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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #352897

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Genes and physiological factors associated with natural variation in rice arsenic concentrations

item Pinson, Shannon
item Edwards, Jeremy
item HEUSCHELE, JO - University Of Minnesota
item TARPLEY, LEE - Texas A&M Agrilife
item Green, Carrie
item SMITH, AARON - Louisiana State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/4/2018
Publication Date: 10/7/2018
Citation: Pinson, S.R., Edwards, J., Heuschele, J.D., Tarpley, L., Green, C.E., Smith, A.P. 2018. Genes and physiological factors associated with natural variation in rice arsenic concentrations. Meeting Abstract. Available:

Interpretive Summary:

Technical Abstract: Previous study of 1763 diverse accessions (the USDA Rice Core), found a 200-fold difference in concentration of total arsenic (tAs) in unmilled rice grains, indicating large genetic variance that could be exploited by breeders to produce varieties with low grain-As. This study identifiedData were used to identify subsets of rice accessions with high grain-tAs concentrations (a.k.a. “grain-tAs Accumulators”) and others with low grain-tAs concentrations (a.k.a. “Excluders”). Interestingly, all the modern USA rice varieties (released since 1980) included in that study were Excluders. This data prompted a series of studies to identify the genes and physiological mechanisms underlying the low grain-tAs of found in modern US varieties so that they could be utilized in breeding efforts in the USA and internationally. Several grain-tAs Accumulators were crossed with Excluders. Among 15 segregating F2 populations, five showed Mendelian segregation patterns (i.e. 1:2:1 or 3:1) for grain-tAs, indicative of single major-gene control. Four F2 populations have been selectively genotyped to date. Marker-trait associations observed in two populations indicate a grain-tAs locus on the short arm of chromosome 11; data from the third population points to the long arm of chromosome 10; and the fourth population points to chromosomes 2 and 8. When subsets of Accumulator and Excluder accessions were compared for As concentration and metabolism in leaves and roots, data suggested that the lower grain-tAs of Excluders might be in part due to more efficient sequestration of As in leaf vacuoles. It is thus notable that chromosome 10 and 11 contain glutathione S-transferase genes (involved in As chelation and sequestration) are near the associated markers on chromosomes 10 and 11. A likely candidate gene on chromosome 2 is Lsi1, a membrane transporter protein known to affect root uptake of both silica and As. Reduced As uptake or enhanced As detoxification and sequestration would be expected to affect improve both grain-As and resistance to As-induced plant stress (e.g., straighthead disease). However, association mapping for these seemingly-related traits in the USDA Rice Minicore (subset of the USDA Rice Core) using 3.3 million SNPs detected no overlapping QTLs, regions. This indicates suggests suggesting that the wide variations for in total grain-tAs and straighthead observed within the Minicore are regulated by different genes and mechanisms.