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Title:Genetic analysis of grain protein concentration and related traits in the Illinois protein strain recombinant inbred population of maize
Author(s):Lucas, Christine
Director of Research:Moose, Stephen P.
Doctoral Committee Chair(s):Moose, Stephen P.
Doctoral Committee Member(s):Brown, Patrick J.; Rodriguez-Zas, Sandra L.; Rayburn, A.L.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):maize
grain protein
kernel composition
grain starch
zein
Illinois Protein Strains
Floury2-mRFP1
Abstract:Maize kernels accumulate nitrogen supplied as amino acids by vegetative source tissues as the abundant zein proteins. However, zein protein is deficient in essential amino acids, and limited knowledge of zein regulation impedes approaches for achieving more nutritious Quality Protein Maize. We employ a candidate gene approach for investigating potential targets of more than a century of divergent selection for grain protein concentration in the Illinois High Protein (IHP) and Illinois Low Protein (ILP) strains. Selection for grain protein concentration has specifically altered α-zein protein abundance, but has also affected whole plant nitrogen metabolism. IHP exibits elevated N uptake, N assimilation and N remobilization from leaves to grain relative to ILP. IHP specifically hyperaccumulates the transport and storage amino acid, asparagine (Asn), in leaves and seeds. Additionally, grain protein and zein protein concentrations are subject to the maternal effect, where the progeny phenotype follows that of the maternal plant. This phenomenon has been observed in a variety of maize genotypes, including IHP and ILP, but its source is unknown. A series of genetic resources derived from the Illinois selection experiment are particularly useful for investigating the genetic regulation of grain protein concentration and can additionally provide information about when candidate genes were targeted. These include inbreds derived from cycle 90, populations from cycles 65 and 100, and a population of recombinant inbred lines (Illinois Protein Strain Recombinant Inbreds or IPSRIs) created from the cross of IHP x ILP (cycle 70). Consistent with protein abundance, we document strong coordinate upregulated expression of all active alpha-zein genes in IHP seeds compared to ILP in inbreds and the cycles (65 & 105). We demonstrate that genes important for regulating Asn-cycling and zein-synthesis pathways exhibit dramatic shifts in allele frequencies and gene expression during the Illinois selection experiment. We find that divergent fixation of expression variants in Asn-cycling genes occurred by cycle 65 of selection, and selection for more strongly-expressed alleles of both Opaque2 and the Prolamin-box factor become important in more recent cycles of the Illinois Protein Strains. Using a GWAS approach on the IPSRI mapping population, we confirm the genetic effects of known gene candidates in Asn-cycling and alpha zein synthesis, and identify novel candidates. Also included in these analyses is a novel phenotype that tracks 22-kD α-zein expression by use of a red fluorescent protein (mRFP1) promoter-reporter transgene, Floury2-mRFP1. This phenotype offers advantages to standard near infrared reflectance (NIR) spectroscopy methods for measuring kernel composition in that it specifically tracks α-zein expression. As a result, this phenotype more readily detected candidate genes annotated as regulatory variants. This phenotypes was also used in a series of reciprocal crosses to investigate possible mechanisms underlying the maternal inheritance of grain protein concentration. These studies provided strong evidence for the role of plant nutrient status as the primary mechanism, which could be explained by the activities of enzymes in the Asn-cycling pathway within vegetative tissues. Collectively, this knowledge will assist breeding for QPM and reveal evolutionary features of regulatory variation. Due to the large impact of selection on nitrogen metabolism, it may also lead to improvements in nitrogen utilization in maize and possibly other cereals.
Issue Date:2014-09-16
URI:http://hdl.handle.net/2142/50467
Rights Information:Copyright 2014 Christine Lucas
Date Available in IDEALS:2014-09-16
2016-09-22
Date Deposited:2014-08


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