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Title:Discovery and characterization of genes controlling nitrogen utilization in maize
Author(s):Liu, Yuhe
Director of Research:Moose, Stephen P.
Doctoral Committee Chair(s):Moose, Stephen P.
Doctoral Committee Member(s):Juvik, John A.; Ming, Ray R.; Brown, Patrick J.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Nitrogen use efficiency (NUE)
quantitative trait loci (QTL)
Gene Discovery
Sustainable Intensification
Plant Breeding
Abstract:Maize (Zea mays, L.) yield has a well-documented response to supplemental nitrogen (N). As a result of this response, supplemental N is applied to nearly all maize grown in the U.S. and other industrialized nations, and the use of N fertilizer in developing countries is on the rise. While sufficient nitrogen fertilization contributes to increased maize yield and better nutritional quality, excessive N inflates the production cost, increases energy consumption, and poses significant risks to the environment and human health. Therefore, improving the nitrogen utilization efficiency (NUtE) of maize hybrids is instrumental to reducing the nitrogen footprint of future agriculture while increasing crop productivity. In order to dissect the genetic architecture of maize N utilization, we conducted a genetic mapping study using a hybrid population created by crossing the intermated B73 x Mo17 recombinant inbred lines (IBMRIL) to the Illinois High Protein 1 (IHP1) inbred line. Agronomic N utilization, component physiological traits, and gene expression variation were used as traits for quantitative trait loci (QTL) analysis. Subsequent fine mapping using dense SNPs generated with genotyping-by-sequencing (GBS) greatly narrowed down primary QTL intervals and resulted in a small number of positional candidates for each locus. Two leading candidate genes were characterized further, ZmHVA22, a regulator of autophagy and nutrient remobilization, and L-asparaginase that mediates nutrient sensing and rate of N flux The functional effects of ZmHVA22 and L-asparaginase on N utilization were investigated in both inbred and hybrid genotypes with different genetic variants for these two genes. Field trial results demonstrated improved N utilization for hybrids with higher expression levels of either ZmHVA22 or L-asparaginase. When examined in populations representative of historical diversity in US Corn Belt maize, patterns of allelic diversity indicated strong divergent selection for ZmHVA22 and approximate 400 other maize genes enriched for regulatory functions and the control of N utilization. This pattern supports the view that heterozygosity at these loci is favored for performance of current elite maize hybrids, perhaps as a compromise breeding solution to developmental, physiological and metabolic tradeoffs such as the remobilization of N from vegetative source to reproductive sink organs. Reliable production of preferred heterozygous genotypes is thus operationally achieved by separation of inbred lines into heterotic groups diversified in part by alternative alleles governing regulatory tradeoffs, and likely represents a current constraint to future genetic improvements in maize. Our study demonstrated the concept and effectiveness of mapping complex field traits using a hybrid mapping population, as well as the efficacy of fine mapping using genetic marker saturation with next-generation-sequencing technology. Candidates identified from our study provided insights on pathways and mechanisms controlling N utilization in maize and possibly other crop species. Our results offer useful resources to marker assisted breeding and lay the foundation for modifying NUtE genes through genetic engineering.
Issue Date:2014-05-30
Rights Information:Copyright 2014 Yuhe Liu
Date Available in IDEALS:2014-05-30
Date Deposited:2014-05

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