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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Identification of QTLs that enhance the nutritional value of rice grain and limit accumulation of undesirable elements such as arsenic

Authors
item Pinson, Shannon
item Tarpley, Lee -
item Yan, Wengui
item Zhang, Min -
item Guerinot, Mary Lou -
item Salt, David -

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 18, 2014
Publication Date: N/A

Technical Abstract: Research into the mineral contents of cereal grains and vegetables is motivated by interest in improving their nutritional value. Biofortification refers to natural enhancement of grain/food products through traditional breeding. Since this approach does not require genetic engineering, it is acceptable to many consumers, and is compatible with organic labeling. Enhancing the nutritional value of rice is of particular interest because rice is a primary dietary component for more than half of the world’s population, and especially so in underdeveloped parts of the world that have higher rates of malnutrition. But new marketing strategies could be employed in developed countries as well, for value-added products naturally high in consumer-desired minerals such as Ca, K, and Fe; or strategically low in undesirable elements such as As or Cd. The first step toward targeted breeding is the identification of genes responsible for orchestrating concentrations of various elements in the rice grain. In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 (human and plant) nutritional and antinutritional elements in whole, unmilled rice grain were identified. Genetic loci were mapped among several progeny populations from biparental crosses as well as among two sets of diverse rice accessions (SNP Diversity Panel 1and the USDA MiniCore). To increase opportunity to detect and characterize grain-element QTLs, the study populations were grown under two contrasting field redox conditions, flooded (reduced soil chemistry) and unflooded (flush-irrigated to maintain aerated soil chemistry while preventing water stress). Soil redox is known to often alter element availability, and so was expected to affect grain element concentrations. Inductively coupled plasma – mass spectrometry (ICP-MS) was used to analyze the harvested brown rice for variation in accumulation of 16 elements, namely As, Ca, Cd, Co, Cu, Fe, K, Mg, Mn, Mo, Ni, P, Rb, S, Sr, and Zn. Correlations among the individual elements and between each element with grain shape, plant height, and time of heading were studied. When the elements were considered individually, more than 150 grain-element QTLs were identified. However, in agreement with known shared transporters and element networks, many of the QTLs were co-located or clustered into 40 chromosomal regions associated with grain concentration of more than one element. Grain shape, heading time and plant height proved to have little direct influence on rice grain element concentrations. Numerous element × element patterns were found, including strong positive correlations between P, Mg, and K. The two elements most strongly affected by soil flooding were As and Cd, with grains produced in flooded fields containing 30x higher concentrations of As but 10x lower Cd than rice produced in aerated soils. Fifty accessions exhibiting extreme concentrations of one or more grain elements were selected from among a set of 1700 accessions to be used in further gene-mapping, agronomic, and physiological studies. Analysis of seed from F2 progeny from some of these crosses reveal 1:2:1 or 3:1 segregation ratios, suggesting that, at least in some accessions and for some elements, single major genes affecting grain element concentrations can be found. Rice accessions in the indica ancestral lineage showed higher grain concentrations of most elements than other rice lineages, including arsenic, while japonica accessions showed higher average grain concentrations of Cd, Cu, Fe, Mo, and Zn. Principal component analysis identified six elements (P, K, Mg, As, Cu and Fe) as key to explaining most of the variance among the 1700 diverse rice accessions, with the same six elements proving significant regardless of ancestral lineage or flooding condition. Learning which chromosomal regions contain genes affecting grain element concentrations is a critical first step toward understanding how those genes can be most effectively used to improve grain nutritional value or rice plant nutrition. The fact that chromosomal regions were often associated with more than one element suggests the importance of studying multiple elements at a time as well as the importance of carefully controlling factors such as soil fertility, temperature, and pH that can affect the ability of plants to take elements up from the soil. Variation in grain elemental concentrations was not strongly associated with plant height, heading time, or grain shape, suggesting that variation for these traits will not confound efforts to identify genes for other mechanisms, such as element transporters. Because rice can be grown under both flooded and unflooded field conditions, and metal transporter proteins and genes have been shown orthologous between species as diverse as Arabidopsis, rice, and yeast, knowledge of the genetic and environmental factors affecting the rice grain elemental concentrations (ionome) can have applications well beyond rice.

Last Modified: 10/23/2014
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