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Natural Variation of the FLOWERING BHLH1 Contributes to Flowering Time Divergence in Rice
Min-Young Yoon,Aye Aye Khaing,Win Htet Oo,Tae-Sung Kim,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. The floral transition from vegetative to reproductive development is a very important step in the life cycle of a flowering plant. Although the genetic pathway for short-day flowering in rice is relatively well understood, the naturally occurring molecular mechanisms underlying flowering time diversity of the cultivated rice are still not clear. Resequencing of 295 rice accessions including 137 HS and 158 KB rice accessions, was recently finished with an average of approximately 10x depth and > 90% coverage. A wide range of variation in flowering time was observed within a diversity research set of 295 accessions ranging from 28 to 72 days. GWAS was performed using the resequencing data to investigate the candidate genes associated with flowering time in rice. Our GWAS result suggests that two SNPs in the promoter or 3’ UTR of the ‘Arabidopsis CO’ homolog FBH1 are potentially associated with early flowering. The new SNPs found in the FBH1 locus would be useful in developing markers to screen the varieties with early flowering time in the future molecular breeding.
Genome Wide Association Study on the Preharvest Sprouting Resistance in Rice
Aye Aye Khaing,Min-Young Yoon,Byung-Kook Yun,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Preharvest sprouting resistance (PHS) causes the reduction of grain yield and also affects the quality of grains, resulting significant economic losses. PHS and its related traits were evaluated and observed in wide range among the 137 diverse rice accessions. To mine the associated signals for PHS resistance, genome wide association study (GWAS) was performed using phenotype data and whole genome resequencing data of 137 diverse rice accessions. This study not only could detect the previously identified dormancy and PHS associated genes but also explore the new candidate genes associated with the PHS and related traits. An example of them is seed dormancy 4 (Sdr4) gene which was found to be associated with germination % at day 14 (D14). This study provided the potential associated candidate genes which might be very useful to improve the PHS resistance in future rice breeding.
Variation and haplotypes in LOX1, LOX2, and LOX3 genes related to the see longevity in rice
Sun-Kyung Min,Aye Aye Khaing,Win Htet Oo,Tae-Sung Kim,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Rice is the most important staple food crop of almost half of the world`s population. In rice, seed longevity is major factor for production and storage potential of seeds. But it is faced with grain degradation and loss of seed viability. Lipoxygenases(LOX) are a family of enzymes related to the seed longevity. LOX activity in rice grain is present in a bran-milling fraction. It is also observed that rice embryos contains three isozymes activites, Lox1, Lox2 and Lox3. Among those, the Lox3 isozyme is known as the major component in the embryonic tissue. In this study, genetic structure variability of three seed longevity related genes, Lox1, Lox2 and Lox3 were examined by using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels in the exon regions identified through haplotyping analysis would be useful to develop new varieties with improved storage ability of rice in the future molecular breeding.
Qiang He,Byung-Kook Yun,Min-Young Yoon,Xiao-Qiang Wang,Feng-Peng Li,Aye-Aye Khaing,Won-Hee Ra,Win Htet Oo,Cheol-Soon Park,Sun-Kyung Min,Wei Tong,Jie Yu,Bu-Woong Choi,Eun-Beom Heo,Khandakar Md.Rayhanul 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.
Genome-wide association studies approach and post-GWAS study in rice
Gang Li,Min-Young Yoon,Won-Hee Ra,Jae-Wan Park,Qiang He,Aye Aye Khaing,Xiao-Qiang Wang,Win Htet Oo,Feng-Peng Li,Byoung Kook Yun,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.
Learning Curve of ROSA ONE Spine System for Transpedicular Screw Placement
Bing-Hung Hsu,Heng-Wei Liu,Kha-Liang Lee,Ming-Chin Lin,Gao Chen,Jang Yu,Chiao-Ling Chen,I-Chang Su,Chien-Min Lin 대한척추신경외과학회 2022 Neurospine Vol.19 No.2
Objective: The study investigated our institutional learning curve for the ROSA ONE spine system (ROSA) based on ROSA usage time. Methods: ROSA was designed to provide high accuracy for spinal pedicle screw placement through a built-in tracking technique. This study was conducted from November 2018 to January 2021. The time taken to complete each step of the robotic workflow was recorded. Patient demographics, comorbidities, surgical indications, and number of screw placements were examined in subgroup analysis. The Curve Fitting-General package (a part of NCSS 2021 software) was used to fit a mathematical model to the learning curve. Patient demographics, imaging data, and surgical time were reviewed retrospectively. Results: A total of 167 patients who had undergone surgery were included. The mean total ROSA usage time was 107.1 ± 27.3 minutes. The estimated learning rate was 90.4%, and the largest slope change occurred close to the time of the 20th surgery. The observed overall learning trend in the 4-screw group could be attributed to screw planning. The presence of scoliosis (p = 0.73) or spondylolisthesis (p = 0.70) did not significantly influence the mean total time (TT) for all patients; however, the mean TT differed significantly (p < 0.01) among subgroups stratified by body mass index, screw number placement, and thoracic spine involvement. Conclusion: To the best of our knowledge, this is the first study to examine the learning curve for the various crucial steps of ROSA-guided pedicle screw placement. The indicative learning curve involved 20 patients who had undergone surgery.