Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)
Abstract Background Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results To...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-08-01
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| Series: | Biotechnology for Biofuels |
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| Online Access: | http://link.springer.com/article/10.1186/s13068-020-01774-0 |
| _version_ | 1818263731587514368 |
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| author | Tengyue Wang Lijuan Wei Jia Wang Ling Xie Yang Yang Li Shuyao Ran Lanyang Ren Kun Lu Jiana Li Michael P. Timko Liezhao Liu |
| author_facet | Tengyue Wang Lijuan Wei Jia Wang Ling Xie Yang Yang Li Shuyao Ran Lanyang Ren Kun Lu Jiana Li Michael P. Timko Liezhao Liu |
| author_sort | Tengyue Wang |
| collection | DOAJ |
| description | Abstract Background Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments. |
| first_indexed | 2024-12-12T19:23:41Z |
| format | Article |
| id | doaj.art-9d5c4ab3046d4990831226f55ba22f4e |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-12-12T19:23:41Z |
| publishDate | 2020-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-9d5c4ab3046d4990831226f55ba22f4e2022-12-22T00:14:33ZengBMCBiotechnology for Biofuels1754-68342020-08-0113111910.1186/s13068-020-01774-0Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)Tengyue Wang0Lijuan Wei1Jia Wang2Ling Xie3Yang Yang Li4Shuyao Ran5Lanyang Ren6Kun Lu7Jiana Li8Michael P. Timko9Liezhao Liu10Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityDepartment of Biology, University of VirginiaChongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityAbstract Background Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.http://link.springer.com/article/10.1186/s13068-020-01774-0Brassica napusGrowth period traitsGWASLinkage mappingRNA sequencing |
| spellingShingle | Tengyue Wang Lijuan Wei Jia Wang Ling Xie Yang Yang Li Shuyao Ran Lanyang Ren Kun Lu Jiana Li Michael P. Timko Liezhao Liu Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) Biotechnology for Biofuels Brassica napus Growth period traits GWAS Linkage mapping RNA sequencing |
| title | Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) |
| title_full | Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) |
| title_fullStr | Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) |
| title_full_unstemmed | Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) |
| title_short | Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.) |
| title_sort | integrating gwas linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed brassica napus l |
| topic | Brassica napus Growth period traits GWAS Linkage mapping RNA sequencing |
| url | http://link.springer.com/article/10.1186/s13068-020-01774-0 |
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