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PubMed2004

Dissecting the maize genome by using chromosome addition and radiation hybrid lines.

We have developed from crosses of oat (Avena sativa L.) and maize (Zea mays L.) 50 fertile lines that are disomic additions of individual maize chromosomes 1-9 and chromosome 10 as a short-arm telosome. The whole chromosome 10 addition is available only in haploid oat background. Most of the maize chromosome disomic addition lines have regular transmission; however, chromosome 5 showed diminished paternal transmission, and chromosome 10 is transmitted to offspring only as a short-arm telosome. To further dissect the maize genome, we irradiated monosomic additions with gamma rays and recovered radiation hybrid (RH) lines providing low- to medium-resolution mapping for most of the maize chromosomes. For maize chromosome 1, mapping 45 simple-sequence repeat markers delineated 10 groups of RH plants reflecting different chromosome breaks. The present chromosome 1 RH panel dissects this chromosome into eight physical segments defined by the 10 groups of RH lines. Genomic in situ hybridization revealed the physical size of a distal region, which is represented by six of the eight physical segments, as being approximately 20% of the length of the short arm, representing approximately one-third of the genetic chromosome 1 map. The distal approximately 20% of the physical length of the long arm of maize chromosome 1 is represented by a single group of RH lines that spans >23% of the total genetic map. These oat-maize RH lines provide valuable tools for physical mapping of the complex highly duplicated maize genome and for unique studies of inter-specific gene interactions.

Avena↗

PubMed2005

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.

Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of MAGIs are correctly assembled. Because the rates at which junction-testing PCR primers for genomic survey sequences (90-92%) amplify genomic DNA are not significantly different from those of control primers ( approximately 91%), we conclude that a very high percentage of genic MAGIs accurately reflect the structure of the maize genome. EST alignments, ab initio gene prediction, and sequence similarity searches of the MAGIs are available at the Iowa State University MAGI web site. This assembly contains 46,688 ab initio predicted genes. The expression of almost half (628 of 1,369) of a sample of the predicted genes that lack expression evidence was validated by RT-PCR. Our analyses suggest that the maize genome contains between approximately 33,000 and approximately 54,000 expressed genes. Approximately 5% (32 of 628) of the maize transcripts discovered do not have detectable paralogs among maize ESTs or detectable homologs from other species in the GenBank NR nucleotide/protein database. Analyses therefore suggest that this assembly of the maize genome contains approximately 350 previously uncharacterized expressed genes. We hypothesize that these "orphans" evolved quickly during maize evolution and/or domestication.

Chromosomes, Artificial, Bacterial↗

PubMed1998

Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions.

A set of oat-maize chromosome addition lines with individual maize (Zea mays L.) chromosomes present in plants with a complete oat (Avena sativa L.) chromosome complement provides a unique opportunity to analyze the organization of centromeric regions of each maize chromosome. A DNA sequence, MCS1a, described previously as a maize centromere-associated sequence, was used as a probe to isolate cosmid clones from a genomic library made of DNA purified from a maize chromosome 9 addition line. Analysis of six cosmid clones containing centromeric DNA segments revealed a complex organization. The MCS1a sequence was found to comprise a portion of the long terminal repeats of a retrotransposon-like repeated element, termed CentA. Two of the six cosmid clones contained regions composed of a newly identified family of tandem repeats, termed CentC. Copies of CentA and tandem arrays of CentC are interspersed with other repetitive elements, including the previously identified maize retroelements Huck and Prem2. Fluorescence in situ hybridization revealed that CentC and CentA elements are limited to the centromeric region of each maize chromosome. The retroelements Huck and Prem2 are dispersed along all maize chromosomes, although Huck elements are present in an increased concentration around centromeric regions. Significant variation in the size of the blocks of CentC and in the copy number of CentA elements, as well as restriction fragment length variations were detected within the centromeric region of each maize chromosome studied. The different proportions and arrangements of these elements and likely others provide each centromeric region with a unique overall structure.

Base Sequence↗

PubMed1998

Investigation of the bottleneck leading to the domestication of maize.

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize-maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians-but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length.

Agriculture↗

PubMed2003

Extractable soil lipids and microbial activity as affected by Bt and non Bt maize grown on a silty clay loam soil.

