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Keumsun Kim,Hyunsuk Shin,Youngjae Oh,Sewon Oh,Jungyeon Won,Hyeondae Han,Yoon-Kyeong Kim,Seolah Kim,Sung-Il Oh,Mingi Lee,Daeil Kim 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
In this study, we sought to identify primary pears species and Korean native pears, without the use of morphological characteristics. In addition, this study was to establish pear DNA fingerprinting data for Korean native pears using 12 microsatellite markers, and to accurately classify a database for management of the Korean pear collection. Forty two pear accessions (7 primary pears, 5 Asian pears, 29 Korean pears, and 2 reference pears) were analyzed with twelve primers covering whole pear genome. In the present study, all pear accessions were successfully classified along with their pedigrees, and the distribution of primary pears was parallel to those of the previous taxonomic results. Korean pears were divided into 3 groups. Group I was characterized by Pyrus calleryana, and included Korean pea pears. Group II was characterized by P. pyrifolia, and was classified into 2 small groups. The first small group comprised of ‘Najucheongbae’, ‘Sunchanggulimdolbae’, ‘Andongmookbae’, ‘Andongdangsilri’, and ‘Najucheongbae’ and was presumed to be cultivars of P. pyrifolia. The second small group consisted of ‘Cheongdangrori’ and ‘Pyeongchangsuhyangri’. These two accessions were assumed to be a hybrid of P. pyrifolia and the other cultivar. Group III was characterized by P. ussuriensis. ‘Goesanhwangbae’, ‘Andongcheongsilri’, ‘Gongjucheongsilri’, and ‘Yecheoncheongbae’ were assumed to be cultivars of P. ussuriensis. Contrary to ‘Ulreungdocheongbae A’, ‘Ulreungdocheongbae B’ was classified as belonging to the P. ussuriensis group. It is possible that this is a consequence of, P. ussuriensis genes being transferred into ‘Ulreungdocheongbae B’. The result of this research reaffirmed the efficiency of a standard set of microsatellite markers and provides data, which will be useful for developing a core collection of pears.
Youngjae Oh,Seolah Kim,Hyunsuk Shin,Jungyeon Won,Sam-Seok Kang,Yoon-Kyeong Kim,Cheol Choi,Daeil Kim 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Single nucleotide polymorphisms (SNPs) are the most frequent type among variations found in genomic regions and are valuable markers for genetic mapping, genetic diversity studies and association mapping in plants. There are three basic species known as Korean native which are Pyrus ussuriensis, P. pyrifolia, and P. fauriei. Genetic relationship among Korean pear cultivars compared with their parents was identified that they are closely related P. pyrifolia, P. ussuriensis and/or hybrids between two species. Lack of genetic resources, including molecular markers to study pears are very severe. Recently developed next generation sequencing (NGS) platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objective of this study was to develop polymorphic SNP markers in ‘Whangkeumbae’ and ‘Minibae’, which were chosen as the representative cultivars of P. pyrifolia and P. ussuriensis × pyrifolia in each among Korean pears, using genomic sequences generated by NGS technology. In this study, more than 18.6 Gbp and 15.8 Gbp sequences were obtained from NGS of ‘Whangkeumbae’ and ‘Minibae’, respectively. ‘Whangkeumbae’ and ‘Minibae’ contained 2,712,288 and 2,747,224 SNPs, respectively. In SNPs validations between ‘Whangkeumbae’ and ‘Minibae’, the number of polymorphic SNPs were 2,516,438 and non-polymorphic SNPs were 1,179,391. For HRM primer design, 2,125,479 HRM candidate primers were obtained from polymorphic SNPs and 343,731 SNP primers were developed. This study shows that the utility of NGS technology to discover efficiently a large number of SNPs and SNP primers can provide valuable information in the genome study of Pyrus spp.
