Panthita Ruang-areerate
Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach
Ruang-areerate, Panthita; Travis, Anthony J.; Pinson, Shannon R. M.; Tarpley, Lee; Eizenga, Georgia C.; Guerinot, Mary Lou; Salt, David E.; Douglas, Alex; Price, Adam H.; Norton, Gareth J.
Authors
Anthony J. Travis
Shannon R. M. Pinson
Lee Tarpley
Georgia C. Eizenga
Mary Lou Guerinot
DAVID SALT David.Salt@nottingham.ac.uk
Professor of Genome Enabled Biology
Alex Douglas
Adam H. Price
Gareth J. Norton
Abstract
Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.
Citation
Ruang-areerate, P., Travis, A. J., Pinson, S. R. M., Tarpley, L., Eizenga, G. C., Guerinot, M. L., …Norton, G. J. (2021). Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach. Heredity, 126(3), 505-520. https://doi.org/10.1038/s41437-020-00390-w
Journal Article Type | Article |
---|---|
Acceptance Date | Nov 6, 2020 |
Online Publication Date | Nov 24, 2020 |
Publication Date | Mar 1, 2021 |
Deposit Date | Mar 3, 2021 |
Publicly Available Date | May 25, 2021 |
Journal | Heredity |
Print ISSN | 0018-067X |
Electronic ISSN | 1365-2540 |
Publisher | Nature Publishing Group |
Peer Reviewed | Peer Reviewed |
Volume | 126 |
Issue | 3 |
Pages | 505-520 |
DOI | https://doi.org/10.1038/s41437-020-00390-w |
Keywords | Genetics(clinical); Genetics |
Public URL | https://nottingham-repository.worktribe.com/output/5088603 |
Publisher URL | https://www.nature.com/articles/s41437-020-00390-w |
Files
Ms GWAS Mn Heredity Supplementary
(1.6 Mb)
PDF
Ms GWAS Mn Heredity
(933 Kb)
PDF
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