• Journal of Plant Biotechnology
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• v.47 no.3
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• pp.209-217
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• 2020

The presence of high amounts of seed storage proteins (SSPs) improves the overall quality of soybean seeds. However, these SSPs pose a major limitation due to their high abundance in soybean seeds. Although various technical advancements including mass-spectrometry and bioinformatics resources were reported, only limited information has been derived to date on soybean seeds at proteome level. Here, we applied a tandem mass tags (TMT)-based quantitative proteomic analysis to identify the significantly modulated proteins in the seeds of two soybean cultivars showing varying protein contents. This approach led to the identification of 5,678 proteins of which 13 and 1,133 proteins showed significant changes in Daewon (low-protein content cultivar) and Saedanbaek (high-protein content cultivar) respectively. Functional annotation revealed that proteins with increased abundance in Saedanbaek were mainly associated with the amino acid and protein metabolism involved in protein synthesis, folding, targeting, and degradation. Taken together, the results presented here provide a pipeline for soybean seed proteome analysis and contribute a better understanding of proteomic changes that may lead to alteration in the protein contents in soybean seeds.

• The Plant Pathology Journal
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• v.36 no.2
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• pp.111-120
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• 2020

Powdery mildew of Indian mustard (Brassica juncea), caused by Erysiphe cruciferarum, is emerging as major problem in India. All the Indian mustard cultivars presently grown in India are highly susceptible to powdery mildew and so far no resistance source has been reported. In this study, with an aim to identify resistant source, 1,020 Indian mustard accessions were evaluated against E. cruciferarum PMN isolate, at Wellington, The Nilgiris, Tamil Nadu, India under natural hot spot conditions. The study identified one accession (RDV 29) with complete resistance against E. cruciferarum PMN isolate for the first time, which was consistent in five independent evaluations. Genetic analysis of F₁, F₂ and backcross populations obtained from the cross RSEJ 775 (highly susceptible) × RDV 29 (highly resistant) for two season revealed that the resistance is governed by two genes with semi-dominant and gene dosage effect. Further, a new disease rating system using six scales (0, 1, 2, 3, 4, and 5) has also been proposed in this study to score powdery mildew based on progress of fungal growth in different plant parts of the F₂ population. The outcome of this study viz. newly identified powdery mildew-resistant Indian mustard accession (RDV 29), information on inheritance of resistance and the newly developed disease rating scale will provide the base for development of powdery mildew-resistant cultivars of Indian mustard.

• Korean Journal of Plant Resources
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• v.35 no.6
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• pp.785-795
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• 2022

Traditional germplasms are unsuitable for mechanized production, limiting adzuki bean production. The creation of cultivars that can be harvested by mechanized means is an urgent task for breeders. The bottom pod height (BPH), lodging resistance, and synchronous maturing of adzuki beans are critical factors for the reduction of losses due to mechanized harvesting. In this study, 14 traits of 806 adzuki bean accessions were analyzed. All growth stages and the yield, lodging score, and synchronous maturing correlated negatively with the BPH. These negative correlations reflect the increased difficulty of breeding to simultaneously satisfy the needs for no lodging, high synchronous maturing rates, BPHs > 10 cm, and high yield. We screened three germplasms with no lodging, high synchronous maturing rates, and BPHs > 10 cm that were used as mechanization-adapted breeding material for crossing with high-yield cultivars. Agronomic trait diversity in adzuki beans was also examined in this study. Principal component and cluster analyses were conducted for 806 germplasms resulting in three clusters with the yield and three growth stage traits serving as the main discriminating factors. Cluster 1 included high-yield germplasms with the number of pods per plant and the number of seeds per pod being the major discriminant factors. Cluster 2 included germplasms with long growth periods and large 100-seed weights while cluster 3 contained germplasms with high BPHs. In general, the characteristics that make mechanical harvesting feasible and those assessed in this study could be utilized to choose and enhance adzuki beans production.

• Molecules and Cells
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• v.37 no.2
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• Horticultural Science & Technology
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• v.29 no.1
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• pp.53-60
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• 2011

Cytoplasmic male sterility (CMS) induced by mutant mitochondria genome, has been used for commercial seed production of $F_1$ hybrid cultivars in diverse crops. In pepper (Capsicum annuum L.), two sterile cytoplasm specific gene organization, atp6-2 and coxII were identified. An open reading frame, orf456 nearby coxII gene has been speculated to induce male sterility (MS) by mutagenic analysis. Moreover, molecular markers for atp6-2 and coxII of mitochondrial genotype (mitotype) were developed. However, the Cytoplasmic MS specific markers, atp6SCAR and coxIISCAR markers appeared in both N and S cytoplasms when polymerase chain reaction (PCR) cycles prolonged more than 40 cycles. Since the reported molecular markers were dominant markers, the presence of the faint sterile-specific band in normal cytoplasm may lead to the mis-classification of pepper breeding lines. To solve this problem, one common forward primer and two different reverse primers specific to normal coxII and sterile orf456 genes were designed after analyzing their gene organizations. By using these three primers, N and S coxII specific bands were co-amplified in male-sterile lines, but only normal coxII specific band was amplified in maintainer lines. Since the reverse primer for sterile coxII was specifically designed 275 bp downstream of orf456, relatively stable PCR amplification patterns were observed regardless of the number of PCR cycles. These primer sets easily identified different mitotypes among the divergent breeding lines, commercial cultivars and diverse germplasms.

