The maize rough sheath2 gene and leaf development programs in monocot and dicot plants.

Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.

Cell interactions in plants.

Plant cells interact during development through diverse mechanisms that range from genetically encoded signals to physical stresses. Pollen self-incompatibility is the best understood cell interaction in plants. Analysis of genes that appear to be involved in specific developmental signals, such as liguleless1 from maize and GLABROUS1 from Arabidopsis, will provide clues as to the nature of cell interactions in plant development. Recent data suggest that intercellular connections may be more similar in plants and animals than previously thought.

Purification of maize alcohol dehydrogenase-1 allozymes and comparison of their tryptic peptides.

Two naturally occurring allozymes of alcohol dehydrogenase-1 in maize have been purified to homogeneity. Specific activity, molecular weight and amino acid composition have been determined. The difference between these two allozymes was further studied by comparisons of tryptic peptides using a fingerprinting technique. Excellent maps were obtained which resolved 29 out of the 30 peptides which were maximally possible. These allozymes differ in one peptide, consistent with a single, charged amino acid replacement. These results are related to the differences which have been shown to exist between the genes which specify these two allozymes.

Intragenic recombination in maize: pollen analysis methods and the effect of parental adh1 isoalleles.

The ability to stain mature pollen grains for the presence of alcohol dehydrogenase (ADH) activity permits the quantitation of ADH( +) gametophytes at frequencies below 10(-6). This resolution allows reversion and genetic fine structure analyses. The rationale of pollen analysis follows Nelson's prototype studies with waxy. As with the waxy gene, revertant frequencies for seven Adh1-deficient ( Adh1(-)) alleles appear to be in excess of microbially derived expectations. Each of the seven Adh1(-) alleles were derived from one of three naturally occurring isoalleles. Based on Schwartz's protein level characterizations of the mutants' products, it was anticipated that the seven Adh1(-) alleles should recombine to yield ADH(+) cistrons in certain pairwise combinations. This expectation was not met. The parental "wild-type" isoalleles from which the mutants were derived appear to be structurally divergent. The discussion interprets these data in view of understanding naturally occurring cistronic variation.

Further Studies on the Balance between Adh and Adh in Maize: Gene Competitive Programs.

Two unlinked genes which specify alcohol dehydrogenase (ADH) enzymes in maize are coordinately regulated by competition for a factor which limits the rate of total ADH expression during anaerobiosis. The "gene competition hypothesis" and the existence of organ-specific competitive programs, as proposed by Schwartz (1971), is further supported. The potential balance of expression between these two genes appears to be organ-specific and may be "locked-in" and inherited via meristematic growth. The actual expression of these two genes is dependent on the mode of ADH induction. The discussion examines alternative hypotheses explaining gene competition and reinterprets extant data on the adaptive significance of maize ADH polymorphism.

Allelic variation at the level of intragenic recombination.

This report examines five different naturally occurring alcohol dehydrogenase-1 alleles via the recombinational behavior of Adh1(-) mutants induced within them. Twenty-two biochemically characterized Adh1(-) mutants have been assessed for ability to recombine intragenically, using data generated by specifically staining for the presence of ADH in pollen grains. Each of the five naturally occurring Adh1 progenitor isoalleles appears unique. Allelic variation exists in (1) the rate of intragenic recombination sustained by an allele, and (2) the pattern of recombinational success or failure based on the ancestry of each mutant in a heteroallelic pair. In other words, we find quantitative and qualitative Adh1 allelic variation at the level of intragenic recombination. I have experimentally excluded several explanations for recombinational restriction. These results will be related to the structure, function and naturally occurring variability of the gene in higher organisms. Specifically, the "recon" (unit of recombination) has been resurrected as a potentially useful unit of natural selection. The reasonableness of several genres of hypotheses in evolutionary/population genetics, particularly those involving linkage disequilibrium, is called into question.

The Mu transposable elements of maize: evidence for transposition and copy number regulation during development.

