Multi-experiment and multi-locus genome-wide association mapping for grain arsenic in rice population

Authors: CHEN, CAIJIN - University Of Aberdeen; PANTHITA, RUANG - National Center For Genetic Engineering And Biotechnology (BIOTEC); TRAVIS, ANTHONY - University Of Aberdeen; DOUGLAS, ALEX - University Of Aberdeen; SALT, DAVID - University Of Nottingham; Pinson, Shannon; Eizenga, Georgia; PRICE, ADAM - University Of Aberdeen; NORTON, GARETH - University Of Aberdeen

Submitted to: Plant Direct
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2025
Publication Date: 5/4/2025
Citation: Chen, C., Panthita, R., Travis, A.J., Douglas, A., Salt, D., Pinson, S.R., Eizenga, G.C., Price, A.H., Norton, G.J. 2025. Multi-experiment and multi-locus genome-wide association mapping for grain arsenic in rice population. Plant Direct, 9, Article 5. https://doi.org/10.1002/pld3.70064.
DOI: https://doi.org/10.1002/pld3.70064

Interpretive Summary: Rice is a globally important crop and is particularly efficient in assimilating arsenic (As) from paddy soils. Rice grown in some geographic areas has been found to contain concerning levels of arsenic, and human intake from human As intake from rice consumption has been associated with several health problems. To be more precise, only inorganic As is toxic enough to warrant regulation in food products, but due to expenses, this and most studies measure total As which includes both the highly toxic inorganic As and the much less toxic organic As, and it would be beneficial to reduce all As in food products. An essential step toward breeding rice cultivars with low grain As content is the identification of quantitative trait loci (QTLs) and genes that restrict grain As accumulation. To identify these genes, a genetically diverse collection of rice cultivars known as the Rice Diversity Panel 1 (RDP1) was grown in five diverse field environments - one year each in Bangladesh, China and Texas, USA plus two years in Arkansas, USA. Grains from these five field experiments were evaluated for their As concentrations. While some QTLs were reported in 2014 after analyzing marker-trait association with the 44,000 molecular markers that were available at the time, subsequently a set of 3.5 million molecular markers was made available, as well as several improved statistical procedures for analyzing marker-trait associations were developed that vastly improve the ability to identify QTLs, and support the identification of genetic differences within the very genes that are impacting a trait like the accumulation of As in the rice plant. In this study, the prior grain As data was re-analyzed using 3.5 SNP markers and a total of eight statistical analysis procedures. These reanalyzes detected 21 QTL with higher confidence because they were identified using two or more statistical analyses. These QTLs further led to the identification of 10 candidate genes, i.e., genes in the QTL regions whose predicted gene functions are known or expected to be associated with As accumulation, therefore warranting further research to validate their value to breeders. One of these candidate genes (OsABCC1) proved especially interesting for US rice breeding because characterization of the many versions (alleles) of this gene within the RDP1 population indicated that one allele not already widespread among US rice varieties could be used to produce new varieties with reduced grain As concentrations. Further study will be required to determine if the novel allele reduces total grain As content by reducing inorganic arsenic, organic arsenic, or by reducing both types of arsenic. However, the fact that this study also determined that the desired OsABCC1 allele is already within two historically grown US germplasm lines makes it more readily available to US rice researchers and breeders today.

Technical Abstract: Rice is a globally important crop and is particularly efficient in assimilating arsenic (As) from paddy soils. Human As intake from rice consumption is associated with many health problems. Identifying quantitative trait loci (QTLs) and genes associated with grain As is essential for breeding low As rice cultivars. In this study, data on As accumulation in grains of the Rice Diversity Panel 1 (RDP1) in five field environments at four diverse geographic sites were re-analysed to compare genome-wide association (GWA) methods, including multi-experiment and multi-locus mapping approaches. Two single-locus (EMMAX for single-trait and GEMMA for multi-experiments) and six multi-loci (FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB and FASTmrMLM) GWA methods were used to identify the QTLs (QTNs) for grain As. A total of 117 and 205 QTLs were detected using EMMAX and GEMMA, respectively, across all five field experiments. A total of 2, 11, 12, 19, 21, and 23 quantitative trait nucleotides (QTNs) were identified by FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB and FASTmrMLM, respectively. Among them, 22 QTLs (QTNs) were co-detected by single-locus and multi-loci GWAS methods. From these QTL/QTNs a total of 10 candidate genes were identified. Analysis of the haplotype variants of two candidate genes, OsPIP 2;4 and OsABCC1, revealed that a greater than 10% reduction in grain As could be achieved. The QTLs/QTNs and candidate genes identified give insight into the molecular mechanisms regulating As in rice, and serve as breeding targets for producing rice cultivars that accumulate lower grain concentrations of As.