Genetic loci and agronomic traits impacting grain-arsenic concentrations revealed by GWA and biparental QTL analyses

Authors: Pinson, Shannon; Edwards, Jeremy; Jackson, Aaron; HEUSCHELE, D. - University Of Minnesota; Barnaby, Jinyoung; TARPLEY, LEE - Texas A&M Agricultural Experiment Station; Green, Carrie; Codling, Eton; SMITH, AARON - Louisiana State University

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/4/2019
Publication Date: 1/6/2021
Citation: Pinson, S.R., Edwards, J., Jackson, A.K., Heuschele, D.J., Barnaby, J.Y., Tarpley, L., Green, C.E., Codling, E.E., Smith, A.P. 2021. Genetic loci and agronomic traits impacting grain-arsenic concentrations revealed by GWA and biparental QTL analyses. Proceedings of 38th Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. Pp 89-90. Electronic Publication.

Interpretive Summary:

Technical Abstract: There is global concern that rice grains and foods can contain harmful amounts of arsenic (As). While US rice nearly always meets the CODEX limit of 0.2 ppm inorganic As (iAs) in milled rice, not all US rice meets the more stringent limit of 0.1 ppm iAs for baby food products. We conducted a series of studies to identify rice genes and physiological factors that can be used to develop rice varieties with lower grain-As. Arsenic is also toxic to plants, with rice straighthead disease being associated with As-toxicity. Known variance in straighthead resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, sequestration/detoxification or a combination of all three. Because these mechanisms could also be contributing to the wide (200-fold) differences in grain-As observed among diverse rice accessions, we considered associations between grain-As, days to heading (DHD), and straighthead resistance in our gene identification studies. During the initial study of 1763 widely diverse rice accessions (the USDA Rice Core), association between late heading and increased grain-As was observed in rice produced in flooded paddies, but not when the same rice accessions were grown unflooded. This observation is consistent with the redox conditions in flooded paddies converting soil iAs from arsenate into the more bioavailable form of arsenite. Flooding also encourages growth of anaerobic bacteria that scavenge oxygen from soil minerals, thereby releasing mineral-bound As. Bacteria can also synthesize and release organic As compounds (e.g., DMA). Producing rice without a flood for all or part of the season can reduce grain-As up to 10-fold. Early maturity could also reduce grain-As concentrations. From the USDA Rice Core, 8 accessions with higher than average grain-As concentrations (a.k.a. “grain-As Accumulators”) plus 8 accessions with low grain-As (a.k.a. “Excluders”) were selected for further study, including ‘Lemont’ and ‘Jefferson’ as Excluders. All of the Accumulators proved highly susceptible to straighthead, while most but not all Excluders were resistant, suggesting that some mechanisms that reduce grain-As also impart straighthead resistance. When the Accumulators and Excluders were compared for As concentration and metabolism in leaves and roots under field and hydroponic conditions, data indicated that reduced grain-As concentrations were not due to reduced root uptake or root-to-shoot transfer rates, but were associated with more efficient sequestration of As in leaves, a process that involves chelation with multiple sulfur (S) molecules per As molecule. While this suggested that increased S in plants might decrease grain-As by increasing As-sequestration, a follow-on study showed that foliar application of S-fertilizer increased grain-S but did not reduce grain-As or straighthead severity. Linkage between grain-As and SSRs among F2 progeny from four Excluder × Accumulator biparental crosses indicated QTLs on chromosomes 8, 10 and 11 whose effects on grain-As were not due to DHD. QTLs were also mapped in the USDA Rice Minicore population using high resolution genome wide association studies (GWAS). Phenotypic data for 16 grain elements and hull-Si came from previous studies, and resistance to MSMA-induced straighthead disease was rated in 2015 and 2016, two replications/year. Since reduced As uptake or enhanced As detoxification and sequestration would be expected to reduce both grain-As and straighthead, we anticipated finding some straighthead QTLs co-located with grain-As QTLs. Arsenic enters roots through phosphorus (P) and silica (Si) transporters, and As-detoxification involves S. Therefore, overlap with grain-P, grain-S, or hull-Si QTLs would provide additional knowledge on the mechanisms underlying grain-As and straighthead QTLs. While GWAS indicat