Maize Inbred Line B73 Research Articles

Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.

Maize early endosperm growth and development: from fertilization through cell type differentiation.

• Given the worldwide economic importance of maize endosperm, it is surprising that its development is not the most comprehensively studied of the cereals. We present detailed morphometric and cytological descriptions of endosperm development in the maize inbred line B73, for which the genome has been sequenced, and compare its growth with four diverse Nested Association Mapping (NAM) founder lines.• The first 12 d of B73 endosperm development were described using semithin sections of plastic-embedded kernels and confocal microscopy. Longitudinal sections were used to compare endosperm length, thickness, and area.• Morphometric comparison between Arizona- and Michigan-grown B73 showed a common pattern. Early endosperm development was divided into four stages: coenocytic, cellularization through alveolation, cellularization through partitioning, and differentiation. We observed tightly synchronous nuclear divisions in the coenocyte, elucidated that the onset of cellularization was coincident with endosperm size, and identified a previously undefined cell type (basal intermediate zone, BIZ). NAM founders with small mature kernels had larger endosperms (0-6 d after pollination) than lines with large mature kernels.• Our B73-specific model of early endosperm growth links developmental events to relative endosperm size, while accounting for diverse growing conditions. Maize endosperm cellularizes through alveolation, then random partitioning of the central vacuole. This unique cellularization feature of maize contrasts with the smaller endosperms of Arabidopsis, barley, and rice that strictly cellularize through repeated alveolation. NAM analysis revealed differences in endosperm size during early development, which potentially relates to differences in timing of cellularization across diverse lines of maize.

A pair of homoeolog ClpP5 genes underlies a virescent yellow-like mutant and its modifier in maize.

Gene-background interaction is a commonly observed phenomenon in many species, but the molecular mechanisms of such an interaction is less well understood. Here we report the cloning of a maize mutant gene and its modifier. A recessive mutant with a virescent yellow-like (vyl) phenotype was identified in an ethyl methanesulfonate-mutagenized population derived from the maize inbred line B73. Homozygous mutant maize plants exhibited a yellow leaf phenotype after emergence but gradually recovered and became indistinguishable from wild-type plants after approximately 2 weeks. Taking the positional cloning approach, the Chr.9_ClpP5 gene, one of the proteolytic subunits of the chloroplast Clp protease complex, was identified and validated as the candidate gene for vyl. When introgressed by backcross into the maize inbred line PH09B, the mutant phenotype of vyl lasted much longer in the greenhouse and was lethal in the field, implying the presence of a modifier(s) for vyl. A major modifier locus was identified on chromosome 1, and a paralogous ClpP5 gene was isolated and confirmed as the candidate for the vyl-modifier. Expression of Chr.1_ClpP5 is induced significantly in B73 by the vyl mutation, while the expression of Chr.1_ClpP5 in PH09B is not responsive to the vyl mutation. Moreover, expression and sequence analysis suggests that the PH09B Chr.1_ClpP5 allele is functionally weaker than the B73 allele. We propose that functional redundancy between duplicated paralogous genes is the molecular mechanism for the interaction between vyl and its modifier.

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

Maize (Zea mays) is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis). Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs). Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL) of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and mycorrhizal fungi.

Copy number variation detection using next generation sequencing read counts.

BackgroundA copy number variation (CNV) is a difference between genotypes in the number of copies of a genomic region. Next generation sequencing (NGS) technologies provide sensitive and accurate tools for detecting genomic variations that include CNVs. However, statistical approaches for CNV identification using NGS are limited. We propose a new methodology for detecting CNVs using NGS data. This method (henceforth denoted by m-HMM) is based on a hidden Markov model with emission probabilities that are governed by mixture distributions. We use the Expectation-Maximization (EM) algorithm to estimate the parameters in the model.ResultsA simulation study demonstrates that our proposed m-HMM approach has greater power for detecting copy number gains and losses relative to existing methods. Furthermore, application of our m-HMM to DNA sequencing data from the two maize inbred lines B73 and Mo17 to identify CNVs that may play a role in creating phenotypic differences between these inbred lines provides results concordant with previous array-based efforts to identify CNVs.ConclusionsThe new m-HMM method is a powerful and practical approach for identifying CNVs from NGS data.

Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines

DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-inherited DMRs provide an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at these DMRs during the generations of the NIL population development. DNA methylation level was associated with local genotypes in nearly all of the >30,000 potential cases of inheritance. The majority of the DMRs were not associated with small RNAs. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits locally (cis) inherited patterns, is highly stable, and does not require active programming by small RNAs for maintenance. DNA methylation may contribute to heritable epigenetic information in many eukaryotic genomes. In this study, we have documented the inheritance patterns and trans-generational stability for nearly 1000 DNA methylation variants in a segregating maize population. At most loci studied, the DNA methylation differences are locally inherited and are not influenced by the other allele or other genomic regions. The inheritance of DNA methylation levels across generations is quite robust with almost no examples of unstable inheritance, suggesting that DNA methylation differences can be quite stably inherited, even in segregating populations.

Identification of drought‐responsive genes by cDNA‐amplified fragment length polymorphism in maize

AbstractThe cDNA‐AFLP (amplified fragment length polymorphism) technique was performed to detect transcript‐derived fragments related to drought tolerance in maize inbred lines X178 and B73 to identify and understand drought‐responsive genes at the transcriptional level. By comparing the sequences of fragments differentially expressed between these lines under water‐stressed and well‐watered conditions, 72 drought‐responsive unique expressed sequence tags (ESTs) were identified with 41 primer combinations targeting PstI/MseI restriction sites. Most of the fragments isolated in these experiments were found to be associated with genes responsive to abiotic or biotic stresses. Subsequently, a putative R1‐type MYB transcription factor gene corresponding to ZmMYB‐R1 on bin 9.03 was obtained by in silico cloning by homology to EST sequence P36M87‐366, which matched one of the AFLPs identified in this study. The 1881 bp sequence encodes a protein of 626 amino acids that contains a single conserved MYB‐like DNA‐binding domain. Expression of green fluorescence protein fusions showed that ZmMYB‐R1 was localised in the cell nucleus. Quantitative real‐time polymerase chain reaction revealed that ZmMYB‐R1 was induced by drought, high salt, heat, cold and exogenous ABA in maize. The expression of ZmMYB‐R1 initially reaches its highest levels in leaves, then is subsequently also detected in stems and roots. This work revealed genes potentially responsible for drought tolerance in maize, and a new gene, ZmMYB‐R1, was shown to be associated with water stress.

High segregation distortion in maize B73 x teosinte crosses

Two genetic linkage maps of cultivated maize inbred lines and teosinte species were constructed. One population comprised 81 F(2) individuals derived from a cross between maize inbred line B73 and Zea mays ssp parviglumis, while the second consisted of 63 backcross individuals from a cross of maize inbred line B73 with Z. mays ssp diploperennis. In the B73 x Z. mays ssp parviglumis F(2) population, 172 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 2210.8 cM. In the B73 x Z. mays ssp diploperennis backcross population, 258 SSR markers were mapped to 10 chromosomes, covering 1357.7 cM. Comparison of the two maps revealed that the total map length of Z. mays ssp diploperennis covers 1357.7 cM, which is about 61.4% of that of Z. mays ssp parviglumis (2210.8 cM). Extensive segregation distortion regions were found on chromosomes 1, 2, 3, 5, 6, 7, and 10 in the B73 x Z. mays ssp parviglumis F(2) population and on chromosomes 1-5 and 8-10 in the B73 x Z. mays ssp parviglumis backcross population. Segregation distortion analysis confirmed that the segregation distortion ratio in the interspecific population B73 x Z. mays ssp diploperennis was higher than in B73 x Z. mays ssp parviglumis. We found that the recombination distances are highly variable in these genetic crosses between cultivated and wild species of maize.

Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome

BackgroundAs a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes. Helitrons have contributed significantly to the intra-specific genome diversity in maize. Although many characteristics of helitrons in the maize genome have been well documented, the sequence of an intact autonomous helitrons has not been identified in maize. In addition, the process of gene fragment capturing during the transposition of helitrons has not been characterized.ResultsThe whole genome sequences of maize inbred line B73 were analyzed, 1,649 helitron-like transposons including 1,515 helAs and 134 helBs were identified. ZmhelA1, ZmhelB1 and ZmhelB2 all encode an open reading frame (ORF) with intact replication initiator (Rep) motif and a DNA helicase (Hel) domain, which are similar to previously reported autonomous helitrons in other organisms. The putative autonomous ZmhelB1 and ZmhelB2 contain an extra replication factor-a protein1 (RPA1) transposase (RPA-TPase) including three single strand DNA-binding domains (DBD)-A/-B/-C in the ORF. Over ninety percent of maize helitrons identified have captured gene fragments. HelAs and helBs carry 4,645 and 249 gene fragments, which yield 2,507 and 187 different genes respectively. Many helitrons contain mutilple terminal sequences, but only one 3'-terminal sequence had an intact "CTAG" motif. There were no significant differences in the 5'-termini sequence between the veritas terminal sequence and the pseudo sequence. Helitrons not only can capture fragments, but were also shown to lose internal sequences during the course of transposing.ConclusionsThree putative autonomous elements were identified, which encoded an intact Rep motif and a DNA helicase domain, suggesting that autonomous helitrons may exist in modern maize. The results indicate that gene fragments captured during the transposition of many helitrons happen in a stepwise way, with multiple gene fragments within one helitron resulting from several sequential transpositions. In addition, we have proposed a potential mechanism regarding how helitrons with multiple termini are generated.

