Distribution of sequences related to the Bg transposable element of maize in Zea and related genera

Thirty-four accessions from Zea and 10 accessions from related genera were assayed for the presence of Bg, a transposable element originally found in maize (Zea mays ssp. mays). Bg-like sequences, identified as hybridizing bands on Southern blots, were visualized in all Zea accessions and were present in approximately equal numbers in teosinte and maize. With the exception of Tripsacum dactyloides, all accessions from related genera failed to hybridize with the Bg probes, even at reduced stringency. A comparison of the restriction patterns of related inbred lines revealed numerous common hybridizing fragments. An index of molecular similarity (MS) was used to determine the degree of similarity between pairs of inbred lines. Computed MS values endorse an inbred relationship and are in good agreement with published results of cluster analysis on these inbred lines.     

Molecular evolution of human T-cell leukemia virus

Summary In light of previous data, which suggested thatAc-like sequences might have undergone a significant radiation in the recent past, I examined the copy number ofAc-like sequences in representatives of all theZea taxa, both maize and teosinte. The maize and teosinte samples contained approximately equal numbers ofAc-like sequences. FewAc-like sequences were in unmethylated regions of DNA. Unmethylated elements were distributed randomly among both maize and teosinte lines. The appearance in a line of a discrete band resulting from digestion with one methylation-sensitive restriction enzyme was correlated with the appearance of discrete bands with other methylation-sensitive bands. This suggests that individualAc-like elements are occasionally demethylated in many sites. No unmethylated element having restriction fragments of the lengths predicted from the publishedAc sequence was seen in the approximately 326 elements examined.     

Variation for Root Aerenchyma Formation in Flooded and Non-Flooded Maize and Teosinte Seedlings

Morphological and anatomical factors such as aerenchyma formation in roots and the development of adventitious roots are considered to be amongst the most important developmental characteristics affecting flooding tolerance. In this study we investigated the lengths of adventitious roots and their capacity to form aerenchyma in three- and four-week-old seedlings of two maize (Zea mays ssp. mays, Linn.) inbred accessions, B64 and Na4, and one teosinte, Z. nicaraguensis Iltis & Benz (Poaceae), with and without a flooding treatment. Three weeks after sowing and following a seven day flooding treatment, both maize and teosinte seedlings formed aerenchyma in the cortex of the adventitious roots of the first three nodes. The degree of aerenchyma formation in the three genotypes increased with a second week of flooding treatment. In drained soil, the two maize accessions failed to form aerenchyma. In Z. nicaraguensis, aerenchyma developed in roots located at the first two nodes three weeks after sowing. In the fourth week, aerenchyma developed in roots of the third node, with a subsequent increase in aerenchyma in the second node roots. In a second experiment, we investigated the capacity of aerenchyma to develop in drained soil. An additional three teosinte species and 15 maize inbred lines, among them a set of flooding-tolerant maize lines, were evaluated. Evaluations indicate that accessions of Z. luxurians (Durieu & Asch. Bird) and two maize inbreds, B55 and Mo20W, form aerenchyma when not flooded. These materials may be useful genetic resources for the development of flooding-tolerant maize accessions.     

Maize seedling morphology and defence hormone profiles,but not herbivory tolerance,were mediated by domestication and modern breeding

