Spoiling the Whole Bunch: Quality Control Aimed at Preserving the Integrity of High-Throughput Genotyping

False-positive or false-negative results attributable to undetected genotyping errors and confounding factors present a constant challenge for genome-wide association studies (GWAS) given the low signals associated with complex phenotypes and the noise associated with high-throughput genotyping. In the context of the genetics of kidneys in diabetes (GoKinD) study, we identify a source of error in genotype calling and demonstrate that a standard battery of quality-control (QC) measures is not sufficient to detect and/or correct it. We show that, if genotyping and calling are done by plate (batch), even a few DNA samples of marginally acceptable quality can profoundly alter the allele calls for other samples on the plate. In turn, this leads to significant differential bias in estimates of allele frequency between plates and, potentially, to false-positive associations, particularly when case and control samples are not sufficiently randomized to plates. This problem may become widespread as investigators tap into existing public databases for GWAS control samples. We describe how to detect and correct this bias by utilizing additional sources of information, including raw signal-intensity data.     

Use of tropical maize for bioethanol production

Tropical maize is an alternative energy crop being considered as a feedstock for bioethanol production in the North Central and Midwest United States. Tropical maize is advantageous because it produces large amounts of soluble sugars in its stalks, creates a large amount of biomass, and requires lower inputs (e.g. nitrogen) than grain corn. Soluble sugars, including sucrose, glucose and fructose were extracted by pressing the stalks at dough stage (R4). The initial extracted syrup fermented faster than the control culture grown on a yeast extract/phosphate/sucrose medium. The syrup was subsequently concentrated 1.25–2.25 times, supplemented with urea, and fermented using Saccharomyces cerevisiae for up to 96 h. The final ethanol concentrations obtained were 8.1 % (v/v) to 15.6 % (v/v), equivalent to 90.3–92.2 % of the theoretical yields. However, fermentation productivity decreased with sugar concentration, suggesting that the yeast might be osmotically stressed at the increased sugar concentrations. These results provide in-depth information for utilizing tropical maize syrup for bioethanol production that will help in tropical maize breeding and development for use as another feedstock for the biofuel industry.     

Growth and composition of maize kernels cultured in vitro with varying supplies of carbon and nitrogen

This study employed in vitro seed culture to determine how C and N supply influence the growth (i.e. starch accumulation) and protein composition of maize (Zea mays L.) endosperm. Immature kernels were grown to maturity on liquid medium containing various concentrations of C (sucrose at 234 millimolar [low] and 468 millimolar [high]) and N (amino acid mixture ranging in N from 0 to 144 millimolar). Low C supply limited starch, but not N, accumulation in the endosperm. With high C, endosperm starch and protein content increased concomitantly as N supply increased from 0 to 13.4 millimolar. Endosperm growth was unaffected by additional N until concentrations exceeding approximately 72 millimolar reduced starch accumulation. A similar inhibition of starch deposition occurred with lower N concentrations when kernels were grown with low C. Endosperm total N content reached a point of saturation with approximately 36 millimolar N in the medium, regardless of C supply. Zein synthesis in the endosperm responded positively across all N levels, while glutelin content remained static and albumin/globulin proteins were reduced in amount when N supply was greater than 36 millimolar. A reciprocal, inverse relationship was observed in mature endosperm tissue between the concentrations of free amino acids and soluble sugars. Our data suggest that under N stress starch and protein accumulation in the endosperm are interdependent, at least in appearance, but are independent otherwise.     

The effects of ear removal on senescence and metabolism of maize

Ears were removed from field grown maize (Zea mays L.) to determine the effects on senescence and metabolism and to clarify conflicting literature reports pertaining to these effects. Ears were removed at three days after anthesis and comparisons were made of changes in metabolism between eared and earless plants until grain of the eared plants matured as judged by black layer formation.     

Availability of reduced N and carbohydrates for ear development of maize

Changes in dry weights, reduced N, nitrate, and nitrate reductase activity of various plant parts of the above ground vegetation (stover) and ears of field grown maize were measured at intervals between anthesis and grain maturity. Nonstructural carbohydrate contents were also measured in some instances. Changes in dry weight and reduced N content were used to approximate net in situ photosynthetic and nitrate assimilation activities and to determine whether the availability of photosynthate or reduced N was limiting grain production.     