The Mu transposon of maize exists in a highly mutagenic strain called Robertson's Mutator. Plants of this strain contain 10-50 copies of the Mu element, whereas most maize strains and other plants have none. When Mutator plants are crossed to plants of the inbred line 1S2P, which does not have copies of Mu, the progeny plants have approximately the same number of Mu sequences as did their Mutator parent. Approximately one-half of these copies have segregated from their parent and one-half have arisen by transposition and are integrated into new positions in the genome. This maintenance of copy number can be accounted for by an extremely high rate of transposition of the Mu elements (10-15 transpositions per gamete per generation). When Mutator plants are self-pollinated, the progeny double their Mu copy number in the first generation, but maintain a constant number of Mu sequences with subsequent self-pollinations. Transposition of Mu and the events that lead to copy number maintenance occur very late in the development of the germ cells but before fertilization. A larger version of the Mu element transposes but is not necessary for transposition of the Mu sequences. The progeny of crosses with a Mutator plant occasionally lack Mutator activity; these strains retain copies of the Mu element, but these elements no longer transpose.

Developmental genetics of mutants that specify knotted leaves in maize.

Of seven dominant knotted-leaf mutants tested, six mapped at or near Kn1 on the long arm of chromosome 1, and one was not linked to Kn1. Comparisons of phenotypes among these mutants allowed us to focus on a systematic abnormality: the parenchyma cells associated with lateral veins do not fully differentiate into bundle sheath, mesophyll or upper sclerenchyma. The more dramatic expression of Kn1 mutants-knots, ligule alterations and twisting-is sporadic and dependent on the time when the mutant acts in leaf primordium development. Using lw to mark leaf sectors that lose Kn1 following X-irradiation, we show that the knotted-leaf phenotype encoded by chromosome 1L is autonomous. Analysis of sectors lacking a particular Kn1 gene ( Kn1-N2) suggests that Kn1 itself, rather than a linked modifier gene, is autonomous in the leaf primordium. Aneuploid studies using various translocations involving 1L and marked by Adh1 allozymes are compared. The Kn1 mutant appears to encode a "new" function or a considerable overproduction of an extant product in the leaf. Kn1/- 1L hypoploids either express knotted poorly or not at all; transvection is ruled out, but the cause for this modification of Kn1 expression is not yet known.-Our working hypothesis is that Kn1 mutants permit the expression of a product that is usually not produced in leaf primordial cells. We suggest that this product interferes with the early cell-type commitments of cells near lateral veins. Thus, relatively uncommitted cells are present in more mature blades, where they may divide unexpectedly into knots or may induce bits of ligule.

Interactions of liguleless1 and liguleless2 function during ligule induction in maize.

The maize ligule is an adaxial membranous structure on the leaf that develops at the boundary of the sheath and blade. The ligule and the associated auricle are dispensable structures, amenable to genetic manipulation. We present here a genetic analysis of liguleless1 (lg1) and liguleless2 (lg2), the two genes known to be uniquely necessary for ligule and auricle development. We show that both reference mutant alleles, lg1-R and lg2-R, are null alleles. The double mutant phenotype suggests that lg1 and lg2 act in the same pathway. Indeed, the dosage of a functional allele at either gene affects the null phenotype of the other. While lg1 function has previously been shown to be cell-autonomous, here we show that the lg2-R phenotype is cell-nonautonomous, suggesting lg1 and lg2 play different roles in the ligule-auricle induction mechanism. We present a model in which early lg2 function specifies the precise position where ligule and auricle will develop. Later lg2 function interacts with lg1 function (either directly or indirectly) to transmit and receive a make-ligule-make-auricle inductive signal.

Mutator-suppressible alleles of rough sheath1 and liguleless3 in maize reveal multiple mechanisms for suppression.