Pyrolysis-gas (Py-GC) chromatography was used to characterize extractable lipids from Bt and non-Bt maize shoots and soils collected at time of harvesting. Py-GC-MS (mass spectrometry) showed that the concentrations of total alkenes identified in non-Bt shoots and soils were 47.9 and 21.3% higher than in Bt maize shoots and soils, respectively. N-alkanes identified were of similar orders of magnitude in Bt and non-Bt maize shoots, but were 28.6% higher in Bt than in non-Bt soils. Bt maize shoots contained 29.7% more n-fatty acids than non-Bt maize shoots, whereas the concentrations of n-fatty acids in Bt soils were twice as high as those in non-Bt soils. Concentrations of unsaturated fatty acids in Bt maize shoots were 22.1% higher than those in non-Bt maize shoots, while concentrations of unsaturated fatty acids were 22.5% higher in non-Bt than in Bt soils. The cumulative CO2-C evolved from soils under Bt and non-Bt crops was 30.5% lower under Bt as compared to non-Bt crops, whereas when maize shoots were added to Bt and non-Bt soils, the decrease in CO2-C evolved were 16.5 and 23.6%, respectively. Our data showed that the cultivation of Bt maize significantly increased the saturated to unsaturated lipid ratios in soils which appeared to negatively affect microbial activity.

Bacillus thuringiensis↗

PubMed2006

Zinc absorption in Guatemalan schoolchildren fed normal or low-phytate maize.

BACKGROUND: Poor bioavailability of zinc from high-phytate diets is an important contributory factor to zinc deficiency in low-income populations. OBJECTIVE: The objective of this study was to determine the effect of low-phytate maize consumption on zinc absorption. DESIGN: The participants were apparently healthy children from the Central Highlands of Guatemala. Sixty children (20 per group) were randomly assigned to be fed only the low-phytate maize or 1 of 2 control maizes, the isohybrid wild-type maize or a local maize, for a 10-wk period. During the final week, the fractional absorption of zinc for all meals was measured during 1 d with the use of zinc stable isotopes and a dual isotope ratio technique based on urine enrichment data. RESULTS: Mean (+/-SD) phytate intakes for the low-phytate, wild-type, and local maize groups were 1536 +/- 563, 2056 +/- 517, and 2253 +/- 687 mg/d, respectively. Corresponding zinc intakes were 8.6 +/- 2.5, 8.1 +/- 2.0, and 9.7 +/- 2.6 mg/d, and the dietary phytate:zinc molar ratios were 18 +/- 5, 26 +/- 6, and 23 +/- 5. Corresponding fractional absorptions of zinc were 0.32 +/- 0.07, 0.28 +/- 0.07, and 0.29 +/- 0.06. The respective values for total absorbed zinc were 2.72 +/- 0.88, 2.30 +/- 0.96, and 2.78 +/- 1.04 mg/d. No significant differences in either the fractional absorption of zinc or total absorbed zinc were seen between the maize groups. CONCLUSION: Under the conditions of the present study, zinc absorption was not increased by the long-term use of low-phytate maize in children whose major dietary staple is maize.

Anthropometry↗

PubMed2006

Panzea: a database and resource for molecular and functional diversity in the maize genome.

Serving as a community resource, Panzea (http://www.panzea.org) is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every approximately 100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.

Chromosome Mapping↗

PubMed2004

Close split of sorghum and maize genome progenitors.

It is generally believed that maize (Zea mays L. ssp. mays) arose as a tetraploid; however, the two progenitor genomes cannot be unequivocally traced within the genome of modern maize. We have taken a new approach to investigate the origin of the maize genome. We isolated and sequenced large genomic fragments from the regions surrounding five duplicated loci from the maize genome and their orthologous loci in sorghum, and then we compared these sequences with the orthologous regions in the rice genome. Within the studied segments, we identified 11 genes that were conserved in location, order, and orientation. We performed phylogenetic and distance analyses and examined the patterns of estimated times of divergence for sorghum and maize gene orthologs and also the time of divergence for maize orthologs. Our results support a tetraploid origin of maize. This analysis also indicates contemporaneous divergence of the ancestral sorghum genome and the two maize progenitor genomes about 11.9 million years ago (Mya). On the basis of a putative conversion event detected for one of the genes, tetraploidization must have occurred before 4.8 Mya, and therefore, preceded the major maize genome expansion by gene amplification and retrotransposition.

Chromosomes, Artificial, Bacterial↗

PubMed1990

Molecular Characterization of the Brittle-2 Gene Effect on Maize Endosperm ADPglucose Pyrophosphorylase Subunits.