• Korean Journal of Agricultural Science
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• v.38 no.2
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• pp.285-294
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• 2011

Glucosinolate (GSL) contents were investigated (i) at 1~7 days after sowing (DAS) in seed sprouts and (ii) at 3-7 weeks after sowing for the time-course. Moreover, (iii) They were compared with five different cultivars of rocket salad (Eruca sativa). Seventeen GSLs were separated by HPLC analysis, and 10 GSLs among them were identified as glucoraphanin, sinigrin, glucoalyssin, diglucothiobeinin, glucobrassicanapin, glucoerucin, glucobrassicin, dimeric, 4-mercaptobutyl GSL, 4-methoxy glucobrassicin, gluconasturttin by using LC-APCI-MS analysis, but 7 compounds were not identified. (i) The total GSL content in seed sprouts initially increased up to 3 DAS and then decreased according to their seedling growth. In particular, glucoraphanin known as a strong anti-cancer reagent was found the highest level (5.05 ${\mu}mol/g$ dry wt.) at 3 DAS. The most abundant GSL was glucoerucin ranged from 26.0~49.6 ${\mu}mol/g$ dry wt. (ii) In the time-course, the total GSL contents increased dramatically from 3-week (5.91 ${\mu}mol/g$ dry wt.) to 7-week after sowing (32.2 ${\mu}mol/g$ dry wt.). The major GSLs were glucoraphanin, glucoerucin and 4-methoxy glucobrassicin. (iii) By comparing GSL contents with five different cultivars, the total GSL contents increased from 4-week to 6-week after sowing, regardless of cultivar. In 4-week-old, the order with the total GSL content was "Rucola" > "Rocket Herbs" ${\geqq}$ "Odyssey" > "Takii" > "Herb", but in 6-week-old it is changed as "Takii" > "Herb" > "Odyssey" > "Rucola" > "Rocket Herbs" even there was almost no significantly difference between them.

• Journal of Ginseng Research
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• v.33 no.1
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• pp.55-58
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• 2009

Generally, the direct sequencing through PCR is faster, easier, cheaper, and more practical than clone sequencing. Frequently, standard PCR amplification is usually interpreted by mispriming internal or external regions of the target template. Normally, DNA fragments were eluted from the gel using Gel extraction kit and subjected to direct sequencing or cloning sequencing. Cloning sequencing has often troublesome and needs more time to analyze for many samples. Since touchdown (TD) PCR can generate sufficient and highly specific amplification, it reduces unwanted amplicon generation. Accordingly, TD PCR is a good method for direct sequencing due to amplifying wanted fragment. In plants the 5S-rRNA gene is separated by simple spacers. The 5S-rRNA gene sequence is very well-conserved between plant species while the spacer is species-specific. Therefore, the sequence has been used for phylogenetic studies and species identification. But frequent occurrences of spurious bands caused by complex genomes are encountered in the product spectrum of standard PCR amplification. In conclusion, the TD PCR method can be applied easily to amplify main 5S-rRNA and direct sequencing of panax ginseng cultivars.

• Molecules and Cells
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• v.20 no.3
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• pp.416-422
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• 2005

We previously used Southern blot analysis to detect restriction-length polymorphisms between male fertile and cytoplasmic male sterile (CMS) cytoplasms at the coxII and atp6 loci of the mtDNA of Capsicum annuum L. Two copies of atp6 were found in each male fertile and CMS pepper lines. Interestingly, one of the copies of atp6 in CMS pepper was a 3'-truncated pseudogene. The open reading frame of the coxII gene was the same in the fertile (N-) and CMS (S-) lines. However, the nucleotide sequence in the S-cytoplasm diverged from that in the N-cytoplasm 41 bp downstream of the stop codon. To develop CMS-specific sequence-characterized amplified region (SCAR) markers, inverse PCR was performed to characterize the nucleotide sequences of the 5' and 3' flanking regions of mitochondrial atp6 and coxII from the cytoplasms of male fertile (N-) and CMS (S-) pepper plants. Based on these data, two CMS-specific SCAR markers, 607 and 708 bp long, were developed to distinguish N-cytoplasm from S-cytoplasm by PCR. The CMS-specific PCR bands were verified for 20 cultivars containing either N- or S-cytoplasm. PCR amplification of CMS-specific mitochondrial nucleotide sequences will allow quick and reliable identification of the cytoplasmic types of individual plants at the seedling stage, and assessment of the purity of $F_1$ seed lots. The strategy used in this report for identifying CMS-specific markers could be adopted for many other crops where CMS is used for F1 seed production.

