Distribution and organization of a tandemly repeated 352-bp sequence in the oryzae family

Summary A 352-bp EcoRI fragment from rice DNA was cloned and shown to be a member of a tandem repeat. Sequence determination revealed homologies with human alpha satellite DNA and maize knob heterochromatin specific repeat. This 352-bp sequence is highly specific for the AA genome of rice. However, copy number and sequence organization are variable, depending on the accession analyzed. Several examples of amplification were observed in O. rufipogon and O. longistaminata. Use of resolutive polyacrylamide gel electrophoresis and 4-bp cutter enzymes allowed one to distinguish between the Indica and Japonica subtypes of O. sativa. The same method also discriminates between two groups of O. rufipogon, the presumed ancestor of O. sativa, suggesting that the present day Indica and Japonica subtypes originated independently from two O. rufipogon distinct populations.     

Feature article

Domesticated maize emerged from human selection, exploitation, and cultivation of natural recombinants between two wild grasses that had novel characteristics desired by humans for food. Crossing experiments reconstructing prototypes of ancient archaeological specimens demonstrate how the simple flowering spike of the wild relatives of maize was transformed into the prolific grain-bearing ear within a few generations of intergenomic recombination between teosinte andTripsacum. The high degree of morphological similarities of segregating intercross progeny to archaeological specimens from Tehuacán, Oaxaca, and Tamaulipas provides strong support for this evolutionary scenario. Comparative genomic analysis of maize, teosinte, andTripsacum confirms that maize has inherited unique polymorphisms from aTripsacum ancestor and other unique polymorphisms from a teosinte progenitor. This supports the hypothesis thatTripsacum introgression provided the mutagenic action for the transformation of the teosinte spike into the maize ear. This model for the origin of maize explains its sudden appearance, rapid evolutionary trajectory, and genesis of its spectacular biodiversity.     

Molecular characterization of a family of tandemly repeated DNA sequences,TR-1, in heterochromatic knobs of maize and its relatives

Two families of tandem repeats, 180-bp and TR-1, have been found in the knobs of maize. In this study, we isolated 59 clones belonging to the TR-1 family from maize and teosinte. Southern hybridization and sequence analysis revealed that members of this family are composed of three basic sequences, A (67 bp); B (184 bp) or its variants B' (184 bp), 2/3B (115 bp), 2/3B' (115 bp); and C (108 bp), which are arranged in various combinations to produce repeat units that are multiples of approximately 180 bp. The molecular structure of TR-1 elements suggests that: (1) the B component may evolve from the 180-bp knob repeat as a result of mutations during evolution; (2) B' may originate from B through lateral amplification accompanied by base-pair changes; (3) C plus A may be a single sequence that is added to B and B', probably via nonhomologous recombination; and (4) 69 bp at the 3' end of B or B', and the entire sequence of C can be removed from the elements by an unknown mechanism. Sequence comparisons showed partial homologies between TR-1 elements and two centromeric sequences (B repeats) of the supernumerary B chromosome. This result, together with the finding of other investigators that the B repeat is also fragmentarily homologous to the 180-bp repeat, suggests that the B repeat is derived from knob repeats in A chromosomes, which subsequently become structurally modified. Fluorescence in situ hybridization localized the B repeat to the B centromere and the 180-bp and TR-1 repeats to the proximal heterochromatin knob on the B chromosome.     

Molecular analysis of crosses between Tripsacum dactyloides and Zea diploperennis (Poaceae)

 DNA fingerprinting verified hybrid plants obtained by crossing Eastern gamagrass, Tripsacum dactyloides L., and perennial teosinte, Zea diploperennis Iltis, Doebley & R. Guzmán. Pistillate inflorescences on these hybrids exhibit characteristics intermediate to the key morphological traits that differentiate domesticated maize from its wild relatives: (1) a pair of female spikelets in each cupule; (2) exposed kernels not completely covered by the cupule and outer glumes; (3) a rigid, non-shattering rachis; (4) a polystichous ear. RFLP analysis was employed to investigate the possibility that traits of domesticated maize were derived from hybridization between perennial teosinte and Tripsacum. Southern blots of restriction digested genomic DNA of parent plants, F₁, and F₂ progeny from two different crosses were probed with RFLP markers specifically associated with changes in pistillate inflorescence architecture that signal maize domestication. Pairwise analysis of restriction patterns showed traits considered missing links in the origin of maize correlate with alleles derived from Tripsacum, and the same alleles are stably inherited in second generation progeny from crosses between Tripsacum and perennial teosinte. Received: 11 October 1996/Accepted:8 November 1996     