Grain Protein Accumulation and the Relationship between Leaf Nitrate Reductase and Protease Activities during Grain Development in Maize (Zea mays L.): I. VARIATION BETWEEN GENOTYPES

Four maize hybrids, two with high and two with low levels of postanthesis nitrate reductase activity were grown under field conditions. The characteristic enzyme patterns had been established in previous work. Nitrate reductase and proteases were measured in three representative leaves (ear leaf, fourth leaf above and fourth leaf below the ear) at intervals throughout the period of grain development. Concurrent with enzyme sampling, other plants were harvested and subdivided into top, middle and lower leaves, husks, stalks, and ear. Dry weights, nitrate, and reduced N were determined on all plant parts for each sampling. These data established the rate of N accumulation by the grain and depletion from the vegetative material and provide some insight into the relation between newly reduced and remobilized N and accumulation of grain N. Other plants were harvested at maturity for yield and harvest indices for dry weight and N.     

Response of enzymes and storage proteins of maize endosperm to nitrogen supply

To examine the effects of N nutrition upon endosperm development, maize (Zea mays) kernels were grown in vitro with either 0, 3.6, 7.1, 14.3, or 35.7 millimolar N. Kernels were harvested at 20 days after pollination for determination of enzyme activities and again at maturity for quantification of storage products and electrophoretic separation of zeins. Endosperm dry weight, starch, zein-N, and nonzein-N all increased in mature kernels as N supply increased from zero to 14.3 millimolar. The activities of sucrose synthase, aldolase, phosphoglucomutase, glutamate-pyruvate transaminase, glutamate-oxaloacetate transaminase, and acetolactate synthase increased from 1- to 2.5-fold with increasing N supply. Adenosine diphosphate-glucose pyrophosphorylase and both ATP- and PPi-dependent phosphofructokinases increased to lesser extents, while no significant response was detected for hexose kinases and glutamine synthetase. Nitrogen-induced changes in enzyme activities were often highly correlated with changes in final starch and/or zein-N contents. Separation of zeins indicated that these peptides were proportionately enhanced by N supply, with the exception of C-zein, which was relatively insensitive to N. These data indicate that at least a portion of the yield increase in maize produced by N fertilization is induced by a modification of kernel metabolism in response to N supply.     

Differential Senescence of Maize Hybrids following Ear Removal : I. Whole Plant

Visual senescence symptoms and associated changes in constituent contents of three field-grown maize (Zea mays L.) hybrids (Pioneer brand 3382, B73 × Mo17, and Farm Service brand 854) were compared in response to ear removal. Whole plants were harvested at eight intervals during the grain-filling period, and analyzed for dry matter, total N and nitrate N, phosphorus, sugars, and starch.

Upper leaves of earless P3382 and B73 × Mo17 showed reddish discoloration by 25 days after anthesis (DAA) and all leaves had lost most of their chlorophyll by 40 DAA. In striking contrast, leaves of earless FS854 plants remained green and similar in appearance to eared controls throughout the grain-filling period.

For all hybrids, ear removal led to a decrease in dry weight, reduced N, total N, and phosphorus contents of the total plant, and an increase in carbohydrate content of the leaves and stalks, relative to respective controls. Although changes in carbohydrate and N contents, which previously had been associated with senescence, were observed for all earless hybrids, these changes were followed by accelerated senescence and early death only for P3382 and B73 × Mo17. By 30 DAA, earless P3382 and B73 × Mo17 plants ceased to accumulate dry weight, total N, and phosphorus, indicating a termination of major metabolic activities. In contrast, earless FS854 plants retained a portion of these metabolic activities until 58 DAA, indicating a role for roots in determining rate of senescence development. Thus, the course of senescence was more accurately reflected by measurements of metabolic activities than by measurements of metabolite contents at any given time. These results show that the ear per se does not dictate the rate or completion of the senescence process, and implicated an association between the continued accumulation of N and associated root activities with the delayed senescence pattern of the earless FS854 plants. It is evident that studies involving control of senescence among species must also consider genotypic influences within species.

     

Effect of foliar applications of urea on accelerated senescence of maize induced by ear removal

Field grown maize (Zea mays L. cv B73 × Mo17) plants, with and without ears, were sprayed with urea solutions to determine whether foliar application of N could prevent or delay the accelerated loss of reduced N from the leaf and leaf senescence induced by ear removal. Urea sprays were applied at 7, 14, and 21 days after anthesis in three separate and equal applications that provided a total of 67 kilograms N per hectare or 1 gram N per plant. Treatments were arranged in a 2 × 2 factorial in a randomized complete block with five replicates. Appropriate plant and leaf samplings and assays were made.

In response to spray treatments, net increases of reduced N were detected in the whole shoot and plant parts, especially the stalk of the earless plants and grain of the eared plants. There was no effect of urea spray treatment on the normal loss of N from the leaves or rate of senescence of the eared plants or on the accelerated loss of N from the leaves or rate of senescence induced by ear removal. Grain and stover yields were unaffected by the spray treatment.

Apparently the plants were unable to utilize the urea N applied to the vegetation (primarily leaves) after anthesis to enhance or extend the accumulation of dry weight by either eared or earless plants.