Activity of the enzyme ADPglucose pyrophosphorylase is known to be reduced in maize (Zea mays L.) endosperm mutants at two independent loci, Shrunken-2 (Sh(2)) and Brittle-2 (Bt(2)). Spinach leaf ADPglucose pyrophosphorylase has previously been shown to comprise two subunits of 51 and 54 kilodaltons. Anti-bodies raised to each of the two subunits of spinach leaf ADPglucose pyrophosphorylase were found to cross-react to different bands on Western blots prepared from polyacrylamide gel electrophoresis separated wild-type maize endosperm proteins. The anti-spinach leaf 51 kilodalton subunit antibody cross-reacted with a 55 kilodalton maize endosperm protein and the anti-spinach leaf 54 kilodalton subunit antibody cross-reacted with a 60 kilodalton maize endosperm protein. These immunological reactions were observed in maize endosperm extracts and with a highly purified preparation of maize endosperm ADPglucose pyrophosphorylase. Mutant bt(2) endosperm lacked the 55 kilodalton subunit while mutant sh(2) endosperm lacked the 60 kilodalton subunit on Western blots. These results suggest that the maize endosperm ADPglucose pyrophosphorylase is made up of two immunologically dissimilar subunits and that the bt(2) and sh(2) mutations cause reduction in ADPglucose pyrophosphorylase activity through the lack of one of these two subunits. An ADPglucose pyrophosphorylase cDNA clone antigenically selected from a rice seed cDNA expression library was found to hybridize strongly with a cDNA corresponding to a maize endosperm transcript which is absent in a W64A bt(2) mutant. Thus, the bt(2) mutant causes the absence not only of the small subunit but of the corresponding transcript. Bt(2) is implicated as the structural gene for the small (54 kilodalton) subunit of maize endosperm ADPglucose pyrophosphorylase.

Journal Article↗

PubMed1990

Cloning, sequence analysis, and expression of a cDNA encoding a plastid-localized heat shock protein in maize.

We have cloned and characterized a cDNA encoding a maize (Zea mays L.) heat shock protein (HSP), HSP26. The mRNA of HSP26 is present as a single mRNA species of 1.1 kilobase pairs in size and is detectable when maize seedlings are treated at 40 degrees C but not at 28 degrees C. Accumulation of HSP26 mRNA was detected after 10 minutes of incubation at 40 degrees C, reaching the maximum level after 1 hour. Comparison of the deduced amino acid sequence of maize HSP26 to other HSPs indicated a strong homology to the sequences of two nuclear encoded HSPs that are transported into the chloroplasts during heat shock: pea HSP21 and soybean HSP22. Maize HSP26 was also found to cross-react with anti-pea chloroplast HSP21 antibodies. Because of the sequence homology between maize HSP26, soybean HSP22, and pea HSP21, in vitro chloroplast protein import experiments were conducted. The in vitro synthesized maize HSP26 is specifically imported to the soluble fraction of the chloroplast and processed to a smaller polypeptide. The sequence homology and antibody cross-reactivity between maize HSP26 and pea HSP21 have allowed us to conclude that maize HSP26 is a nuclear-encoded, plastid-localized protein in maize.

Journal Article↗

PubMed2003

The maize genome contains a helitron insertion.

The maize mutation sh2-7527 was isolated in a conventional maize breeding program in the 1970s. Although the mutant contains foreign sequences within the gene, the mutation is not attributable to an interchromosomal exchange or to a chromosomal inversion. Hence, the mutation was caused by an insertion. Sequences at the two Sh2 borders have not been scrambled or mutated, suggesting that the insertion is not caused by a catastrophic reshuffling of the maize genome. The insertion is large, at least 12 kb, and is highly repetitive in maize. As judged by hybridization, sorghum contains only one or a few copies of the element, whereas no hybridization was seen to the Arabidopsis genome. The insertion acts from a distance to alter the splicing of the sh2 pre-mRNA. Three distinct intron-bearing maize genes were found in the insertion. Of most significance, the insertion bears striking similarity to the recently described DNA helicase-bearing transposable elements termed HELITRONS: Like Helitrons, the inserted sequence of sh2-7527 is large, lacks terminal repeats, does not duplicate host sequences, and was inserted between a host dinucleotide AT. Like Helitrons, the maize element contains 5' TC and 3' CTRR termini as well as two short palindromic sequences near the 3' terminus that potentially can form a 20-bp hairpin. Although the maize element lacks sequence information for a DNA helicase, it does contain four exons with similarity to a plant DEAD box RNA helicase. A second Helitron insertion was found in the maize genomic database. These data strongly suggest an active Helitron in the present-day maize genome.

Alternative Splicing↗

PubMed2005

Duodenal ulcer in South Africa: home-pounded versus milled maize.

