High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing
Abstract Background Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map constr...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5291-8 |
| _version_ | 1819261792442908672 |
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| author | Li-Yi Xu Li-Yuan Wang Kang Wei Li-Qiang Tan Jing-Jing Su Hao Cheng |
| author_facet | Li-Yi Xu Li-Yuan Wang Kang Wei Li-Qiang Tan Jing-Jing Su Hao Cheng |
| author_sort | Li-Yi Xu |
| collection | DOAJ |
| description | Abstract Background Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map. Results A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation. Conclusions To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants. |
| first_indexed | 2024-12-23T19:47:26Z |
| format | Article |
| id | doaj.art-767695db3aed40fe8d90f4b820f5b71d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-23T19:47:26Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-767695db3aed40fe8d90f4b820f5b71d2022-12-21T17:33:30ZengBMCBMC Genomics1471-21642018-12-0119111110.1186/s12864-018-5291-8High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencingLi-Yi Xu0Li-Yuan Wang1Kang Wei2Li-Qiang Tan3Jing-Jing Su4Hao Cheng5National Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural SciencesNational Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural SciencesNational Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural SciencesCollege of Horticulture, Sichuan Agricultural UniversityNational Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural SciencesNational Centre for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural SciencesAbstract Background Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map. Results A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation. Conclusions To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.http://link.springer.com/article/10.1186/s12864-018-5291-8Genetic mapSNPQTL mapping2b-RAD sequencing |
| spellingShingle | Li-Yi Xu Li-Yuan Wang Kang Wei Li-Qiang Tan Jing-Jing Su Hao Cheng High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing BMC Genomics Genetic map SNP QTL mapping 2b-RAD sequencing |
| title | High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing |
| title_full | High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing |
| title_fullStr | High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing |
| title_full_unstemmed | High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing |
| title_short | High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing |
| title_sort | high density snp linkage map construction and qtl mapping for flavonoid related traits in a tea plant camellia sinensis using 2b rad sequencing |
| topic | Genetic map SNP QTL mapping 2b-RAD sequencing |
| url | http://link.springer.com/article/10.1186/s12864-018-5291-8 |
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