journal article·2025-05Open access

Genome‐Wide Association Studies Reveal the Genetic Architecture of Ionomic Variation in Grains of Tartary Buckwheat

Zhirong Wang, Yuqi He, Mengyu Zhao, Xiang‐Qian Liu, Hao Lin, Yaliang Shi, Kaixuan Zhang, Guijie Lei, Dili Lai, Tong Liu, Xiaoyang Peng, Jiayue He, Wei Li, Xiangru Wang, Sun‐Hee Woo, Muriel Quinet, Alisdair R. Fernie, Xin‐Yuan Huang, Meiliang Zhou

Advanced Science· Volume 12· Issue 17

Abstract

Abstract Tartary buckwheat ( Fagopyrum tataricum ) is esteemed as a medicinal crop due to its high nutritional and health value. However, the genetic basis for the variations in Tartary buckwheat grain ionome remains inadequately understood. Through genome‐wide association studies (GWAS) on grain ionome, 52 genetic loci are identified associated with 10 elements undergoing selection. Molecular experiments have shown that the variation in FtACA13 ’s promoter (an auto‐inhibited Ca 2+ ‐ATPase) is accountable for grain sodium concentration and salt tolerance, which underwent selection during domestication. FtYPQ1 (a vacuolar amino acid transporter) exhibits zinc transport activity, enhancing tolerance to excessive zinc stress and raising zinc accumulation. Additionally, FtNHX2 (a Na + /H + exchanger) positively regulates arsenic content. Further genomic comparative analysis of “20A1” (wild accession) and “Pinku” (cultivated accession) unveiled structural variants in key genes involved in ion uptake and transport that may result in considerable changes in their functions. This research establishes the initial comprehensive grain ionome atlas in Tartary buckwheat, which will significantly aid in genetic improvement for nutrient biofortification.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Seed and Plant Biochemistry · Genetic and Environmental Crop Studies · Genetic Mapping and Diversity in Plants and Animals

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

National Key Facility for Crop Gene Resources and Genetic Improvement/Key laboratory Grain Crop Genetic Resources Evaluation and Utilization Ministry of Agriculture and Rural Affairs Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 P. R. China

State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization College of Resources and Environmental Sciences Nanjing Agricultural University Nanjing 210095 P. R. China

State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan Key Laboratory of Biology and Germplasm Innovation of Perennial Rice School of Agriculture Yunnan University Kunming 650500 P. R. China

Department of Crop Science Chungbuk National University Cheong‐ju 28644 Republic of Korea

Groupe de Recherche en Physiologie Végétale (GRPV) Earth and Life Institute‐Agronomy (ELI‐A) Université catholique de Louvain Croix du Sud 45, boîte L7.07.13 Louvain‐la‐Neuve B‐1348 Belgium

Department of Molecular Physiology Max‐Planck‐Institute of Molecular Plant Physiology 14476 Potsdam Germany

Sanya Institute of Nanjing Agricultural University Sanya 572024 P. R. China

Funding

National Key Research and Development Program of China · National Natural Science Foundation of China · Fundamental Research Funds for the Central Universities

References (64)

