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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

Title: Genetic diversity for rice grain mineral concentrations observed among genetically and geographically giverse rice accessions

Authors
item Pinson, Shannon
item Tarpley, Lee -
item Yeater, Kathleen
item Yan, Wengui
item Guerinot, Mary Lou -
item Salt, David -

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: March 7, 2012
Publication Date: February 1, 2013
Citation: Pinson, S.R., Tarpley, L., Yeater, K.M., Yan, W., Guerinot, M., Salt, D. 2012. Genetic diversity for rice grain mineral concentrations observed among genetically and geographically giverse rice accessions. 35th Rice Technical Working Group Meeting Proceedings. Feb. 27-March 1, 2012, Hot Springs, Arkansas. CDROM.

Technical Abstract: With about half of the world’s people dependent on rice as their main food source, improving the nutritional value of rice could have major impact on human health. While rice in the USA is often artificially fortified, natural enhancement of the rice grain’s nutritional value, i.e. from genetic improvement, could open new marketing strategies for the nutritionally enhanced, value-added products. Biofortification is a term referring to natural enhancement of the grain/food product through traditional breeding. Since biofortification does not require genetic engineering, it is acceptable to many consumers, and is able to acquire organic certification if grown under organic field conditions. The first step toward breeding rice cultivars with enhanced element composition (ionomics) is to understand the genetic diversity available to breeders in germplasm collections. Furthermore, the element × element interactions and element × plant trait relationships observed therein can implicate mechanisms of mineral uptake, transport, and grain accumulation influencing grain nutritional quality and rice plant nutrition. A core subset of 1640 accessions from among the 17,000+ rice accessions in the USDA National Small Grains Collection was grown over two years in Beaumont, TX. Because soil redox is known to significantly alter the availability of soil mineral nutrients to plant uptake, the diverse rice accessions from more than 100 countries of origin were grown under both flooded and unflooded (flush irrigated) field conditions, two replications per treatment per year. ICP-MS was used to analyze the harvested brown rice for grain concentrations of Mg, P, K, S, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Mo, and Cd. Fifteen repeated check-plots per replication documented that environmental variance was low compared to genetic variance, but also revealed a gradient among the rice grains harvested throughout the plots that may have been due to soil variance or water depth, both of which varied in a north-south direction within the present study. To account for this environmental trend in the subsequent calculations, subsequent analyses were based on best linear unbiased estimates (BLUEs) calculated for each genotype and element. Wide differences (from 2x to 100x) in grain concentration were seen among the diverse rice genotypes for all 16 elements. Unflooded fields generally provided greater ionomic variance than did flooded fields, but spatial analysis indicated that for many of the elements, this increased variance was due to environmental variance rather than enhanced genotypic variance. None of the elements were strongly associated with plant height, heading time, or grain shape, suggesting that genetic differences in mineral uptake/transport/accumulation have more effect on grain mineral concentrations than these plant and grain traits. Statistically significant element × element correlations included P×K (r = -0.97 across both flooded and unflooded conditions), P×Mg (r = 0.95), and Sr×Ca (r = 0.64). K and Mg were more directly correlated with P than each other (r = -0.89). The high association between Ca and Sr was expected because these elements are chemically similar and known to follow the same routes of plant uptake and transport. Although Arabidopsis seed studies have also found high correlations between P, Mg, and –K, no underlying chemical network or physiological cause of a P-Mg-K complex are known. All element histograms were skewed with more accessions having low grain concentrations than those having notably high concentrations. This skewing plus the 2- to 100-fold range in grain concentration observed for each element among the set of diverse rices suggest that the high-concentration phenotypes result from a change in one or few genes and such simply inherited traits can often be molecularly mapped among F2 progeny. Accessions high in specific elements were sometimes found to have similar genetic or geographic origins. For example, genotypes high in Ca, Mg, P, or K were more likely to be of the japonica than of the indica subspecies. Other elements were more associated with tropical vs. temperate origins, e.g., high Cu was less prevalent among the temperate japonicas than among the tropical japonicas or indicas, and low As was most common among the temperate japonica accessions followed by the tropical japonica group, then indicas. Four of the five lines highest in Mo-concentration originated from Malaysia, suggesting they share a heritable mechanism underlying their high Mo-concentration. Accessions exhibiting extreme grain mineral concentration for one or more of the observed minerals were crossed to develop segregating progeny populations in which to molecularly map genes affecting rice grain nutritional value and rice plant nutrition.

Last Modified: 10/1/2014
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