BACKGROUND: In South Africa there is suggestive evidence that home-pounded maize protects against duodenal ulceration. Therefore the purpose of the present paper was to test, in an animal model, whether oil from home-pounded maize gives protection against ulceration and whether this effect is present in commercially prepared maize oil. METHODS: Gastric ulceration was induced in rats with topical ethanol 1 h after giving oil prepared either from fresh-pounded or from commercially treated maize. The lengths of the linear ulcers produced were measured with a planimeter and summed in each rat. Control observations were made using arachis oil (which is known not to be ulceroprotective) and horse gram lipid (which is known to be strongly ulceroprotective). Statistical comparisons were performed mainly with the Mann-Whitney U-test, but also with reference to the normal distribution. Thin-layer chromatography (TLC) was performed on the oil from fresh maize, and the fractions similarly investigated for ulceroprotective activity. RESULTS: Fresh maize oil was strongly ulceroprotective (P = 0.0039), commercial maize oil was not (P = 0.2864). The active ingredient in the fresh maize oil was located in the fraction near the solvent front. CONCLUSION: These findings support the hypothesis that home-pounded maize protects against duodenal ulceration.

Animal Feed↗

PubMed2006

Genetically engineered plants, endangered species, and risk: a temporal and spatial exposure assessment for Karner blue butterfly larvae and Bt maize pollen.

Genetically engineered maize (Zea mays) containing insecticidal endotoxin proteins from Bacillus thuringiensis (Bt) delta-endotoxin proteins has been adopted widely in the Midwestern United States. The proteins are toxic to several lepidopteran species and because a variety of maize tissues, including pollen, may express the endotoxins, the probability of exposure to nontarget species, including endangered species, needs to be understood. The objective of this study was to assess the potential temporal and spatial exposure of endangered Karner blue butterfly larvae (Lycaeides melissa samuelis) to Bt maize pollen in Wisconsin using probabilistic exposure techniques and geographic information systems analysis. Based on degree-day modeling of butterfly phenology and maize pollen shed, there is some potential for temporal exposure of larvae to maize pollen. However, in the majority of years and locations, maize pollen shed most likely will occur after the majority of larval feeding on wild lupine (Lupinus perennis). The spatial analysis indicates that some Karner blue butterfly populations occur in close proximity to maize fields, but in the vast majority of cases the butterfly's host plant and maize fields are separated by more than 500 m. A small number of potential or existing Karner blue butterfly sites are located near maize fields, including sites in two of the four counties where temporal overlap is most likely. The exposure assessment indicates that these two counties should receive the highest priority to determine if Karner blue butterfly larvae are actually at risk and then, if needed, to reduce or prevent exposure.

Animals↗

PubMed1997

Comparison of milk and maize based diets in kwashiorkor.

UNLABELLED: The dual sugar test of intestinal permeability is a reliable non-invasive way of assessing the response of the small intestinal mucosa to nutritional rehabilitation. AIM: To compare a local mix of maize-soya-egg to the standard milk diet in the treatment of kwashiorkor. DESIGN: The diets were alternated three monthly in the sequence milk-maize-milk. There were a total of 533 kwashiorkor admissions of at least five days during the study who received either milk or maize. Intestinal permeability was assessed at weekly intervals by the lactulose-rhamnose test in 100 kwashiorkor cases, including 55 on milk and 45 on the maize diet. RESULTS: Permeability ratios (95% confidence interval) on the milk diet improved by a mean of 6.4 (1.7 to 11.1) compared with -6.8 (-16.8 to 5.0) in the maize group. The improved permeability on milk occurred despite more diarrhoea, which constituted 34.8% of hospital days (29.8 to 39.8) compared with 24.3% (17.8 to 30.8) in the maize group. Case fatality rates for all 533 kwashiorkor admissions were 13.6% v 20.9%, respectively, giving a relative risk of death in the maize group of 1.54 (1.04 to 2.28). The maize group also had more clinical sepsis (60% v 31%) and less weight gain (2.9 v 4.4 g/kg/day) than the milk group. IMPLICATIONS: Milk is superior to a local maize based diet in the treatment of kwashiorkor in terms of mortality, weight gain, clinical sepsis, and improvement in intestinal permeability.

Animals↗

PubMed2005

A selfish gene governing pollen-pistil compatibility confers reproductive isolation between maize relatives.