Evolution of Ac and Dsl elements in select grasses (Poaceae)

We present data on evolution of the Ac/Ds family of transposable elements in select grasses (Poaceae). An Ac-like element was cloned from a DNA library of the grass Pennisetum glaucum (pearl millet) and 2387 bp of it have been sequenced. When the pearl millet Ac-like sequence is aligned with the corresponding region of the maize Ac sequence, it is found that all sequences corresponding to intron II in maize Ac are absent in pearl millet Ac. Kimura's evolutionary distance between maize and pearl millet Ac sequences is estimated to be 0.429±0.020 nucleotide substitutions per site. This value is not significantly different from the average number of synonymous substitutions for coding regions of the Adh1 gene between maize and pearl millet, which is 0.395±0.051 nucleotide substitutions per site. If we can assume Ac and Adh1 divergence times are equivalent between maize and pearl millet, then the above calculations suggest Ac-like sequences have probably not been strongly constrained by natural selection. The level of DNA sequence divergence between maize and pearl millet Ac sequences, the estimated date when maize and pearl millet diverged (25–40 million years ago), coupled with their reproductive isolation/lack of current genetic exchange, all support the theory that Ac-like sequences have not been recently introduced into pearl millet from maize. Instead, Ac-like sequences were probably present in the progenitor of maize and pearl millet, and have thus existed in the grasses for at least 25 million years. Ac-like sequences may be widely distributed among the grasses. We also present the first 2 Dsl controlling element sequences from teosinte species: Zea luxurians and Zea perennis. A total of 10 Dsl elements had previously been sequenced from maize and a distant maize relative, Tripsacum. When a maximum likelihood network of genetic relationships is constructed for all 12 sequenced Dsl elements, the 2 teosinte Dsl elements are as distant from most maize Dsl elements and from each other, as the maize Dsl elements are from one another. Our new teosinte sequence data support the previous conclusion that Dsl elements have been accumulating mutations independently since maize and Tripsacum diverged. We present a scenario for the origin of Dsl elements.     

Complex structure of knobs and centromeric regions in maize chromosomes

The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat x maize crosses enables us to analyze the structure and composition of individual maize chromosomes via the isolation and characterization of chromosome-specific cosmid clones. Restriction fragment fingerprinting, sequencing, and in situ hybridization were applied to discover a new family of knob associated tandem repeats, the TR1, which are capable of forming fold-back DNA segments, as well as a new family of centromeric tandem repeats, CentC. Analysis of knob and centromeric DNA segments revealed a complex organization in which blocks of tandemly arranged repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration/association of certain retrotransposable elements into knobs or centromere regions as well as for integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. DNA hybridization to a blot panel of eight individual maize chromosome addition lines revealed that CentC, TR1, and 180-bp tandem repeats are found in each of these maize chromosomes, but the copy number of each can vary significantly from about 100 to 25,000. In situ hybridization revealed variation among the maize chromosomes in the size of centromeric tandem repeats as well as in the size and composition of knob regions. It was found that knobs may be composed of either 180-bp or TR1, or both repeats, and in addition to large knobs these repeated elements may form micro clusters which are detectable only with the help of in situ hybridization. The association of the fold-back elements with knobs, knob polymorphism and complex structure suggest that maize knob may be consider as megatransposable elements. The discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes.     

Organization and chromosomal localization of a B1-like containing repeat of Microtus subarvalis

A repetitive DNA sequence, MS2, was isolated from EcoRI-digested genomic DNA of the vole, Microtus subarvalis. The fragment was cloned and sequenced. Sequence analysis of this 1194-bp fragment revealed a 156-bp region demonstrating a 55% homology with the mouse B1 repeat. The remaining MS2 sequence shows no significant homology with other known GenBank sequences. The results of in situ hybridization of MS2 on vole metaphase chromosomes indicate the fragment is confined to heterochromatin blocks of the sex chromosomes in all but one species (M. arvalis). Distribution of MS2 sequences provides evidence for heterogeneity of the giant heterochromatin blocks of the XY Chromosomes (Chrs) in voles, for the unique cluster-like localization of MS2 within these blocks. Received: 10 October 1995 / Accepted: 30 March 1996     

Rapid amplification and fixation of new restriction sites in the ribosomal dna repeats in the derivatives of a cross between maize and Tripsacum dactyloides

