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.