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The Establishment of a Standard SSR System Fitting for Pear Germplasm Management
Seolah Kim,Youngjae Oh,Hyunsuk Shin,Hyoundae Han,Yoon-Kyeong,Kim, Nahla Bassil,Daeil Kim 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Pear (Pyrus spp.) is one of the most important temperate fruit species in the world. The identification of Pyrus spp. based on analysis and comparison of their phenotypes has been causing a number of synonyms and homonyms among Pyrus spp. For accurate identification, genotype analysis with molecular marker such as microsatellite is necessarily to use. However, It is difficult to share and compare of microsatellite profiles obtained among different laboratories because no effort has made to standardize equipment or protocols. A strategy for data comparison by dint of reference to the alleles detected in well-known cultivars will be helpful for co-work with laboratories and developing international databases. Thus the study was performed to compare results between laboratories of microsatellite DNA profiling for reproducibility and standardize allele scoring by defining reference alleles efficiently. In this study, ninety pear species including forty-four comparison Asian pears, six of comparison suspicious Asian pears and reference pears, seven basic pear species, and twenty-seven Korean native pear cultivars to development of a standard set of SSR reference alleles. Twelve primers covering most of pear genome were chosen, which are CH02b10, CH03g07, CH04e03, CH03d12, EMPc117, CH01f07a, EMPc11, CH01d09, GD147, CH01d08, CH05c06, and GD96 located in pear chromosome of 2, 3, 5, 6, 7, 10, 11, 12, 13, 15, 16, and 17 respectively. Genotyping was conducted with Fragment Analyzer. After genotyping, a set of defined standard alleles based on reference pear cultivars can facilitate data comparison among laboratories and will permit the improvement of a common international database.
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,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.