• The Plant Pathology Journal
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• v.21 no.1
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• pp.47-54
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• 2005

Identification of host genes involved in disease progresses and/or defense responses is one of the most critical steps leading to the elucidation of disease resistance mechanisms in plants. Soybean mosaic virus (SMV) is one of the most prevalent pathogen of soybean (Glycine max). Although the soybeans are placed one of many important crops, relatively little is known about defense mechanism. In order to obtain host genes involved in SMV disease progress and host defense especially for virus resistance, two different cloning strategies (DD RT-PCR and Subtractive hybridization) were employed to identify pathogenesis- and defenserelated genes (PRs and DRs) from susceptible (Geumjeong 1) and resistant (Geumjeong 2) cultivars against SMV strain G7H. Using these approaches, we obtained 570 genes that expressed differentially during SMV infection processes. Based upon sequence analyses, differentially expressed host genes were classified into five groups, i.e. metabolism, genetic information processing, environmental information processing, cellular processes and unclassified group. A total of 11 differentially expressed genes including protein kinase, transcription factor, other potential signaling components and resistant-like gene involved in host defense response were selected to further characterize and determine expression profiles of each selected gene. Functional characterization of these genes will likely facilitate the elucidation of defense signal transduction and biological function in SMV-infected soybean plants.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.27 no.4
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• pp.371-384
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• 1982

Highly cold tolerant varieties are requested not only at high latitute cool area but also tropical high elevated areas, and the required tolerance is different from location to location. IRRI identified 6 different types of cold tolerance required in the world for breeding purpose; a) Hokkaido type, b) Suweon type, c) Taipei 1st season type, d) Taipei 2nd season type, e) Tropical alpine type and, f) Bangladesh type. The cold tolerance requested in Korea is more eargent in Tongil group cultivars and their required tolerance is the one such as the physiological activities at low temperature are as active as in Japonica group cultivars at least during young seedling stage and reproduction stage. With conventional Japonica cultivars, such cold tolerant characters are requested as short growth duration but stable basic vegetative growth, less sensitive to high temperature and less prolonged growth duration at low temperature. The methods screening for cold tolerance were developed rapidly after the Tongil cultivar was reliesed. The facilities of screening for cold tolerance, such as, low temperature incubator, cold water tank, growth cabinet, phytotron, cold water nursery in Chuncheon, breeding nursery located in Jinbu, Unbong and Youngduk, are well established. Foreign facilities such as, cold water tank with the rapid generation advancement facilities, cold nurseries located in Banaue, Kathmandu and Kashimir may be available for the screening of some limitted breeding materials. For the reference, screening methods applied at different growth stages in Japan are introduced. The component characters of cold tolerance are not well identified, but the varietal differences in a) germinability, b) young seedling growth, c) rooting, d) tillering, e) discolation, f) nutrition uptake, g) photosynthesis rate, h) delay in heading, i) pollen sterility, and j) grain fertility at low temperature are reported to be distinguishable. Relationships among those traits are not consistent. Reported studies on the inheritance of cold tolerance are summarized. Four or more genes are controlling low temperature germinability, one or several genes are controlling seedling tolerance, and four or more genes are responsible for the pollen fertility of the rice treated with cold air or grown in the cold water nursery. But most of those data indicate that the results may come out in different way if those were tested at different temperature. Many cold tolerant parents among Japonicas, Indicas and Javanicas were identified as the results of the improvement of cold tolerance screening techniques and IRTP efforts and they are ready to be utilized. Considering a) diversification of germ plasm, b) integration of resistances to diseases and insects, c) identification of adaptability of recommending cultivars and, d) systematic control of recommending cultivars, breeding strategies for short term and long term are suggested. For short term, efforts will be concentrated mainly to the conventional cultivar group. Domestic cultivars will be used as foundation stock and ecologically different foreign introductions such as from Hokkaido, China or from Taiwan, will be used as cross parents for the adjustment of growth durations and synthsize the prototype of tolerances. While at the other side, extreme early waxy Japonicas will be crossed with the Indica parents which are identified for their resistances to the diseases and insects. Through the back corsses to waxy Japonicas, those Indica resistances will be transfered to the Japonicas and these will be utilized to the crosses for the improvement of resistances of prototype. For the long term, efforts will be payed to synthsize all the available tolerances identified any from Japonicas, Indicas and Javanicas to diversify the germ plasm. The tolerant cultivars newly synthsized, should be stable and affected minimum. to the low temperature at all the growing stages. The resistances to the diseases and insects should be integrated also. The rapid generation advancement, pollen culture and international cooperations were emphasized to maximize the breeding efficiency.