A platform for research: civil engineering, architecture and urbanism
A platform for research: civil engineering, architecture and urbanism
Construction of an SNP linkage map using genotyping-by-sequencing in Capsicum chinense
학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부 원예과학전공, 2016. 2. 강병철. ; Construction of linkage map is important for genetic studies and marker-assisted breeding programs. Recent advances in next-generation sequencing technologies allow the rapid and efficient generation of high-density linkage maps. In this study, we used a modified genotyping-by-sequencing (GBS) protocol involving two restriction enzymes (PstI-MseI). A total of 87 F2 individuals derived from a cross of C. chinense ‘Habanero’ and C. chinense ‘Jolokia’ were used to construct an SNP linkage map. To imputate missing data, a novel method combining sliding window and bin mapping was used to obtain reliable genotype data. A total of 1,000 bin markers selected from 217,152 SNPs were used for construction of a linkage map. The total genetic distance was about 3654.1 cM, and the average distance between bin markers was 3.9 cM. These bin markers were evenly distributed over 14 linkage groups, corresponding to 12 pepper chromosomes. This research shows that GBS together with the sliding window imputation method enabled us to rapidly develop a genetic map in an F2 generation. Using the linkage map, QTL mapping was performed for capsaicinoids content in the placenta and pericarp tissues. Also, we analyzed Pun1 expression to test whether capsaicinoids are synthesized in the pericarp. The results showed that only Jolokia showed Pun1 expression whereas Habanero and F1 hybrid showed no expression in pericarp. Distribution of capsaicinoids content in the pericarp of F2 plants also indicated that capsaicinoids might be regulated by a recessive gene(s). When QTL analysis was performed using the GBS linkage map and capsaicinoids content data, one QTL was identified for capsaicinoids in the placenta. Six QTLs were detected on chromosome 6 and 9 for capsaicinoids content in the pericarp. Bin markers linked to the two major QTLs will be used for selection plants containing high capsaicinoids content. ; INTRODUCTION 1 LITERATURE REVIEW 4 Linkage map 4 Genetic map in pepper 5 Single nucleotide polymorphism 6 Next-generation sequencing 6 Genotyping-by-sequencing 7 Sliding window and bin map 8 MATERIALS AND METHODS 9 Plant materials and DNA extraction 9 Library preparation and sequencing 9 Sequencing data processing and SNP calling 9 SNP dataset filtering and genotyping 10 Bin map and SNP linkage map construction 13 Alignment of linkage map to physical map 14 Isolation of RNA and cDNA synthesis 14 Expression analysis of Pun1 by semi-qPCR 15 Measurement of capsaicinoids content by HPLC analysis 15 QTL analysis 16 RESULTS 17 Genotyping by sequencing 17 Bin map construction 19 SNP linkage map construction 23 Relationship between linkage map and physical map 26 Measurement of capsaicinoids content in placenta and pericarp 30 QTL analysis for capsaicinoids content in placenta and pericarp 39 DISCUSSION 43 REFERENCES 47 ABSTRACT IN KOREAN 58 ; Master
Construction of an SNP linkage map using genotyping-by-sequencing in Capsicum chinense
학위논문 (석사)-- 서울대학교 대학원 : 식물생산과학부 원예과학전공, 2016. 2. 강병철. ; Construction of linkage map is important for genetic studies and marker-assisted breeding programs. Recent advances in next-generation sequencing technologies allow the rapid and efficient generation of high-density linkage maps. In this study, we used a modified genotyping-by-sequencing (GBS) protocol involving two restriction enzymes (PstI-MseI). A total of 87 F2 individuals derived from a cross of C. chinense ‘Habanero’ and C. chinense ‘Jolokia’ were used to construct an SNP linkage map. To imputate missing data, a novel method combining sliding window and bin mapping was used to obtain reliable genotype data. A total of 1,000 bin markers selected from 217,152 SNPs were used for construction of a linkage map. The total genetic distance was about 3654.1 cM, and the average distance between bin markers was 3.9 cM. These bin markers were evenly distributed over 14 linkage groups, corresponding to 12 pepper chromosomes. This research shows that GBS together with the sliding window imputation method enabled us to rapidly develop a genetic map in an F2 generation. Using the linkage map, QTL mapping was performed for capsaicinoids content in the placenta and pericarp tissues. Also, we analyzed Pun1 expression to test whether capsaicinoids are synthesized in the pericarp. The results showed that only Jolokia showed Pun1 expression whereas Habanero and F1 hybrid showed no expression in pericarp. Distribution of capsaicinoids content in the pericarp of F2 plants also indicated that capsaicinoids might be regulated by a recessive gene(s). When QTL analysis was performed using the GBS linkage map and capsaicinoids content data, one QTL was identified for capsaicinoids in the placenta. Six QTLs were detected on chromosome 6 and 9 for capsaicinoids content in the pericarp. Bin markers linked to the two major QTLs will be used for selection plants containing high capsaicinoids content. ; INTRODUCTION 1 LITERATURE REVIEW 4 Linkage map 4 Genetic map in pepper 5 Single nucleotide polymorphism 6 Next-generation sequencing 6 Genotyping-by-sequencing 7 Sliding window and bin map 8 MATERIALS AND METHODS 9 Plant materials and DNA extraction 9 Library preparation and sequencing 9 Sequencing data processing and SNP calling 9 SNP dataset filtering and genotyping 10 Bin map and SNP linkage map construction 13 Alignment of linkage map to physical map 14 Isolation of RNA and cDNA synthesis 14 Expression analysis of Pun1 by semi-qPCR 15 Measurement of capsaicinoids content by HPLC analysis 15 QTL analysis 16 RESULTS 17 Genotyping by sequencing 17 Bin map construction 19 SNP linkage map construction 23 Relationship between linkage map and physical map 26 Measurement of capsaicinoids content in placenta and pericarp 30 QTL analysis for capsaicinoids content in placenta and pericarp 39 DISCUSSION 43 REFERENCES 47 ABSTRACT IN KOREAN 58 ; Master
Construction of an SNP linkage map using genotyping-by-sequencing in Capsicum chinense
한지웅 (author) / 강병철 / 농업생명과학대학 식물생산과학부(원예과학전공)
2016-01-01
Theses
Electronic Resource
English
DDC:
690
Genotyping by sequencing in almond: SNP discovery, linkage mapping, and marker design
| BASE | 2018
Identification of Commercial Cultivars in the Tabebuia Alliance Using Genotyping-by-Sequencing
| DOAJ | 2023