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수박 덩굴마름병 저항성 판별을 위한 SNP 표지인자 탐색
이혜은,홍종필,서혜영,허윤찬,안율균,김진희,김도선 忠北大學校 農業科學硏究所 2015 農業科學硏究 Vol.31 No.2
:Watermelon (Citrullus lanatus) is an important vegetable crop in the world and contains various health promoting compounds including many antioxidants such as lycopene and beta-carotene. Genetic diversity of cultivated watermelon is very narrow, which is one of major factors limiting the improvement of watermelon breeding program. Gummy stem blight (Didymella bryoniae (Auersw.)) is one of the most destructive diseases and causes crown blight, defoliation and fruit rot, resulting in severe production loss in watermelon. Single nucleotide polymorphisms (SNPs), important molecular markers for genetic studies are frequent sequence variation in the plant genome. This study was performed to develop SNP markers related to gummy stem blight resistance from three watermelon lines, one susceptible and two resistant to gummy stem blight. Of them, 22 SNP primers which were sequence information on SNPs derived from comparing a resistant and susceptible line was used for high resolution melt analysis. A total of 14 candidate SNP primers were detected melt temperature difference. These SNP primers can be useful for developing disease resistance-related markers and, therefore, beneficial to watermelon breeding program.
Ahn, Yul-Kyun,Cho, Young-Il,Tripathi, Swati,Kim, Do-Sun,Kim, Jeong-Ho,Lee, Hye-Eun Cambridge University Press 2014 Plant genetic resources Vol.12 No.1
<P>Based on the sequences of <I>Brassica rapa</I> ssp. <I>pekinensis</I>, we carried out a single-nucleotide polymorphism (SNP) study for genes controlling disease resistance (clubroot, turnip mosaic virus and soft rot) and leaf traits in <I>B. rapa</I> leafy genotypes ‘<I>VC40</I>’ and ‘<I>SR5</I>’. In total, 7645 SNP markers were obtained based on the annotation of a <I>B. rapa</I> database for disease resistance. Among these 7645 SNP markers, 141 were related to 125 genes linked to leaf traits. From these 141 SNP markers, 63 were screened and High Resolution Melt (HRM) primers were designed for genomic studies. A total of 20 polymorphic SNP primers were finally obtained. Eventually, these markers will be further used for the detection of quantitative trait loci and mapping studies.</P>
Ahn, Yul-Kyun,Karna, Sandeep,Kim, Jeong-Ho,Lee, Hye-Eun,Kim, Jin-Hee,Kim, Do-Sun The Korean Society of Plant Biotechnology 2016 식물생명공학회지 Vol.43 No.3
The efficacy of plant breeding has been enhanced by application of molecular markers in population screening and selection. Pepper (Capsicum annuum L.) is a major staple crop that is economically important with worldwide distribution. It is valued for its spicy taste and medicinal effect. The aim of this study was to discover single nucleotide polymorphisms (SNPs), microsatellite markers information, and percentage sharing through orthologous analysis of pepper-specific pungency-related genes. Here, we report the results of transcriptome analysis and microsatellite markers for four pepper varieties that possess a pungency-related gene. Orthologous analyses was performed to identify species-specific pungency-related genes in pepper, Arabidopsis thaliana L., potato (Solanum tuberosum L.), and tomato (Solanum lycopersicum L.). Advancements in next-generation sequencing technologies enabled us to quickly and cost-effectively assemble and characterize genes to select molecular markers in various organisms, including pepper. We identified a total of 9762, 7302, 8596, and 6886 SNPs for the four pepper cultivars Blackcluster, Mandarine, Saengryeg 211, and Saengryeg 213, respectively. We used 454 GS-FLX pyrosequencing to identify microsatellite markers and tri-nucleotide repeats (54.4%), the most common repeats, followed by di-, hexa-, tetra-, and penta-nucleotide repeats. A total of 5156 (15.9%) pepper-specific pungency-related genes were discovered as a result of orthologous analysis.
Ahn, Yul-Kyun,Tripathi, Swati,Cho, Young-Il,Kim, Jeong-Ho,Lee, Hye-Eun,Kim, Do-Sun,Woo, Jong-Gyu Cambridge University Press 2014 Plant genetic resources Vol.12 No.1
<P>Next-generation sequencing technique has been known as a useful tool for <I>de novo</I> transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from <I>de novo</I> assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.</P>