Root Infection and Systematic Colonization of DsRed-Labeled Fusarium verticillioides in Maize

Fusarium verticillioides (Sacc.) Nirenberg [syn. F. moniliforme J. Sheld., teleomorph: Gibberella fujikuroi (Sawada) Ito in Ito & K. Kimura] is an important causal agent of diseases in maize (Zea mays L.) worldwide, which invades maize plants at all growth stages. This filamentous fungus not only incites obvious symptoms on maize root, stem, and ear, but also is able to infect plants without any visible symptom (endophytic infection). Fluorescent reporter gene-labeled filamentous fungus permits in vitro and in planta monitoring growth and development of the fungus. In this study, gene DsRed encoding red fluorescent protein was delivered into F. verticillioides strain Fv-1 via Agrobacterium tumefaciens-mediated transformation. Using the DsRed-tagged F. verticillioides, systemic colonization of the fungus in root and stem of the susceptible maize inbred line B73 was investigated to understand the interaction between F. verticillioides and maize. The fungus invaded and multiplied inside the lateral root tissues. Some conidia tended to colonize on the veins of maize root surface and grow along the veins after their germination. Whereas, some others penetrated the plant cells where they attached and formed hyphae for attacking cells nearby. Usually, the mycelia migrated from root to stem through intercellular parts of tissues, while some mycelia ran across different host cells. The colony forming unit (CFU) values from root tended to decrease following the inoculation time, but those from stem inclined to increase. This indicates that F. verticillioides is able to attack the aboveground parts of plant via systemic colonization on root. The results from the present study are useful in disclosing the interaction between F. verticillioides and maize, and can be extended to studying interactions between other soil-borne fungi and plants.

Identification and characterization of putative CIPK genes in maize

Calcium (Ca) plays a crucial role as a second messenger in intracellular signaling elicited by developmental and environmental cues. Calcineurin B-like proteins (CBLs) and their target proteins, CBL-interacting protein kinases (CIPKs) have emerged as a key Ca(2+)-mediated signaling network in response to stresses in plants. Bioinformatic analysis was used to identify 43 putative ZmCIPK (Zea mays CIPK) genes in the genome of maize inbred line B73. Based on gene structures, these ZmCIPKs were divided into intron-rich and intron-poor groups. Phylogenetic analysis indicated that the ZmCIPK family had a high evolutionary relationship with the rice CIPK family of 30 members. Microarray data and RT-PCR assay showed that ZmCIPK genes transcriptionally responded to abiotic stresses, and that 24, 31, 20 and 19 ZmCIPK genes were up-regulated by salt, drought, heat and cold stresses, respectively. There were different expression patterns of ZmCIPKs between cold-tolerant inbred line B73 and cold-sensitive inbred line Mo17 under cold stress. Our findings will aid further molecular dissection of biological functions of the CIPKs in maize, and provide new insight into the CBL-CIPK signaling network in plants.

Differential Expression of microRNAs in Maize Inbred and Hybrid Lines during Salt and Drought Stress

Here, we analyzed whether the microRNA (miRNA) expression levels differ between maize inbred lines B73 and Mo17 and their reciprocal hybrids under salt and drought stress. We found that miR156, miR164, miR166, miR168, miR171 and miR319 are differentially expressed under abiotic stress. Interestingly, Mo17 × B73 showed the strongest change in miRNA expression in response to salt or drought stress, and was also the most resilient line when under abiotic stress in terms of water loss. In summary, our findings open the possibility that differential miRNA expression levels might be involved in heightened stress tolerance in maize hybrids.

A Single Molecule Scaffold for the Maize Genome

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars.

