High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing
Abstract Background Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high...
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3712-8 |
| _version_ | 1819079480872796160 |
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| author | Aifen Tao Long Huang Guifen Wu Reza Keshavarz Afshar Jianmin Qi Jiantang Xu Pingping Fang Lihui Lin Liwu Zhang Peiqing Lin |
| author_facet | Aifen Tao Long Huang Guifen Wu Reza Keshavarz Afshar Jianmin Qi Jiantang Xu Pingping Fang Lihui Lin Liwu Zhang Peiqing Lin |
| author_sort | Aifen Tao |
| collection | DOAJ |
| description | Abstract Background Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. Results An F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance. Conclusions To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute. |
| first_indexed | 2024-12-21T19:29:40Z |
| format | Article |
| id | doaj.art-47898d7c1f324f29a904c3a5922d2432 |
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| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T19:29:40Z |
| publishDate | 2017-05-01 |
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| spelling | doaj.art-47898d7c1f324f29a904c3a5922d24322022-12-21T18:52:45ZengBMCBMC Genomics1471-21642017-05-0118111210.1186/s12864-017-3712-8High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencingAifen Tao0Long Huang1Guifen Wu2Reza Keshavarz Afshar3Jianmin Qi4Jiantang Xu5Pingping Fang6Lihui Lin7Liwu Zhang8Peiqing Lin9Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityBiomarker Technologies CorporationGuangxi UniversityEastern Agricultural Research Center, Montana State UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Key Laboratory of Crops by Design, Fujian Agriculture and Forestry UniversityAbstract Background Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. Results An F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance. Conclusions To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.http://link.springer.com/article/10.1186/s12864-017-3712-8Corchorus capsularis LSLAFGenetic mapQTLPlant height |
| spellingShingle | Aifen Tao Long Huang Guifen Wu Reza Keshavarz Afshar Jianmin Qi Jiantang Xu Pingping Fang Lihui Lin Liwu Zhang Peiqing Lin High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing BMC Genomics Corchorus capsularis L SLAF Genetic map QTL Plant height |
| title | High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing |
| title_full | High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing |
| title_fullStr | High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing |
| title_full_unstemmed | High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing |
| title_short | High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing |
| title_sort | high density genetic map construction and qtls identification for plant height in white jute corchorus capsularis l using specific locus amplified fragment slaf sequencing |
| topic | Corchorus capsularis L SLAF Genetic map QTL Plant height |
| url | http://link.springer.com/article/10.1186/s12864-017-3712-8 |
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