Insertions of Mutator transposons into maize genes can generate suppressible alleles. Mu suppression is when, in the absence of Mu activity, the phenotype of a mutant allele reverts to that of its progenitor. Here we present the characterization of five dominant Mu-suppressible alleles of the knox (knotted1-like homeobox) genes liguleless3 and rough sheath1, which exhibit neomorphic phenotypes in the leaves. RNA blot analysis suggests that Mu suppression affects only the neomorphic aspect of the allele, not the wild-type aspect. Additionally, Mu suppression appears to be exerting its effects at the level of transcription or transcript accumulation. We show that truncated transcripts are produced by three alleles, implying a mechanism for Mu suppression of 5' untranslated region insertion alleles distinct from that which has been described previously. Additionally, it is found that Mu suppression can be caused by at least three different types of Mutator elements. Evidence presented here suggests that whether an allele is suppressible or not may depend upon the site of insertion. We cite previous work on the knox gene kn1, and discuss our results in the context of interactions between Mu-encoded products and the inherently negative regulation of neomorphic liguleless3 and rough sheath1 transcription.

Genetics of dominant gibberellin-insensitive dwarfism in maize.

D8 and Mpl1 are two dominant dwarfing mutations of maize. Although they differ in severity of dwarfism, both D8 and Mpl1 mutants are unresponsive to gibberellin (GA). Because of their close phenotypic resemblance to the recessive GA-sensitive dwarf mutants these dominant mutations may identify a gene whose product is involved in the reception of GA. With this possibility in mind we have studied the genetic properties of D8 and Mpl1. Both mutations map close to Adh1 on chromosome 1L. By marking normal and translocated 1L arms with different Adh1 electrophoretic mobility alleles, we investigated the effect of gene dosage on dominant dwarf phenotype. The results suggest that D8 and Mpl1 encode novel product functions and that these functions are relatively insensitive to the presence of the (presumed) wild-type product. Using X-ray induced chromosome breakage we created sectors of wild-type cells within D8 or Mpl1 tissue; these sectors were marked by the linked recessive lw mutation. The phenotypes of these sectors demonstrated that, at least in certain plant organs and tissues, dominant dwarfism can be an autonomous phenotype. These results are consistent with the hypothesis that the wild-type gene product acts as a GA receptor. The potential utility of dominant dwarf phenotype in plant developmental analysis is discussed, and possible mechanisms for the action of the D8 and Mpl1 mutations are considered.

Genetic analysis of Rough sheath1 developmental mutants of maize.

Maize Rough sheath1 (Rs1) mutants are dominant and cause a proliferation of sheath-like tissue at the base of the blade and throughout the ligular region. They also cause ligule displacement, a chaotic pattern of vasculature and abnormal cellular structure of vascular bundles. The affected region of Rs1-O leaves displays genetic and morphological attributes of both sheath and auricle, suggesting an overlap of these genetic programs. The rs1 locus maps approximately 26 map units distal to opaque2 (o2) on chromosome 7S, defining a new distal-most locus on the genetic map. Three mutant alleles, Rs1-O, Rs1-1025 and Rs1-Z, all display similar phenotypes. The mutations are completely dominant and the Rs1-O phenotype is not affected by dosage of the chromosome arm carrying the rs1+ allele, indicating that these alleles are neomorphic. Analysis of genetic mosaics showed that the Rs1-O phenotype is non-cell-autonomous, suggesting that intercellular signals convey the phenotype. Rs1 mutant phenotypes are affected by modifiers present in particular genetic backgrounds. An enhancer of Rs1-O was identified; segregation data imply a single recessive gene, ers1. Rs1 mutants were also found to enhance the expression of unlinked rs2 and Rs4 mutants, suggesting that these mutations affect similar developmental processes. We discuss the phenotypic and genetic similarities between Rs1 and Knotted 1 (Kn1) mutants that led to the identification of rs1 as a kn1-like homeobox gene (unpublished data).

Genetic characterization of the Mutator system in maize: behavior and regulation of Mu transposons in a minimal line.

