QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis
Abstract Background Toxic heavy metal elements in soils are major global environmental issues and easily migrate to crop grains to cause severe problems in human health, whereas moderately essential elements such as selenium are beneficial for human health. The accumulation of heavy metals and essen...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-025-06087-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832585916719300608 |
|---|---|
| author | Min Li Mengxue Gao Jinmei Huang Shaojuan Jin Yamei Lv Lin Wang Tao Huang Fengcai Wu Zhijian Xu Yinghua Pan Zhixia Liu Chaopu Zhang Yuntao Liang Lijun Meng Jianlong Xu |
| author_facet | Min Li Mengxue Gao Jinmei Huang Shaojuan Jin Yamei Lv Lin Wang Tao Huang Fengcai Wu Zhijian Xu Yinghua Pan Zhixia Liu Chaopu Zhang Yuntao Liang Lijun Meng Jianlong Xu |
| author_sort | Min Li |
| collection | DOAJ |
| description | Abstract Background Toxic heavy metal elements in soils are major global environmental issues and easily migrate to crop grains to cause severe problems in human health, whereas moderately essential elements such as selenium are beneficial for human health. The accumulation of heavy metals and essential elements in rice grains and their genetic mechanisms are still poorly understood. Results We conducted genetic dissection of four toxic heavy metal elements (lead, cadmium, mercury, and chromium), one quasi metallic element (arsenic), and one essential element (selenium) in grains of 290 Xian and 308 Geng rice accessions through a genome-wide association study (GWAS) based on three statistical models and assays of element concentrations from three environments. A total of 99 quantitative trait loci (QTLs) were identified. Among these QTLs, 18.2% overlapped between/among two or more elements, indicating that some QTLs related to the accumulation of certain elements may depend on other heavy metal elements or be involved in the collaborative transport of other elements. Moreover, at least 14 QTLs/regions were identified in the same regions, containing 12 cloned genes reported to be associated with element accumulation or tolerance-related traits, while the remaining 85 were new QTLs. A total of 62 promising candidate genes were identified from 50 major QTLs, of which 25 genes were newly discovered in this study. More importantly, population genetic analysis revealed 26 and 15 intraspecies divergent regions affecting element concentrations in the Xian and Geng subspecies, respectively, including 25 QTLs identified in this study and 13 previously reported and cloned genes. Conclusions Our findings will facilitate further gene cloning and dissection of the genetic mechanisms of element accumulation in rice grains to improve grain quality. |
| format | Article |
| id | doaj-art-65cd40f8907d45cab62e1299d8ae2802 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-65cd40f8907d45cab62e1299d8ae28022025-01-26T12:23:30ZengBMCBMC Plant Biology1471-22292025-01-0125111110.1186/s12870-025-06087-8QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysisMin Li0Mengxue Gao1Jinmei Huang2Shaojuan Jin3Yamei Lv4Lin Wang5Tao Huang6Fengcai Wu7Zhijian Xu8Yinghua Pan9Zhixia Liu10Chaopu Zhang11Yuntao Liang12Lijun Meng13Jianlong Xu14School of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversitySchool of Agronomy, Anhui Agricultural UniversityRice Research Institute, Guangxi Academy of Agricultural SciencesRice Research Institute, Guangxi Academy of Agricultural SciencesRice Research Institute, Guangdong Academy of Agricultural SciencesSchool of Agronomy, Anhui Agricultural UniversityRice Research Institute, Guangxi Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesAbstract Background Toxic heavy metal elements in soils are major global environmental issues and easily migrate to crop grains to cause severe problems in human health, whereas moderately essential elements such as selenium are beneficial for human health. The accumulation of heavy metals and essential elements in rice grains and their genetic mechanisms are still poorly understood. Results We conducted genetic dissection of four toxic heavy metal elements (lead, cadmium, mercury, and chromium), one quasi metallic element (arsenic), and one essential element (selenium) in grains of 290 Xian and 308 Geng rice accessions through a genome-wide association study (GWAS) based on three statistical models and assays of element concentrations from three environments. A total of 99 quantitative trait loci (QTLs) were identified. Among these QTLs, 18.2% overlapped between/among two or more elements, indicating that some QTLs related to the accumulation of certain elements may depend on other heavy metal elements or be involved in the collaborative transport of other elements. Moreover, at least 14 QTLs/regions were identified in the same regions, containing 12 cloned genes reported to be associated with element accumulation or tolerance-related traits, while the remaining 85 were new QTLs. A total of 62 promising candidate genes were identified from 50 major QTLs, of which 25 genes were newly discovered in this study. More importantly, population genetic analysis revealed 26 and 15 intraspecies divergent regions affecting element concentrations in the Xian and Geng subspecies, respectively, including 25 QTLs identified in this study and 13 previously reported and cloned genes. Conclusions Our findings will facilitate further gene cloning and dissection of the genetic mechanisms of element accumulation in rice grains to improve grain quality.https://doi.org/10.1186/s12870-025-06087-8Element accumulationGWASQTLDivergent regionGene |
| spellingShingle | Min Li Mengxue Gao Jinmei Huang Shaojuan Jin Yamei Lv Lin Wang Tao Huang Fengcai Wu Zhijian Xu Yinghua Pan Zhixia Liu Chaopu Zhang Yuntao Liang Lijun Meng Jianlong Xu QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis BMC Plant Biology Element accumulation GWAS QTL Divergent region Gene |
| title | QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis |
| title_full | QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis |
| title_fullStr | QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis |
| title_full_unstemmed | QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis |
| title_short | QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis |
| title_sort | qtl mapping and candidate gene analysis of element accumulation in rice grains via genome wide association study and population genetic analysis |
| topic | Element accumulation GWAS QTL Divergent region Gene |
| url | https://doi.org/10.1186/s12870-025-06087-8 |
| work_keys_str_mv | AT minli qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT mengxuegao qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT jinmeihuang qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT shaojuanjin qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT yameilv qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT linwang qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT taohuang qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT fengcaiwu qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT zhijianxu qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT yinghuapan qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT zhixialiu qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT chaopuzhang qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT yuntaoliang qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT lijunmeng qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis AT jianlongxu qtlmappingandcandidategeneanalysisofelementaccumulationinricegrainsviagenomewideassociationstudyandpopulationgeneticanalysis |