Identification and validation of QTLs associated with concentrations of mineral nutrients in unmilled grain of two mapping populations derived from 'Lemont' × 'TeQing'

Authors: Pinson, Shannon; MIN, ZHANG - Purdue University; TARPLEY, LEE - Texas Agrilife; LAHNER, BRETT - Purdue University; GUERINOT, MARY LOU - Dartmouth College; SALT, DAVID - University Of Aberdeen

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 3/7/2012
Publication Date: 7/1/2012
Citation: Pinson, S.R., Min, Z., Tarpley, L., Lahner, B., Guerinot, M., Salt, D. 2012. Identification and validation of QTLs associated with concentrations of mineral nutrients in unmilled grain of two mapping populations derived from 'Lemont' × 'TeQing'. 35th Rice Technical Working Group Meeting Proceedings,Feb.27-March 1, 2012, Hot Springs, Arkansas. CDROM.

Interpretive Summary:

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 the grain/food product through traditional breeding. Since it does not require genetic engineering, it is acceptable to many consumers, and readily acquires organic certification if the crop is grown under organic field conditions. 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. One critical step toward developing nutritionally improved rice varieties is to identify where the underlying genes reside along the rice chromosomes. 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. Two rice mapping populations were used so that putative QTLs could be identified in one, and verified in the other. The first population analyzed was a set of 280 ‘Lemont’ x ‘TeQing’ recombinant inbred lines (LT-RILs), complemented by analysis of a set of 123 TeQing-into-Lemont backcross introgression lines (TILs). To increase opportunity to detect and characterize grain-mineral QTLs, the TILs were grown under two contrasting field redox conditions, flooded and unflooded (flush-irrigated). Soil redox is known to alter mineral availability, and so was expected to affect grain mineral concentrations. The LT-RILs were grown flooded over 5 years, one replication per year, while the TILs were grown under flooded and unflooded conditions over two years, two replications per treatment per year. ICP-MS was used to analyze the harvested brown rice for variation in accumulation of 16 elements, namely Mg, P, K, S, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Mo, and Cd. Correlations between the individual elements and between each element with grain shape, plant height, and time of heading were also studied. Transgressive segregation was observed among the LT-RILs for all 16 elements. We identified 127 QTLs that affect the grain concentration of individual mineral elements. More QTLs were found significant among flooded TILs (92) than among unflooded TILs (42) or among flooded LT-RILs (40). The 127 QTLs identified as associated with a single-element were found clustered into 40 genomic regions, with each region being often associated with multiple grain elements. Nearly all of the grain element loci were linked to QTLs affecting additional elements, supporting the concept of element networks within plants. Several of the grain element QTLs co-located with QTLs for grain shape, plant height, and days to heading; but did not always differ for grain elemental concentration as predicted by those traits alone. A number of interesting element × element patterns were found, including a strong P-Mg-K complex. Gene-identification studies such as this one are considered exploratory studies. 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 nutrient