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유희주(Hee-Ju Yu),박신기(Sin-Gi Park),오미진(Mijin Oh),황현주(Hyun-Ju Hwang),김남신(Namshin Kim),정희(Hee Chung),손성한(Seong-Han Sohn),박범석(Beom-Seok Park),문정환(Jeong-Hwan Mun) 한국원예학회 2011 원예과학기술지 Vol.29 No.6
Brassica rapa is an A genome model species for Brassica crop genetics, genomics, and breeding. With the completion of sequencing the B. rapa genome, functional analysis of the genome is forthcoming issue. The expressed sequence tags are fundamental resources supporting annotation and functional analysis of the genome including identification of tissue-specific genes and promoters. As of July 2011, 147,217 ESTs from 39 cDNA libraries of B. rapa are reported in the public database. However, little information can be retrieved from the sequences due to lack of organized databases. To leverage the sequence information and to maximize the use of publicly-available EST collections, the Brassica rapa tissue-specific EST database (BrTED) is developed. BrTED includes sequence information of 23,962 unigenes assembled by StackPack program. The unigene set is used as a query unit for various analyses such as BLAST against TAIR gene model, functional annotation using MIPS and UniProt, gene ontology analysis, and predict ion of tissue-specific unigene sets based on statistics test. The database is composed of two main units, EST sequence processing and information retrieving unit and tissue-specific expression profile analysis unit. Information and data in both units are tightly inter-connected to each other using a web based browsing system. RT-PCR evaluation of 29 selected unigene sets successfully amplified amplicons from the target tissues of B. rapa. BrTED provided here allows the user to identify and analyze the expression of genes of interest and aid efforts to interpret the B. rapa genome through functional genomics. In addition, it can be used as a public resource in providing reference information to study the genus Brassica and other closely related crop crucifer plants.
복숭아 NGS 분석에 의한 다형성 SSR 마커 개발과 활용
김정선(Jung Sun Kim),구윤숙(Yoon Suk Ku),박신기(Sin-Gi Park),김세희(Se Hee Kim),박현우(Hyun Woo Park),원소윤(So Youn Won) 한국육종학회 2021 한국육종학회지 Vol.53 No.4
Prunus persica “Mihong” cultivar is a domesticated white peach that was generated from the crossing between “Yumyeong” and“Chiyomaru” cultivars in the Republic of Korea in 1995. We launched “Mihong” genome sequencing in 2018 and “Mihong” reached to 200scaffold and 241 Mb sequences using long-read sequencing and Hi-C technology. F1 populations of ”Kawanakajima Hakuto,” “Mihong,”“Changhowon Hwangdo,” and “Yumi” were developed in NIHHS. These four cultivars were sequenced and assembled using the SOAPdenovoversion 2.04. First, we surveyed the SSRs in “Mihong” assembly sequences and extracted the ±300 bp flanking sequences containing SSRs. Second, the assembly sequences of three cultivars were aligned and mapped against “Mihong” ±300 bp flanking sequences using BLASTn(version 2.2.29+). We anticipated the differential length in SSRs among the four cultivars. We sorted the primers with a standard deviationover 4.5 (STEV > 4.5) among the four cultivars. In addition, we surveyed the primers having difference in over 10 bp with “KawanakajimaHakuto” and “Mihong” for polymorphic markers in the mapping population. All primer pairs were designed to generate amplicons of 150-200bp in coating SSR regions using primer3 (version 3-2.2.3). We selected 260 SSR markers with a physical distance of average per 1 Mb. These SSR markers accounted for 74% polymorphism in the four genotypes. Finally, a F1 population of “Kawanakajima Hakuto” and “Mihong”covered 884.5 cM with 465 SNPs and 86 SSRs and this genetic map matched correctly to the HI-C pseudomolecule of P. persica.