Most Mutator lines of maize harbor several different classes of Mu transposons, each of which may be present in high copy number. The regulatory element is also often found in high copy number, and it is this element's behavior that is presumed to cause the non-Mendelian inheritance of Mutator activity. Using a very simple Mutator line, we demonstrate tha MuDR-1, a regulator of the Mutator system, can functionally replace standard non-Mendelian Mutator activity and that MuDR-1 is associated with the loss of methylation of the termini of another Mu transposon. Further, we show that Mu transposons can transpose duplicatively, that reinsertion tends to be into unlinked sites, and that MuDR-1 frequently suffers deletions. Changes in chromosomal position and the mode of sexual transmission are shown to be associated with changes in the frequency of MuDR-1 duplication and with the activity of MuDR-1 as monitored by the excision frequency of a reporter transposon of the Mu family, Mu1. Our data are derived from a Minimal Mutator Line in which there are relatively few Mu transposons, including one MuDR-1 regulator and as few as one Mu1 reporter. The seemingly enigmatic results that have been obtained using more complicated Mu genotypes are reinterpreted using simple Mendelian principles. We have borrowed a gap-repair model from Drosophila biologists to explain both duplications and deletions of MuDR-1.

Identification of a genetic element that controls the organ-specific expression of adh1 in maize.

Allozyme balances serve as markers of quantitative behavior of electrophoretically distinguishable alleles. By the use of ADH Set I allozyme balances, it is demonstrated that all Adh1-S/Adh1-F individuals from more than 20 diverse S/F families exhibit a reciprocal correlation between Adh1 quantitative behavior in two maize organs: the scutellum and primary root. Within an electrophoretic mobility class, the Adh1 allele that is relatively underexpressed in the scutellum is relatively overexpressed in the primary root, and vice versa. Segregation tests prove that this "reciprocal effect" is the property of a cis-acting site that is closely linked to or within the Adh1 structural gene, and it is not affected by diverse genetic backgrounds. Immunological and [(3)H]-leucine incorporation experiments establish that Adh1 quantitative variants differ in ADH1.ADH1 synthetic rates in the anaerobic primary root. The reciprocal-effect phenomenon suggests that the cis-acting loci controlling Adh1 quantitative expression in each respective organ are at least in close proximity, or may share common DNA sequences. We discuss the possibility that the reciprocal-effect locus is a regulatory component of the Adh1 cistron.

Mosaic analysis of the liguleless3 mutant phenotype in maize by coordinate suppression of mutator-insertion alleles.

Liguleless3-O (Lg3-O) transforms the leaf blade, auricle and ligule into sheath around the midrib region. We conducted a genetic mosaic analysis of the Lg3 phenotype to determine the site of Lg3 gene action. Combining the Mutator (Mu) suppressible Lg3-Or211 and a1-mum2 alleles in a Mu-active background generated a stock wherein somatic loss of Mu activity resulted in anthocyanin-marked clonal sectors expressing Lg3 in the leaf. Lg3-Or211 plants appear wild type in a Mu-active line, but Mu-inactive plants express a severe Lg3 phenotype. We observed four sector classes: wild type, sheath-like with ligule displacement, sheath-like with ectopic ligule, and auricle-like. The mutation does not cause transformation to a specific cell or regional identity. Lg3-Or211 activity in the mesophyll alters wild-type epidermal cell fates; activity in epidermis seems functionless. Lg3 mutant activity has a nonautonomous, cell-layer-specific function in the transverse dimension. In the lateral dimension, sectors of Lg3 mutant phenotype can exhibit either cell-autonomous or nonautonomous effects. Our work demonstrates that mosaic analysis by coordinate suppression of Mu-induced alleles is useful for analyzing the cell autonomy of genetically defined functions.

Exceptionally High Levels of Restriction Site Polymorphism in DNA near the Maize Adh1 Gene.

Restriction maps have been prepared for the chromosomal region near seven biochemically and genetically distinct maize alcohol dehydrogenase-1 (Adh1) alleles using a small cDNA probe for Adh1. Five restriction sites spanning about 4 kb in and near the Adh1 transcription unit appear identical in all seven alleles. Outside this conserved region, variation in restriction site position is the rule. Six of the seven alleles are distinguishable, and the alleles appear to fall into four groups. The DNA flanking the 1S-type alleles seems to share no restriction site homology with the DNA near the 1F-type alleles. Several hypotheses are put forward to explain how such high levels of polymorphism could have arisen in a species that has been domesticated for only about 10,000 years.