Genome-Wide Analysis of NBS-Encoding Disease Resistance Genes in Maize Inbred Line B73

Nucleotide-binding site(NBS) disease resistance gene is a largest category in plant disease resistance genes,which is a focus in recent studies on molecular breeding of plant disease resistance.Using maize(Zea mays L.) inbred line B73,the complete set of disease resistance candidate genes that encode NBS was identified in the genome.The putative NBS genes were characterized with respect to structural diversity,phylogenetic relationships and so on.One hundred and sixty-five NBS-coding sequences were identified into two types:nonregular(12) and regular NBS genes(153).The amount of NBS genesis much smaller in maize than in japonica rice(Oryza sativa L.).The 153 regular NBS genes were categorized into eight classes,including CC-NBS-LRR,CC-NBS,NBS,NBS-NBS,NBS-LRR,NBS-NBS-LRR,NBS-X,and X-NBS,according to N-terminal motif and leucine-rich repeat(LRR) domains motif.The 165 NBS genes showed two remarkable branches in the phylogenetic tree,differing from the radiation structure in japonica rice.Gene duplication event was observed based on gene family analysis of the NBS disease-resistance genes in maize;however,the ratio of gene duplication was smaller than that in rice.This might be one of the reasons for less NBS disease-resistance genes in maize than in rice.

Expressional profiling study revealed unique expressional patterns and dramatic expressional divergence of maize α-zein super gene family

The alpha-zein super gene family encodes the most predominant storage protein in maize (Zea mays) endosperm. In maize inbred line B73, it consists of four gene families with 41 member genes. In this study, we combined quantitative real-time PCR and random clone sequencing to successfully profile the expression of alpha-zein super gene family during endosperm development. We found that only 18 of the 41 member genes were expressed, and their expression levels diverge greatly. At the gene family level, all families had characteristic "up-and-down" oscillating expressional patterns that diverged into two major groups. At the individual gene level, member genes showed dramatic divergence of expression patterns, indicating fast differentiation of their expression regulation. A comparison study among different inbred lines revealed significantly different expressed gene sets, indicating the existence of highly diverged haplotypes. Large gene families containing long gene clusters, e.g. z1A or z1C, mainly contributed the highly divergent haplotypes. In addition, allelic genes also showed significant divergence in their expressional levels. These results indicated a highly dynamic and fast evolving nature to the maize alpha-zein super gene family, which might be a common feature for other large gene families.

Registration of High‐Methionine Versions of Maize Inbreds A632, B73, and Mo17

Maize (Zea mays L.) is a primary energy‐supplying grain for animal feed in the United States. However, it is deficient in the essential amino acid methionine. Of the maize used for animal feed, 20% is fed to poultry, where the methionine requirement is particularly important. Significant increases in maize methionine levels in the lines reported here can be effectively used in poultry nutrition as well as in human diets where corn and bean (Phaseolus L.) play a major role. Eleven inbred lines of high‐methionine maize (58611 Inbred A632 [Reg. No. GP‐557, PI 648423], 58609 A632 (Meth) BC5S4 [Reg. No. GP‐558, PI 648424], 58610 A632 (Meth) BC5S4 [Reg. No. GP‐559, PI 648425], 58612 Inbred B73 [Reg. No. GP‐560, PI 648426], 58613 B73 (Meth) BC5S4 [Reg. No. GP‐561, PI 648427], 58614 B73 (Meth) BC5S4 [Reg. No. GP‐562, PI 648428], 58615 B73 (Meth) BC5S4 [Reg. No. GP‐563, PI 648429], 58801 Inbred Mo17 [Reg. No. GP‐564, PI 648430], 58802 Mo17 (Meth) BCS3 [Reg. No. GP‐565, PI 648431], 58803 Mo17 (Meth) BCS3 [Reg. No. GP‐566, PI 648432], and 58804 Mo17 (Meth) BCS3 [Reg. No. GP‐567, PI 648433]) were developed by the University of Minnesota and released on 26 Oct. 2007 by the Minnesota Agricultural Experimental Station. These materials were produced by crossing BSSS53 with inbred lines A632, B73, and Mo17 and backcrossing to the respective inbred with intermittent selfing. Maize inbred lines A632, B73, and Mo17 are released with methionine elevated as much as 12.5, 25.0, and 50.0%, respectively, above the recurrent parent. The germplasm source of the high methionine trait is a random line isolate from the Iowa Stiff Stalk Synthetic, identified as BSSS53 and later released by the Iowa State Experiment Station as B101 after obtaining the high methionine information from the University of Minnesota.