Some populations of maize's closest relatives, the annual teosintes of Mexico, are unreceptive to maize pollen. When present in the pistil (silk and ovary) a number of maize genes discriminate against or exclude pollen not carrying the same allele. An analogous gene Tcb1-s was found in some teosinte populations but not in sympatric or parapatric maize. It was polymorphic among populations of teosinte growing wild, but regularly present in populations growing in intimate association with maize as a weed. Introduction of Tcb1-s into maize substantially to fully restored compatibility with Tcb1-s carrying teosintes. Although Tcb1-s pollen can fertilize tcb1 tcb1 maize, it is at a competitive disadvantage relative to tcb1 pollen. Hence, the influence of Tcb1-s on crossability is bidirectional. In the absence of maize, Tcb1-s can increase in teosinte populations without improving their fitness. In the presence of maize, Tcb1-s appears to have been co-opted to provide reproductive isolation for adaptation to a cultivated habitat.

Breeding↗

PubMed2003

Study on the weed-crop competition for nutrients in maize.

Considering the effect of crop-weed competition the rate of weed growing, the competitiveness of the occurring weed species and the duration of competition are determining factors. Experiments were carried out on fields in order to collect data on the effect of early weed competition on maize, including the competition for nutrients and the possible rate of nutrient removal by weeds. From 7 sampling areas of the 9.2 ha field weeds and maize samples were collected 1 month after the sowing of maize. We determined the total numbers and the species numbers of weeds by plots. The removed plant species and maize were weighed then dried until the weight balance was reached. The samples were tested for N, P, K and Ca. Comparison was done with the weight and nutrient element content of maize plants taken from the treated, weed-free area. At the same time comparative analyses were made with the mass and nutrient contents of maize plants. There were 12 occurring weed species in this experiment. Based on the rate of weed cover the following species were dominant: Datum stramonium L., Cannabis sativa L., Amaranthus chlorostachis Willd., Chenopodium album L., Chenopodium hybridum L. Our experiments revealed that in the areas being likely to produce high weed populations and showing a considerable high nutrient removal by weeds, the competition between weed plants and maize occurs at an earlier stage of the vegetation period of maize than on fields with moderate weed populations. Weeds have utilised significant amount of nutrients which has been many fold of maize in case of unit area.

Amaranthus↗

PubMed1991

Hypoxia enhances phosphorylation of eukaryotic initiation factor 4A in maize root tips.

We have identified two isoforms of initiation factor 4A (eIF-4A) in maize root tips, with distinct isoelectric points and similar molecular mass (approximately 50 kDa). Both isoforms of maize eIF-4A cross-react with antibodies raised against wheat germ eIF-4A, and one of the maize proteins (higher pI isoform) comigrates with purified wheat germ eIF-4A on two-dimensional gels. The two maize eIF-4As were indistinguishable by comparative peptide fingerprint analysis, which also showed a very strong similarity between eIF-4A in maize roots and wheat germ. Maize eIF-4As copurify with eIF-4F and eIF-(iso)4F on a 7-methyl-GTP-Sepharose affinity column, indicating that they are part of the 5'-cap-binding complex. Two-dimensional gel electrophoresis and immunoblotting of proteins from 32P-labeled maize root tips revealed that the lower pI isoform of eIF-4A is phosphorylated. Two-dimensional phosphopeptide maps of trypsin-digested eIF-4A contained one principal phosphorylated fragment; phosphoamino acid analysis indicated phosphorylation of threonine. In oxygenated maize root tips, the ratio of phosphorylated to nonphosphorylated eIF-4A is approximately 0.2. This ratio increases to approximately 1 within 20 min following the onset of hypoxia, due to interconversion between the two maize eIF-4A isoforms. The hypoxia-induced phosphorylation of eIF-4A is discussed with respect to metabolic responses, and the translational control of gene expression, in hypoxic plant tissues.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2002

Genetically modified maize and soybean on the Egyptian food market.

The results of a survey study on food samples produced from genetically modified soybean and maize collected from the Egyptian market are presented. Forty samples of soybean and 40 samples of maize products have been gathered randomly from markets in Cairo and Giza. The genetic modification was detected by polymerase chain reaction (PCR) using official detection methods according to section 35 of the German Foodstuffs Act. Samples were investigated for the presence of material derived from the following genetically modified organisms (GMOs) all of which are approved for food use in Europe: Roundup Ready soybean (RRS) and maize lines Bt176, Bt11, T25 and MON810. In addition, samples were examined in qualitative and quantitative analysis for the presence of material derived from the transgenic maize line StarLink (Aventis) which was approved for animal feed use exclusively in the US. Twenty % of 40 investigated soy samples contained Roundup Ready soybean; 15% of 40 maize samples tested positive for Bt176 and 12.5% positive for Bt11 maize. Furthermore, the presence of StarLink maize could clearly be demonstrated in four samples mixed with Bt176 and Bt11. The percentage of StarLink was less than 1% in quantitative analysis. The maize lines T25 and MON810 were not detected.

DNA, Plant↗