. in a poly-A repeat that has been known to be responsible for frame-shift mutation of $og^c$ was confirmed by resequencing mutant allele and wild-type allele at B locus of several tomato lines. For allele discrimination and detection of $og^c$, derived CAPS (dCAPS) approach was used by designing a primer that artificially introduced restriction enzyme recognition site of Hin fI in PCR products from $og^c$ allele. This dCAPS marker is co-dominant gene-based PCR marker that can be efficiently used for MAS breeding program aiming the development of high lycopene tomato.

• Food Science of Animal Resources
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• v.32 no.6
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• pp.776-782
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• 2012

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.235-235
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• 2022

Genome selection is a promising tool for plant and animal breeding, which uses genome-wide molecular marker data to capture large and small effect quantitative trait loci and predict the genetic value of selection candidates. Genomic selection has been shown previously to have higher prediction accuracies than conventional marker-assisted selection (MAS) for quantitative traits. In this study, the prediction accuracy of 10 agricultural traits in the wheat core group with 567 points was compared. We used a cross-validation approach to train and validate prediction accuracy to evaluate the effects of training population size and training model.As for the prediction accuracy according to the model, the prediction accuracy of 0.4 or more was evaluated except for the SVN model among the 6 models (GBLUP, LASSO, BayseA, RKHS, SVN, RF) used in most all traits. For traits such as days to heading and days to maturity, the prediction accuracy was very high, over 0.8. As for the prediction accuracy according to the training group, the prediction accuracy increased as the number of training groups increased in all traits. It was confirmed that the prediction accuracy was different in the training population according to the genetic composition regardless of the number. All training models were verified through 5-fold cross-validation. To verify the prediction ability of the training population of the wheat core collection, we compared the actual phenotype and genomic estimated breeding value using 35 breeding population. In fact, out of 10 individuals with the fastest days to heading, 5 individuals were selected through genomic selection, and 6 individuals were selected through genomic selection out of the 10 individuals with the slowest days to heading. Therefore, we confirmed the possibility of selecting individuals according to traits with only the genotype for a shorter period of time through genomic selection.

• Proceedings of the Korean Society of Crop Science Conference
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• 2019.04a
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• pp.130-130
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• 2019