Some of the derivatives of a cross of maize (Zea mays L.) × Tripsacum dactyloides (L) L (2n = 72) have abnormal development leading to strange and striking morphologies. The Tripsacum chromosomes in these “tripsacoid” maize plants (with Tripsacum-like characteristics) were eliminated and the maize chromosomes were recovered through repeated backcrossing to maize. As an initial attempt to analyze the DNA alterations in tripsacoid maize, we have detected a few restriction site changes in the ribosomal DNA repeat of these plants (Hpa II, Bal I, Sst I, Mbo II, and Sph I) and a new Sph I site was mapped to the spacer region between the 26S and 17S genes. Several possible mechanisms for the generation of a new restriction site are discussed, and we propose that the transient presence of Tripsacum genome during the backcrossing in some way induced a rapid amplification and fixation of new restriction sites in a relatively short period of time.     

Zeins as indicators of maize-Tripsacum introgression

A survey of zeins in tripsacoid and non-tripsacoid races of maize from Mesoamerica and from South America, annual teosinte, perennial species of Zea and species of Tripsacum revealed at least 33 zein proteins as determined by isoelectric focusing. Zea and Tripsacum and generally also species within these genera are characterized by distinct combinations of zein proteins. Maize is extensively heterogenous, and spans the complete spectrum of zeins present in wild Zea taxa. A comparison of zein proteins failed to distinguish between introgression of maize with Tripsacum or teosinte. The ease with which maize crosses naturally with wild Zea taxa, and the rarity of hybrids with Tripsacum essentially rule out natural Tripsacum introgression as a mode of racial evolution in maize.     

A cross between two maize relatives:Tripsacum dactyloides andZea diploperennis (Poaceae)

Crosses betweenTripsacum dactyloides and teosinte (Zea diploperennis) using standard pollination technique have been successfully attempted and six highly fertile hybrid plants obtained. Previous research had shown other teosintes to be cross-incompatible with Tripsacum and maize to be crossable but highly intersterile withTripsacum. Some investigators believe thatTripsacum played a prominent role in the origin of maize; theTripsacum-diploperennis hybrid provides evidence to support that idea. Ears produced by the hybrid have paired kernel rows, a distinctive characteristic of the oldest archaeological maize that none of the wild relatives have. This unique hybrid is described and discussed in terms of its possible role in the origin and evolution of maize.     

A Scanning Electron Microscopy Survey of Some Maydeae Pollen

Scanning electron microscopy was used to examine the wall sculpturing of pollen from Zea mays L. ssp. mays (maize), Zea mays ssp. mexicana (Schrad.) Iltis (teosinte), Zea perennis (Hitchc.) Reeves and Mangelsdorf (perennial teosinte), and two species of Tripsacum L. The Zea taxa are shown to possess similar pollen types, with spinules scattered regularly over the exine surface. Tripsacum exhibits a distinctly reticuloid pattern, with spinules clumped into isolated lacunae. Hybrids between Zea and Tripsacum are either intermediate in exine pattern or similar to Tripsacum, depending on the genome combination.     

Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative

Knowledge about the composition and structure of centromeres is critical for understanding how centromeres perform their functional roles. Here, we report the sequences of one centromere-associated bacterial artificial chromosome clone from a Coix lacryma-jobi library. Two Ty3/gypsy-class retrotransposons, centromeric retrotransposon of C. lacryma-jobi (CRC) and peri-centromeric retrotransposon of C. lacryma-jobi, and a (peri)centromere-specific tandem repeat with a unit length of 153 bp were identified. The CRC is highly homologous to centromere-specific retrotransposons reported in grass species. An 80-bp DNA region in the 153-bp satellite repeat was found to be conserved to centromeric satellite repeats from maize, rice, and pearl millet. Fluorescence in situ hybridization showed that the three repetitive sequences were located in (peri-)centromeric regions of both C. lacryma-jobi and Coix aquatica. However, the 153-bp satellite repeat was only detected on 20 out of the 30 chromosomes in C. aquatica. Immunostaining with an antibody against rice CENH3 indicates that the 153-bp satellite repeat and CRC might be both the major components for functional centromeres, but not all the 153-bp satellite repeats or CRC sequences are associated with CENH3. The evolution of centromeric repeats of C. lacryma-jobi during the polyploidization was discussed.     

MORPHOLOGY OF TEOSINTOID AND TRIPSACOID MAIZE (ZEA MAYS L.)