Youngjae Oh,Seolah Kim,Hyunsuk Shin,Jungyeon Won,Sam-Seok Kang,Yoon-Kyeong Kim,Daeil Kim 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Currently, the type of short insertions and deletions (InDels) polymorphisms are increasingly focused in genomic research. InDels have been known as a source of genetic markers that are widely spread across the genome. Genetic relationship among Korean pear cultivars compared with their parents was also identified that they are closely related P. pyrifolia, P. ussuriensis and/or hybrids between two species. Lack of genetic resources including molecular markers has made it difficult to study pears severely. Recently developed next generation sequencing (NGS) platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The main goal of this study was to develop polymorphic InDel markers in ‘Whangkeumbae’ and ‘Minibae’, which were chosen as the representative cultivars of P. pyrifolia and P. ussuriensis × pyrifolia in each among Korean pears using genomic sequences generated by NGS technology. In this study, more than 18.6 Gbp and 15.8 Gbp sequences were obtained from NGS of ‘Whangkeumbae’ and ‘Minibae’, respectively. ‘Whangkeumbae’ contained 197,210 InDels and 197,272 InDels in ‘Minibae’. In InDels validations between ‘Whangkeumbae’ and ‘Minibae’, the number of polymorphic InDels were 149,338 and non-polymorphic InDels were 122,572. For InDel primer set designing, 11,308 of primers were designed from polymorphic InDels and 10,919 of InDel primers were recommended. The study shows that the utility of NGS technology to design amount of efficient InDels and the developed InDel primers will be used for genetic mapping, breeding by marker assisted selection (MAS) and QTL mapping of Korea native pear as well as further genetic studies.
Availability of Novel Pear SSR Markers delivered from ‘Golden Delicious’ Apple Genomic Sequences
Jungyeon Won,Youngjae Oh,Seolah Kim,Hyunsuk Shin,Sewon Oh,Cheol Choi,Daeil Kim 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Korea is a origin of three basic species, P. ussuriensis, P. pyrifolia and P. fauriei. Genetic relationship among Korean pear cultivars compared with their parents were also identified that they are closely related P. pyrifolia, P. ussuriensis and/or hybrid between two species. SSRs or Microsatellites are co-dominant and typically neutral inheritance showing high degree of polymorphism, large number of alleles per locus, abundance in genomes, and suitability for automation. SSR markers were developed in apple and pear where they were used for construction of genetic linkage maps, evaluation of the genetic diversity, cultivar identification, genotype identification, and in the determination of genetic relatedness. Many apple (Malus × domestica Borkh.) SSRs would be useful for genetic mapping in European and Asian pears in previous experiments and cross-species amplification was observed between apple and pear. The objectives of this study were to develop polymorphic SSR markers in ‘Whangkeumbae’ and ‘Minibae’, which were chosen as the representative cultivars of P. pyrifolia and P. ussuriensis in each among Korean pears, from ‘Golden Delicious’ genomic sequences generated by next generation sequencing technology and to evaluate the utility of the SSR markers based on ‘Golden Delicious’ sequences. Of 51 SSR markers, 18 were polymorphic in ‘Whangkeumbae’ and ‘Minibae’. The cross-species transportability of primers designed in ‘Golden Delicious’ sequences makes SSR markers more useful, given the current high level of investment in mapping the genomes of related Rosaceae.
Kim Jong Mu,Yoo Min-Gyu,Bae Soon Jong,Kim Jungyeon,Lee Hyungmin 대한의학회 2023 Journal of Korean medical science Vol.38 No.27
Background: Paxlovid is an oral antiviral drug that received emergency use authorization in South Korea for the treatment of patients with mild-to-moderate coronavirus disease 2019 (COVID-19) on January 14, 2022. Since the onset of the severe acute respiratory syndrome coronavirus 2 pandemic, the virus has continued to evolve. The emergence of new variants has raised concerns about possible reductions in the effectiveness of vaccines and drugs. The effectiveness of Paxlovid in patients infected with the omicron variant and subvariants has not yet been determined. This study assessed the effectiveness of Paxlovid at reducing the risk of severe/critical illness or death and death in patients with mild-to-moderate COVID-19 caused by omicron subvariant BA.5. Methods: In this nationwide retrospective cohort study, data on 8,902,726 patients were collected from four sources (the Drug Utilization Review database, COVID-19 Patient Information Management System, confirmed patient information, and basic epidemiological investigation data) between July 1 and November 30, 2022. Multivariable logistic regression analysis was conducted, with adjustment for age, sex, severe acute respiratory syndrome coronavirus 2 immunity (vaccination), and comorbidities. Results: A total of 1,936,925 patients with COVID-19 were included in the analysis, including 420,996 patients treated with Paxlovid, and 1,515,959 patients not treated with Paxlovid. Paxlovid treatment in patients aged ≥ 60 years of age was associated with significantly reduced risk of severe/critical illness or death (46.0%), and death rate (32.5%), and its effectiveness was high, regardless of vaccination status. Conclusion: Paxlovid is effective at reducing the risk of death due to COVID-19 in patients with omicron BA.5 infection, especially in older patients, regardless of vaccination status. This suggests that older patients with COVID-19-related symptoms should be administered Paxlovid, regardless of their vaccination status, to reduce severity and risk of death.