We addressed whether Zea seedling morphology relevant to performance, defence hormone profiles and tolerance of a phloem‐feeding, specialist herbivore were affected by two processes, plant domestication and modern breeding. Domestication effects were inferred through comparisons between Balsas teosintes (Zea mays parviglumis) and landrace maizes (Z. mays mays), and modern breeding effects through comparisons between landrace maizes and inbred maize lines. Specifically, we compared seedling forms (a composite measure of leaf length, average stem diameter, shoot wet weight, shoot dry weight, total root length, root wet weight, and root dry weight), shapes (forms scaled by seedling dry weight, a proxy for seedling size), and defence hormone profiles among Balsas teosinte and landrace and inbred line maizes, exposed or unexposed to feeding by Dalbulus maidis. Our results suggested that domestication as well as modern breeding strongly mediated both seedling form and shape. Form was more similar between landrace and inbred maize than between Balsas teosinte and landrace maize, suggesting that domestication affected seedling form more than modern breeding. In contrast, shape was more similar between Balsas teosinte and landrace maize than between landrace and inbred maizes, suggesting that modern breeding affected seedling shape more than domestication. Additionally, seedling shoot : root ratios appeared to have been mediated by domestication, but not by modern breeding. In broad terms, individual seedling structures relevant to seedling ecology in wild or managed environments, such as leaf and root lengths, and shoot and root masses, were enlarged with domestication and reduced with modern breeding. Herbivory did not affect seedling shape, but had a weak effect on form so that seedlings were slightly larger in the absence versus presence of D. maidis. Also, both domestication and modern breeding seem to have mediated seedling hormone profiles, with breeding more strongly mediating profiles than domestication. Jasmonic acid isoleucine (JA‐Ile) and salicylic acid (SA) were induced by herbivory in both teosinte and maize. The hormone profiles assays collectively suggested that domestication and modern breeding altered constitutive levels of SA, abscisic acid and JA‐related (JA‐Ile and oxo‐phytodienoic acid) hormone levels in seedlings, particularly by increasing the levels of SA and decreasing those of JA‐related hormones. Altogether, our results suggested that maize domestication and modern breeding significantly altered seedling form, shape, ecologically relevant morphological traits (e.g. leaf and root lengths, and shoot and root masses) and hormonal defences, but not tolerance of D. maidis herbivory.     

Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme

Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU_leaf through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU_end, LSU_emb) or breeding (LSU_leaf), two exhibit patterns consistent with diversifying (SSU_leaf) and balancing selection (SSU_emb) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.     

Variation within teosinte. I. Numerical analysis of morphological data

Principal components analysis of 27 morphological characters for 18 accessions of teosinte and 3 accessions of maize separated teosinte into 6 phenetic groups which showed broad agreement with previous taxonomic groupings. Tests for regression suggested significant linear relationships with altitude; teosintes from higher elevations are generally more maize-like for a combination of characters. Introgression from maize may have blurred racial identities within teosinte, but variation among current teosinte accessions cannot be satisfactorily explained solely on the basis of known maize introgression. It appears instead that racial differentiation in teosinte was well established by the time of the domestication of maize. While current racial classification of teosinte is quite useful, it does not adequately reflect the amount of genetic variation, nor does it accurately portray many of the relationships within teosinte.     

Facilitated by nature and agriculture: performance of a specialist herbivore improves with host-plant life history evolution, domestication, and breeding

Plant defenses against herbivores are predicted to change as plant lineages diversify, and with domestication and subsequent selection and breeding in the case of crop plants. We addressed whether defense against a specialist herbivore declined coincidently with life history evolution, domestication, and breeding within the grass genus Zea (Poaceae). For this, we assessed performance of corn leafhopper (Dalbulus maidis) following colonization of one of four Zea species containing three successive transitions: the evolutionary transition from perennial to annual life cycle, the agricultural transition from wild annual grass to primitive crop cultivar, and the agronomic transition from primitive to modern crop cultivar. Performance of corn leafhopper was measured through seven variables relevant to development speed, survivorship, fecundity, and body size. The plants included in our study were perennial teosinte (Zea diploperennis), Balsas teosinte (Zea mays parviglumis), a landrace maize (Zea mays mays), and a hybrid maize. Perennial teosinte is a perennial, iteroparous species, and is basal in Zea; Balsas teosinte is an annual species, and the progenitor of maize; the landrace maize is a primitive, genetically diverse cultivar, and is ancestral to the hybrid maize; and, the hybrid maize is a highly inbred, modern cultivar. Performance of corn leafhopper was poorest on perennial teosinte, intermediate on Balsas teosinte and landrace maize, and best on hybrid maize, consistent with our expectation of declining defense from perennial teosinte to hybrid maize. Overall, our results indicated that corn leafhopper performance increased most with the agronomic transition, followed by the life history transition, and least with the domestication transition.     

