Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits
Abstract Background Lotus corniculatus is a widely distributed perennial legume whose great adaptability to different environments and resistance to barrenness make it an excellent forage and ecological restoration plant. However, its molecular genetics and genomic relationships among populations ar...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-023-01670-7 |
| _version_ | 1797451462060539904 |
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| author | Cheng Chen Kaixuan Zhang Fu Liu Xia Wang Yang Yao Xiaolei Niu Yuqi He Jun Hong Fang Liu Qiu Gao Yi Zhang Yurong Li Meijuan Wang Jizhen Lin Yu Fan Kui Ren Lunhao Shen Bin Gao Xue Ren Weifei Yang Milen I. Georgiev Xinquan Zhang Meiliang Zhou |
| author_facet | Cheng Chen Kaixuan Zhang Fu Liu Xia Wang Yang Yao Xiaolei Niu Yuqi He Jun Hong Fang Liu Qiu Gao Yi Zhang Yurong Li Meijuan Wang Jizhen Lin Yu Fan Kui Ren Lunhao Shen Bin Gao Xue Ren Weifei Yang Milen I. Georgiev Xinquan Zhang Meiliang Zhou |
| author_sort | Cheng Chen |
| collection | DOAJ |
| description | Abstract Background Lotus corniculatus is a widely distributed perennial legume whose great adaptability to different environments and resistance to barrenness make it an excellent forage and ecological restoration plant. However, its molecular genetics and genomic relationships among populations are yet to be uncovered. Result Here we report on a genomic variation map from worldwide 272 L. corniculatus accessions by genome resequencing. Our analysis suggests that L. corniculatus accessions have high genetic diversity and could be further divided into three subgroups, with the genetic diversity centers were located in Transcaucasia. Several candidate genes and SNP site associated with CNglcs content and growth traits were identified by genome-wide associated study (GWAS). A non-synonymous in LjMTR was responsible for the decreased expression of CNglcs synthesis genes and LjZCD was verified to positively regulate CNglcs synthesis gene CYP79D3. The LjZCB and an SNP in LjZCA promoter were confirmed to be involved in plant growth. Conclusion This study provided a large number of genomic resources and described genetic relationship and population structure among different accessions. Moreover, we attempt to provide insights into the molecular studies and breeding of CNglcs and growth traits in L. corniculatus. |
| first_indexed | 2024-03-09T14:55:00Z |
| format | Article |
| id | doaj.art-39cbc6aa37174051aa608aab8a84d144 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-09T14:55:00Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-39cbc6aa37174051aa608aab8a84d1442023-11-26T14:14:26ZengBMCBMC Biology1741-70072023-08-0121111710.1186/s12915-023-01670-7Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traitsCheng Chen0Kaixuan Zhang1Fu Liu2Xia Wang3Yang Yao4Xiaolei Niu5Yuqi He6Jun Hong7Fang Liu8Qiu Gao9Yi Zhang10Yurong Li11Meijuan Wang12Jizhen Lin13Yu Fan14Kui Ren15Lunhao Shen16Bin Gao17Xue Ren18Weifei Yang19Milen I. Georgiev20Xinquan Zhang21Meiliang Zhou22Institute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesAnnoroad Gene Technology (Beijing) Co., Ltd.Institute of Crop Sciences, Chinese Academy of Agricultural SciencesHainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan UniversityInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceNational Herbage Gempiasm Bank of China, National Animal Husbandry ServiceInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityLaboratory of Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of SciencesCollege of Grassland Science and Technology, Sichuan Agricultural UniversityInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesAbstract Background Lotus corniculatus is a widely distributed perennial legume whose great adaptability to different environments and resistance to barrenness make it an excellent forage and ecological restoration plant. However, its molecular genetics and genomic relationships among populations are yet to be uncovered. Result Here we report on a genomic variation map from worldwide 272 L. corniculatus accessions by genome resequencing. Our analysis suggests that L. corniculatus accessions have high genetic diversity and could be further divided into three subgroups, with the genetic diversity centers were located in Transcaucasia. Several candidate genes and SNP site associated with CNglcs content and growth traits were identified by genome-wide associated study (GWAS). A non-synonymous in LjMTR was responsible for the decreased expression of CNglcs synthesis genes and LjZCD was verified to positively regulate CNglcs synthesis gene CYP79D3. The LjZCB and an SNP in LjZCA promoter were confirmed to be involved in plant growth. Conclusion This study provided a large number of genomic resources and described genetic relationship and population structure among different accessions. Moreover, we attempt to provide insights into the molecular studies and breeding of CNglcs and growth traits in L. corniculatus.https://doi.org/10.1186/s12915-023-01670-7Lotus corniculatusResequencingGenomic variationGWASPopulation structureCyanogenic glycosides |
| spellingShingle | Cheng Chen Kaixuan Zhang Fu Liu Xia Wang Yang Yao Xiaolei Niu Yuqi He Jun Hong Fang Liu Qiu Gao Yi Zhang Yurong Li Meijuan Wang Jizhen Lin Yu Fan Kui Ren Lunhao Shen Bin Gao Xue Ren Weifei Yang Milen I. Georgiev Xinquan Zhang Meiliang Zhou Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits BMC Biology Lotus corniculatus Resequencing Genomic variation GWAS Population structure Cyanogenic glycosides |
| title | Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits |
| title_full | Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits |
| title_fullStr | Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits |
| title_full_unstemmed | Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits |
| title_short | Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits |
| title_sort | resequencing of global lotus corniculatus accessions reveals population distribution and genetic loci associated with cyanogenic glycosides accumulation and growth traits |
| topic | Lotus corniculatus Resequencing Genomic variation GWAS Population structure Cyanogenic glycosides |
| url | https://doi.org/10.1186/s12915-023-01670-7 |
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