Publications
Detailed Information
Single Nucleotide Polymorphism Marker Discovery by Transcriptome Sequencing in Capsicum
DC Field | Value | Language |
---|---|---|
dc.contributor.advisor | 강병철 | - |
dc.contributor.author | 최필립 | - |
dc.date.accessioned | 2017-07-14T06:31:04Z | - |
dc.date.available | 2017-07-14T06:31:04Z | - |
dc.date.issued | 2014-08 | - |
dc.identifier.other | 000000021818 | - |
dc.identifier.uri | https://hdl.handle.net/10371/125662 | - |
dc.description | 학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부(원예과학전공), 2014. 8. 강병철. | - |
dc.description.abstract | Backcross breeding is the method most commonly used to introgress new traits into elite lines. Conventional backcross breeding requires at least 4-5 generations to recover the genomic background of the recurrent parent. Marker-assisted backcrossing (MABC) represents a new breeding approach that can substantially reduce breeding time and cost. For successful MABC, highly polymorphic markers with known positions in each chromosome are essential. Single nucleotide polymorphism (SNP) markers have many advantages over other marker systems for MABC due to their high abundance and amenability to genotyping automation. To facilitate MABC in hot pepper (Capsicum annuum), we utilized expressed sequence tags (ESTs) to develop SNP markers in this study. For SNP identification, we used Bukang F1-hybrid pepper ESTs to prepare a reference sequence through de novo assembly. We performed large-scale transcriptome sequencing of eight accessions using the Illumina Genome Analyzer (IGA) IIx platform by Solexa, which generated small sequence fragments of about 90-100 bp. By aligning each contig to the reference sequence, 58,151 SNPs were identified. After filtering for polymorphism, segregation ratio, and lack of proximity to other SNPS or exon/intron boundaries, a total of 1,910 putative SNPs were chosen and positioned to a pepper linkage map. We further selected 412 SNPs evenly distributed on each chromosome and primers were designed for high throughput SNP assays and tested using a genetic diversity panel of 27 Capsicum accessions. The SNP markers clearly distinguished each accession. These results suggest that the SNP marker set developed in this study will be valuable for MABC, genetic mapping, and comparative genome analysis. | - |
dc.description.tableofcontents | ABSTRACT
CONTENTS LIST OF TABLES LIST OF FIGURES LIST OF ABBREVIATIONS INTRODUCTION LITERATURE REVIEWS Molecular marker Developments in the past Use of molecular marker in Capsicum SNP marker discovery EST-derived marker discovery SNP discovery in other crops by using ESTs Sequencing technology development LITERATURE CITED MATERIALS AND METHODS Plant material preparation for eight accessions RNA extraction for each sample Sequencing of transcriptomes for eight accessions Quality trimming for sequences Reference sequence preparation Repeat Masking on the reference sequence Alignment to the reference sequence SNP calling and filtering Linkage mapping Polymorphism survey and genetic diversity RESULTS Sequencing of hot pepper accessions and quality trimming Alignment of each accession to the reference sequence SNP discovering and SNP filtering Development and validation of SNP markers DISCUSSION REFERENCES ABSTRACT IN KOREAN | - |
dc.format | application/pdf | - |
dc.format.extent | 1162790 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject | Capsicum annuum | - |
dc.subject | expressed sequence tag | - |
dc.subject | linkage map | - |
dc.subject | marker-assisted breeding | - |
dc.subject | single mucleotide polymorphism | - |
dc.subject | next generation sequence | - |
dc.subject.ddc | 635 | - |
dc.title | Single Nucleotide Polymorphism Marker Discovery by Transcriptome Sequencing in Capsicum | - |
dc.type | Thesis | - |
dc.contributor.AlternativeAuthor | Phillip Choe | - |
dc.description.degree | Master | - |
dc.citation.pages | x, 92 | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부(원예과학전공) | - |
dc.date.awarded | 2014-08 | - |
- Appears in Collections:
- Files in This Item:
Item View & Download Count
Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.