Modern races of maize (Zea mays L.) are characterized by indurated glume and rachis tissues. The archaeological record, as well as experimental studies indicate that in North America this induration is associated with hybridization between domesticated maize and its closest wild relative Z. mays subsp. mexicana (Schrad.) Iltis (teosinte). Similar induration can also be introduced into maize through introgression from Tripsacum. North and South American indurated races of maize are not all closely allied morphologically. They evolved independently under domestication. Teosinte is absent from South America, but Tripsacum is widely sympatric with maize from about 42 N to 42 S latitude. For these reasons it has been postulated that induration in South American races may be the result of Tripsacum introgression. However, barriers restricting gene exchange between Zea and Tripsacum are difficult to overcome in nature. It is maintained that indurated South American races of maize were derived from indurated Mexican races, and that the presence or absence of such induration is due to different degrees of expression by intermediate alleles of the tunicate locus.     

Fluorescence in situ hybridization analysis reveals multiple loci of knob-associated DNA elements in one-knob and knobless maize lines.

Fluorescence in situ hybridization analyses were conducted to examine the presence or absence of the 180- and 350-bp knob-associated tandem repeats in maize strains previously defined as "one-knob" or "knobless." Multiple loci were found to hybridize to these two repeats in all maize lines analyzed. Our results show that the number of 180- and 350-bp repeat loci do not correlate with the number of knobs in maize and that these tandem repeats are not independently sufficient to confer knob heterochromatin, even when present at megabase sizes.     

A COMPARISON OF CHROMOSOME KNOB FREQUENCIES BETWEEN SYMPATRIC AND ALLOPATRIC POPULATIONS OF TEOSINTE AND MAIZE

Unrestricted gene flow would be expected to lead to similar chromosome knob frequencies in sympatric populations of maize and teosinte. Chi-square tests were therefore used to compare chromosome knob frequencies of 45 collections of Mexican teosinte, grouped according to six geographic regions, with sympatric and allopatric populations of maize. Comparisons of knob frequencies between sympatric and allopatric populations within each region produced an initial classification for each knob-forming position. Further comparisons for each knob position over all regions, led to an interpretation of results for sympatric populations of maize and teosinte in terms of gene flow, selection, differentiation, ancestral similarities, and ancestral differences. Within regions, a high number of knob positions suggesting gene flow was associated with a low number of knob positions suggesting recent differentiation, and vice versa. It is suggested that the teosinte populations most likely to represent unique sources of germplasm are those most susceptible to future genetic erosion by maize. These relationships may represent a general model applicable to a number of crop plants and associated weed races.     

Comparative isozyme polymorphisms of north American eastern gamagrass,Tripsacum dactyloides var.dactyloides and maize,Zea mays L.

Random samples, consisting of at least 100 individual seedlings, were taken from the diploid (2n=2x=36) eastern gamagrass (Tripsacum dactyloides var.dactyloides) and assayed to determine which of 12 enzyme marker loci and isozyme systems would be most informative in providing satisfactory resolution of both maize andTripsacum isozyme systems. For comparison, eight maize inbreds were included in the study to aid evaluation and comparison of the various isozyme systems. In addition, evaluations were conducted to identify if the identified optimum isozyme system could be used to detectTripsacum introgression in maize following a maize ×Tripsacum backcrossing scheme. Using the established isozyme techniques for maize (Zea mays L.), theAdh, Pgd, Cat, Est, B-Glu, Got, Idh, Tpi isozyme systems detected no polymorphism among theTripsacum individuals assayed. TheEst andB-Glu systems forTripsacum were unscorable due to poor staining and resolution. TheAcp, Mdh, Pgm, andPhi isozyme systems were found to be satisfactory markers for differentiating between eastern gamagrass individuals as well as detectingTripsacum introgression in maize. The availability of useful isozyme systems which can simultaneously provide significant isozyme resolution of maize,Tripsacum and maize-Tripsacum backcross hybrids, on a single gel system, will be useful for the detection of marker assistedTripsacum introgression into maize. In addition, the identification of a set of variable biochemical markers should also assist breeding, selection and genetic manipulations in eastern gamagrass.The use of company names in this publication does not imply endorsement by the USDA-ARS, or the product names of criticism of similar ones not mentioned. All programs and services of the U.S. Department of Agriculture are offered on a nondiscriminatory basis without regard to race, color, national origin, religion, sex, age, marital status, or handicap.     

A tale of two centromeres—diversity of structure but conservation of function in plants and animals

The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.