Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.)
Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SN...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01102/full |
| _version_ | 1818853604140777472 |
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| author | Chengming Sun Benqi Wang Lei Yan Kaining Hu Sheng Liu Yongming Zhou Chunyun Guan Zhenqian Zhang Jiana Li Jiefu Zhang Song Chen Jing Wen Chaozhi Ma Jinxing Tu Jinxiong Shen Tingdong Fu Bin Yi |
| author_facet | Chengming Sun Benqi Wang Lei Yan Kaining Hu Sheng Liu Yongming Zhou Chunyun Guan Zhenqian Zhang Jiana Li Jiefu Zhang Song Chen Jing Wen Chaozhi Ma Jinxing Tu Jinxiong Shen Tingdong Fu Bin Yi |
| author_sort | Chengming Sun |
| collection | DOAJ |
| description | Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10-5), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up- and downstream of 65 loci (r2 > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding. |
| first_indexed | 2024-12-19T07:39:27Z |
| format | Article |
| id | doaj.art-8b9f0ab559784437b616ec12a05e1e2a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-19T07:39:27Z |
| publishDate | 2016-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-8b9f0ab559784437b616ec12a05e1e2a2022-12-21T20:30:29ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-07-01710.3389/fpls.2016.01102208578Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.)Chengming Sun0Benqi Wang1Lei Yan2Kaining Hu3Sheng Liu4Yongming Zhou5Chunyun Guan6Zhenqian Zhang7Jiana Li8Jiefu Zhang9Song Chen10Jing Wen11Chaozhi Ma12Jinxing Tu13Jinxiong Shen14Tingdong Fu15Bin Yi16Huazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHunan Agricultural UniversityHunan Agricultural UniversitySouthwest UniversityJiangsu Academy of Agricultural ScienceJiangsu Academy of Agricultural ScienceHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityHuazhong Agricultural UniversityPlant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10-5), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up- and downstream of 65 loci (r2 > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01102/fullBrassica napusAssociation mappingPlant heightselective sweephaplotype block |
| spellingShingle | Chengming Sun Benqi Wang Lei Yan Kaining Hu Sheng Liu Yongming Zhou Chunyun Guan Zhenqian Zhang Jiana Li Jiefu Zhang Song Chen Jing Wen Chaozhi Ma Jinxing Tu Jinxiong Shen Tingdong Fu Bin Yi Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) Frontiers in Plant Science Brassica napus Association mapping Plant height selective sweep haplotype block |
| title | Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) |
| title_full | Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) |
| title_fullStr | Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) |
| title_full_unstemmed | Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) |
| title_short | Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.) |
| title_sort | genome wide association study provides insight into the genetic control of plant height in rapeseed brassica napus l |
| topic | Brassica napus Association mapping Plant height selective sweep haplotype block |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01102/full |
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