Functional analysis of deletion derivatives of the maize transposon MuDR delineates roles for the MURA and MURB proteins.

The regulatory transposon of the Mutator system of transposable elements in maize is MuDR. MuDR elements produce two transcripts, from genes mudrA and mudrB, encoding proteins MURA and MURB, respectively. Like many other transposons, MuDR elements often undergo deletions, usually of internal sequences. Analysis of a deletion that is restricted to the region encoding MURB demonstrates that this gene is not required to cause excisions of a reporter element, although it may be required for transposition or suppression of suppressible alleles. Conversely, a derivative that lacks the region encoding MURA but that produces MURB is nonfunctional for all aspects of Mutator activity. Northern analysis of these derivatives reveals that each of the two transcripts can be independently transcribed, and analysis using an antibody specific for MURB reveals that mudrB transcript can also be successfully translated and its product appropriately localized in the absence of mudrA. A third deletion derivative provides evidence for a source of previously reported antisense transcript.

Organ-specific expression of maize Adh1 is altered after a Mu transposon insertion.

A new, unstable, organ-specific Adh1 mutant was isolated from a Robertson's mutator line by germinating kernels under partial anaerobic conditions. Families of kernels which showed segregation of a conditional anaerobic lethal phenotype were identified. One mutant, Adh1-3F1124, was shown to express approximately 6% normal levels of ADH1 in seed and anaerobically treated seedlings but expresses normal levels of ADH1 in pollen, the male gametophyte. The ADH1 polypeptide encoded by the mutant allele was found to be indistinguishable from that encoded by the Adh1-3F progenitor but its message levels were lower in seed and seedlings. Robertson's mutator lines are known to carry Mu transposons that cause increased mutation rates. Genomic Southern analysis of Adh1-3F1124 and Adh1-3F showed the presence of a 1.85 kbp insertion at the 5' region of Adh1. Comparison of the DNA sequences revealed that a Mu 1-like element was inserted 31 bp 5' from the transcriptional start site of Adh1-3F1124 gene. The insertion of the Mu element creates an additional TATA box by duplicating the 9 bp genomic sequence--ATATAAATC--at the site of insertion. Consequently, there are two potentially functional TATA sequences, separated by the 1.85 kbp Mu element, 5' to the transcriptional start site. It is not yet understood how such an arrangement alters the organ-specific expression of Adh1.

Identification of a regulatory transposon that controls the Mutator transposable element system in maize.

The Mutator system of maize consists of more than eight different classes of transposable elements each of which can be found in multiple copies. All Mu elements share the approximately 220-bp terminal inverted repeats, whereas each distinct element class is defined by its unique internal sequences. The regulation of instability of this system has been difficult to elucidate due to its multigenic inheritance. Here we present genetic experiments which demonstrate that there is a single locus, MuR1, which can regulate the transposition of Mu1 elements. We describe the cloning of members of a novel class of Mu elements, MuR, and demonstrate that a member of the class is the regulator of Mutator activity, MuR1. This conclusion is based on several criteria: MuR1 activity and a MuR-homologous restriction fragment cosegregate; when MuR1 undergoes a duplicative transposition, an additional MuR restriction fragment is observed, and MuR1 activity and the cosegregating MuR fragment are simultaneously lost within clonal somatic sectors. In addition, the MuR element hybridizes to transcripts in plants with Mutator activity. Our genetic experiments demonstrate that the MuR1 transposon is necessary to specify Mutator activity in our lines.

Toward monitoring specific DNA lesions in the gene by using pollen systems.

Specific gene systems expressed in cereal pollen could contribute uniquely to the problem of monitoring our environment for mutagens. This paper considers the development of a mutagen monitor with quantitative endpoints that reflect particular types of lesions at the DNA level, and lesions in particular components of the gene.