Identification of Quantitative Trait Loci for Resistance to Southern Leaf Blight and Days to Anthesis in Two Maize Recombinant Inbred Line Populations

The genetic architecture underlying resistance in maize to southern leaf blight (SLB) caused by Cochliobolus heterostrophus race O is not well understood. The objective of this study was to identify loci contributing to SLB resistance in two recombinant inbred line populations and to compare these to SLB resistance loci in other populations. The two populations used were derived from crosses between maize inbred lines H99 and B73 (HB population-142 lines) and between B73 and B52 (BB population-186 lines). They were evaluated for SLB resistance and for days from planting to anthesis (DTA) in 2005 and 2006. Two replications arranged as randomized complete blocks were assessed in each year for each population. Entry mean heritabilities for disease resistance were high for both populations (0.876 and 0.761, respectively). Quantitative trait loci (QTL) for SLB resistance were identified in bins 3.04 (two QTL), 6.01, and 8.05 in the HB population and in bin 2.07 in the BB population. No overlap of DTA and SLB resistance QTL was observed, nor was there any phenotypic correlation between the traits. A comparison of the results of all published SLB resistance QTL studies suggested that bins 3.04 and 6.01 are 'hotspots' for SLB resistance QTL.

A linkage map of maize × teosinte Zea luxurians and identification of QTLs controlling root aerenchyma formation

The objectives of this study were to construct a linkage map and identify quantitative trait loci (QTLs) controlling root aerenchyma formation in drained soil conditions using 195 F2 individuals derived from a cross between maize inbred line B73 × teosinte Zea luxurians. A 107 SSR marker based map covering 1,331 cM across all ten chromosomes was developed. One significant difference between the parents utilized in the study was that under non-flooding conditions, B73 exhibits a minor capacity to develop root aerenchyma, whereas Z. luxurians exhibits a high tendency to form aerenchyma. Linkage analysis indicated segregation distortion regions on chromosomes 2, 4 and 8, and severe recombination suppression on the long arm of chromosome 4. Multiple interval mapping analysis suggests that five QTLs for aerenchyma formation in non-flooding conditions are located on chromosomes 2, 3, 5, 9 and 10, and these explained 36.3% of the total phenotyphic variance. The Z. luxurians alleles in all five QTLs increased the capacity to form aerenchyma and the locations of these QTLs did not overlap those previously identified in the teosinte Z. nicaraguensis. By transferring aerenchyma-forming QTLs from both Z. luxurians and Z. nicaraguensis, it may be possible to pyramid these genes and develop a maize line with exceptional aerenchyma formation and a high level of tolerance to flooding conditions.

Nonadditive Expression and Parent-of-Origin Effects Identified by Microarray and Allele-Specific Expression Profiling of Maize Endosperm

Plant endosperm cells have a nuclear ratio of two maternal genomes to one paternal genome. This 2 to 1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 d after pollination. The majority of genes exhibited additive expression in reciprocal hybrids based on microarray analyses. However, a substantial number of genes exhibited nonadditive expression patterns, including maternal like, paternal like, high parent like, low parent like, and expression patterns outside the range of the parental inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes, allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues.

Distribution of Genes, Recombination, and Repetitive Elements in the Maize Genome

A high‐density genetic map of maize (Zea mays L.), integrated with a high‐resolution bacterial artificial chromosome (BAC) contig map compiled from two inbred lines, B73 and Mo17, was used to determine gene density and recombination frequency along chromosomes and to compare the distribution of these features as a function of physical distance. Recombination frequency is well correlated with gene density for each chromosome (r = 0.767–0.960), although in centromeric regions, recombination is more depressed than a strict correlation with gene density would indicate. In addition, the distribution of major retrotransposon classes and of Mu and Helitron insertion sites were examined. Overall retrotransposon density is equal at all maize chromosomes (r = 0.996), although different classes of retrotransposons display preferential insertion into different chromosome regions. Cinful, Zeon, and Prem are more common near the centromere, while Opie, Ji, and Huck preferentially reside at the subtelomeric segments of chromosomes. Grande does not show preference in distribution relative to physical location on the chromosome. Comparison of the distribution of genic overgo probe hybridization‐positive BACs from maize inbred line B73 to those of the inbred Mo17 indicates that nonshared genic segments, many of which correspond to pseudogenes carried by the Helitron elements, tend to be less common in the centromeric region. As previously reported, Mu transposons seem to preferentially insert in the vicinity of genes, as indicated by their paucity in centromeric regions, and moderate correlation (r = 0.759) with gene density.