Show source-provided references
1. 10.1146/annurev.arplant.59.032607.09294210.1146/annurev.arplant.59.032607.092942 ↗
2. 10.20307/nps.2020.26.1.5010.20307/nps.2020.26.1.50 ↗
3. 10.1016/j.molp.2021.12.00810.1016/j.molp.2021.12.008 ↗
4. 10.1016/B978-0-323-66162-1.00022-610.1016/B978-0-323-66162-1.00022-6 ↗
5. 10.1126/science.adf325610.1126/science.adf3256 ↗
6. 10.1002/moda.3010.1002/moda.30 ↗
7. 10.1038/s43016-023-00905-810.1038/s43016-023-00905-8 ↗
8. 10.1038/nature0880010.1038/nature08800 ↗
9. 10.1111/tpj.1517710.1111/tpj.15177 ↗
10. 10.1105/tpc.18.0037510.1105/tpc.18.00375 ↗
11. 10.1111/tpj.1608010.1111/tpj.16080 ↗
12. 10.1038/s41598-022-10618-w10.1038/s41598-022-10618-w ↗
13. 10.1111/pce.1382310.1111/pce.13823 ↗
14. 10.1007/s11032-008-9225-z10.1007/s11032-008-9225-z ↗
15. 10.1104/pp.15.0197110.1104/pp.15.01971 ↗
16. 10.3389/fpls.2014.0048510.3389/fpls.2014.00485 ↗
17. Hunt H. V. · Veg. Hist. Archaeobotany · 2018 · 27 · 493
18. 10.1186/s12915-023-01587-110.1186/s12915-023-01587-1 ↗
19. Yang W. · Adv. Sci. · 2024 · 11 · 20
20. 10.1186/s13059-020-02217-710.1186/s13059-020-02217-7 ↗
21. 10.1186/s13059-024-03203-z10.1186/s13059-024-03203-z ↗
22. 10.1016/j.molp.2017.08.01310.1016/j.molp.2017.08.013 ↗
23. 10.1080/07388551.2020.174738710.1080/07388551.2020.1747387 ↗
24. 10.1016/j.molp.2016.05.00310.1016/j.molp.2016.05.003 ↗
25. 10.1111/pbi.1393210.1111/pbi.13932 ↗
26. 10.1038/s41598-022-26619-810.1038/s41598-022-26619-8 ↗
27. 10.1002/jame.2002610.1002/jame.20026 ↗
28. 10.1111/pbi.1425910.1111/pbi.14259 ↗
29. 10.1093/plcell/koac28310.1093/plcell/koac283 ↗
30. 10.1042/BST2021069910.1042/BST20210699 ↗
31. 10.1016/j.gene.2022.14688410.1016/j.gene.2022.146884 ↗
32. 10.1093/jxb/erad17510.1093/jxb/erad175 ↗
33. 10.1111/nph.1702110.1111/nph.17021 ↗
34. 10.1093/plcell/koad05210.1093/plcell/koad052 ↗
35. 10.1016/j.bbamcr.2023.11950810.1016/j.bbamcr.2023.119508 ↗
36. 10.1111/j.1365-3040.2008.01817.x10.1111/j.1365-3040.2008.01817.x ↗
37. 10.1186/s12864-018-5036-810.1186/s12864-018-5036-8 ↗
38. 10.1111/tpj.1235210.1111/tpj.12352 ↗
39. 10.1007/s11103-015-0426-710.1007/s11103-015-0426-7 ↗
40. 10.1111/ppl.1235410.1111/ppl.12354 ↗
41. 10.1038/s41586-024-07487-w10.1038/s41586-024-07487-w ↗
42. 10.1371/journal.pone.022910710.1371/journal.pone.0229107 ↗
43. 10.1111/j.1365-3040.2009.01935.x10.1111/j.1365-3040.2009.01935.x ↗
44. 10.1016/j.jfca.2019.10333510.1016/j.jfca.2019.103335 ↗
45. 10.1007/s12011-014-0099-010.1007/s12011-014-0099-0 ↗
46. 10.1111/nph.1830610.1111/nph.18306 ↗
47. 10.1038/s41467-019-13355-310.1038/s41467-019-13355-3 ↗
48. Cornejo M. · Biochim. Biophys. Acta. Mol. Basis. Dis. · 1867 · 2021
49. 10.1016/j.jgg.2022.05.00710.1016/j.jgg.2022.05.007 ↗
50. 10.3390/biology1005035310.3390/biology10050353 ↗
51. 10.1002/moda.7000210.1002/moda.70002 ↗
52. 10.1016/j.jgg.2022.08.00310.1016/j.jgg.2022.08.003 ↗
53. 10.1016/j.plaphy.2019.12.00410.1016/j.plaphy.2019.12.004 ↗
54. 10.1007/s13237-023-00441-710.1007/s13237-023-00441-7 ↗
55. 10.3389/fpls.2023.127015010.3389/fpls.2023.1270150 ↗
56. Daniel‐Mozo M. · Sci. Adv. · 2024 · 15 · 10
57. 10.1038/ncomms1213810.1038/ncomms12138 ↗
58. 10.1038/nmeth.168110.1038/nmeth.1681 ↗
59. 10.1186/s13059-019-1905-y10.1186/s13059-019-1905-y ↗
60. 10.1002/advs.20240360310.1002/advs.202403603 ↗
61. 10.1016/j.jgg.2023.10.00710.1016/j.jgg.2023.10.007 ↗
62. 10.1093/jxb/erac25810.1093/jxb/erac258 ↗
63. 10.1016/j.molp.2020.11.02210.1016/j.molp.2020.11.022 ↗
64. 10.1016/j.molp.2023.09.01010.1016/j.molp.2023.09.010 ↗