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Identification of Genetic Factors Controlling Capsaicinoid Content in Pepper (Capsicum spp.) : 고추의 캡사이시노이드 함량을 조절하는 유전인자 탐색
DC Field | Value | Language |
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dc.contributor.advisor | 강병철 | - |
dc.contributor.author | 한고은 | - |
dc.date.accessioned | 2018-05-28T16:36:40Z | - |
dc.date.available | 2021-09-23T06:57:04Z | - |
dc.date.issued | 2018-02 | - |
dc.identifier.other | 000000150525 | - |
dc.identifier.uri | https://hdl.handle.net/10371/140813 | - |
dc.description | 학위논문 (박사)-- 서울대학교 대학원 : 농업생명과학대학 식물생산과학부, 2018. 2. 강병철. | - |
dc.description.abstract | Peppers (Capsicum spp.) synthesize a pungent metabolite, capsaicinoid. Capsaicinoid biosynthesis pathway has been predicted based on primary and secondary metabolite synthesis pathway of other plants like Arabidopsis. From gene expression studies, multiple genes showed correlation with capsaicinoid content and designated as candidate genes controlling pungency. However, effects of the capsaicinoid biosynthetic genes for capsaicinoid content still unclear. In this study, we conducted two experiments to figure out the quantitative and qualitative genetic factors controlling the level of capsaicinoid in Capsicum.
To find the quantitative trait loci (QTL) controlling capsaicinoid content, two recombinant inbred lines (RILs) were used. Capsaicinoid content was evaluated from placental tissue, where capsaicinoid mostly synthesized and accumulated. Furthermore, high-density genetic map using single-nucleotide polymorphism (SNPs) from next-generation sequencing (NGS) based genotyping methods. Based on the C. annuum CM334 reference genome, we found five common QTL located on chromosome 1, 2, 3, 4, and 10 which were detected from both RIL populations. To identify the capsaicinoid biosynthetic genes located on QTL, physical location of QTL were compared with the genome-wide association study (GWAS) conducted from Capsicum core collection. A total of ten regions were commonly detected, and five genes involved in capsaicinoid biosynthesis pathway were proposed to regulate pungency level. Since non-pungent accessions has non-functional capsaicinoid biosynthetic gene, they were widely used to identify the genes. RIL and F2 population derived from a cross between non-pungent accession C. annuum YCM334 and pungent accession C. annuum Tean were used to find a novel locus controlling presence of capsaicinoid. High-density genetic map was constructed using genotyping-by-sequencing (GBS) method, and the novel locus designated as Pun3 was genetically mapped on chromosome 7. To find the candidate genes on the Pun3 locus, High-resolution melting (HRM) markers were designed and the locus was mapped between 192.2-193.1 Mbp and 199.3-200.1 Mbp on Zunla-1 and PI159236 reference genome, respectively. Additionally RNA-Seq of parental lines was performed in three developmental stages, and expressions of the genes in fatty-acid biosynthetic pathway were extremely reduced in non-pungent parent YCM334. Three genes including Capana07g001603, Capana07g001604, and Capana07g001614 showed significant difference in expression level. They were only expressed in pungent parent Tean, and all three genes were predicted to encode MYB transcription factors. One of the genes, Capana07g001604, was reported to be related with capsaicinoid level in previous research. Therefore, we proposed that one of the predicted MYB transcription factors will be the candidate gene for Pun3. Taken together, we identified capsaicinoid biosynthetic genes controlling capsaicinoid content and a transcription factor regulates presence of pungency. Although the exact function of genes should be validated in multiple accessions, this result could be helpful to understand the capsaicinoid biosynthetic pathway as well as understanding the genetic control and breeding of pungent pepper. | - |
dc.description.tableofcontents | GENERAL INTRODUCTION 1
CHAPTER I. QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum 11 ABSTRACT 12 INTRODUCTION 14 MATERIALS AND METHODS 18 Plant materials 18 Evaluation of capsaicinoid content 21 gDNA extraction and genotyping-by-sequencing 22 Reference-based SNP calling 22 Bin map construction for the RILs 23 QTL analysis for capsaicinoid content 24 Genome-wide association analyses for capsaicinoid content 24 Haplotype block estimation and candidate gene identification 25 RESULTS 26 Measurement of capsaicinoid content in the biparental populations 26 Bin map of biparental populations 32 QTL mapping for capsaicinoid content 38 Epistatic control of capsaicinoid content 44 SNPs and haplotype blocks of GWAS population 47 GWAS for capsaicinoid content 51 Candidate gene prediction for QTL controlling capsaicinoid content 53 DISCUSSION 58 Global comparison of QTL for capsaicinoid content 58 Candidate genes controlling capsaicinoid content 60 SNP detection by GBS for QTL study 63 REFERENCES 66 CHAPTER II. Identification of a novel locus controlling pungency in Capsicum 76 ABSTRACT 77 INTRODUCTION 79 MATERIALS AND METHODS 82 Plant materials and allelism test 82 Evaluation of pungency 72 Sequence and gene expression analysis of Pun1 83 gDNA extraction and genotyping-by-sequencing (GBS) 83 RNA-Seq of YCM334 and Tean 85 Genetic mapping of Pun3 86 RT-PCR and sequence analysis 86 RESULTS 88 Presence of pungency 88 Allelism test with pun1 and pun2 mutant accessions 90 Genetic mapping of Pun3 93 Fine-mapping of Pun3 96 RNA-Seq for candidate gene identification 101 Candidate gene prediction and sequence variation 105 DISCUSSION 111 Novel gene controlling pungency 111 Next-generation sequencing (NGS) based genetic mapping 112 MYB transcription factor regulates capsaicinoid 114 REFERENCES 117 ABTRACT IN KOREAN 125 | - |
dc.format | application/pdf | - |
dc.format.extent | 3414140 bytes | - |
dc.format.medium | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject | capsaicin | - |
dc.subject | dihydrocapsaicin | - |
dc.subject | pepper | - |
dc.subject | pungency | - |
dc.subject | QTL | - |
dc.subject | GBS | - |
dc.subject.ddc | 633 | - |
dc.title | Identification of Genetic Factors Controlling Capsaicinoid Content in Pepper (Capsicum spp.) | - |
dc.title.alternative | 고추의 캡사이시노이드 함량을 조절하는 유전인자 탐색 | - |
dc.type | Thesis | - |
dc.contributor.AlternativeAuthor | Koeun Han | - |
dc.description.degree | Doctor | - |
dc.contributor.affiliation | 농업생명과학대학 식물생산과학부 | - |
dc.date.awarded | 2018-02 | - |
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