Molecular evidence for post-domestication selection in the <Emphasis Type="Italic">Waxy</Emphasis> gene of Chinese waxy maize

Waxy maize was first reported in China in 1909 and is mainly used in food production in Asia. The evidence for strong domestication selection in the Waxy locus of rice and a selective sweep around its genomic region make us to wonder whether there has been similar selection in Waxy in glutinous maize. To address this issue, DNA sequences of Waxy, three flanking genes and an unlinked gene (Adh1) of 30 accessions sampled from Chinese waxy maize accessions, including representative landraces and inbred lines, were determined in this study. Sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed in the Waxy locus in Chinese waxy maize but not in nonglutinous maize; comparison with the unlinked gene confirmed that this pattern was different to Waxy. Sequence analysis across a 143 kb genomic segment centered on the Waxy locus revealed patterns consistent with a selective sweep in the upstream region of Waxy. The selective sweep detected based on current limited genomic sequences exceeded over 50 kb, indicating strong selection in this or a bigger region. However, No sweep effect was detected in the repetitive downstream region of Waxy. Phylogenetic analysis indicated that Chinese waxy maize was domesticated from the cultivated flint maize (Zea mays ssp. mays) that was introduced from the new world. At least two independent deletions in exon 7 (30 bp) and 10 (15 bp) were identified in the Chinese accessions respectively. These findings demonstrate a similar pattern of domestication selection in the Waxy genomic region in both glutinous maize and rice, suggesting that this pattern in the rise of glutinous phenotype is likely in other cereal crops.     

A maize cryptic Ac-homologous sequence derived from an Activator transposable element does not transpose.

Summary Sequences sharing homology to the transposable element Activator (Ac) are prevalent in the maize genome. A cryptic Ac-like DNA, cAc-11, was isolated from the maize inbred line 4Co63 and sequenced. Cryptic Ac-11 has over 90% homology to known Ac sequences and contains an 11 by inverted terminal repeat flanked by an 8 by target site duplication, which are characteristics of Ac and Dissociation (Ds) transposable elements. Unlike the active Ac element, which encodes a transposase, the corresponding sequence in cAc-11 has no significant open reading frame. A 44 by tandem repeat was found at one end of cAc-11, which might be a result of aberrant transposition. The sequence data suggest that cAc-11 may represent a remnant of an Ac or a Ds element. Sequences homologous to cAc-11 can be detected in many maize inbred lines. In contrast to canonical Ac elements, cAc-11 DNA in the maize genome is hypermethylated and does not transpose even in the presence of an active Ac element.     

Relationships between maize and teosinte of Mexico and Guatemala: Numerical analysis of allozyme data

Electrophoresis revealed 153 variants at 19 enzyme loci among 77 accessions of annual teosinte, 1 accession of diploid perennial teosinte, 1 accession of tetraploid perennial teosinte, and 43 accessions of maize from Mexico and Guatemala. One hundred and thirty-three (87%) variants were found within teosinte, and 95 (61%) variants were found within maize. Seventy-four (48%) variants were distributed among both teosinte and maize, whereas 58 (38%) variants were found only in teosinte and 20 (13%) variants were found only in maize. The majority of alleles were found in low frequency. A single allele predominated across maize and teosinte at 11 loci, 3 loci showed similar trends and 5 loci showed greater variability for the predominant alleles among maize and teosinte. Principal components analysis revealed little overlap between maize and teosinte, involving a minority of maize collections and Balsas teosintes. No clear evidence could be seen suggesting recent introgression between maize and teosinte. The collections of maize and teosinte were seen to represent a rich and contrasted array of germplasm.     

Chromosome polymorphism of teosinte

Florida teosinte from Honduras and Guanajuato teosinte have most of their knobs internally located and a common inversion in the short arm of chromosome 8. Teosintes from northern Guatemala, Huixta and Monajil, have all their knobs terminally located and do not have any inversions. Therefore, Florida teosinte from Honduras appears to be phylogenetically closer to Guanajuato teosinte than it is to Guatemalan teosintes.——The presence of B chromosomes and an In 8 in Guanajuato teosinte and Florida teosinte from Honduras may constitute evidence of introgression between maize and teosinte.     

Variation within teosinte. II. numerical analysis of chromosome knob data

Principal components analysis of 46 chromosome knob positions and B chromosomes for 61 accessions of annual teosinte (in 12 groups) and 207 accessions of maize (in 87 groups) produced results which did not entirely agree with previous groupings. Teosintes of northwest and southeast Guatemala (races Huehuetenango and Guatemala) were widely separated from maize and from all other teosintes; however, teosintes of east Mexico-Distrito Federal (race Chalco) were also widely separated from maize and other teosintes. Teosintes of south Chihuahua (race Nobogame) grouped separately from other teosintes, suggesting that race Nobogame is not simply a northern extreme of race Central Plateau. Teosintes of east Michoacan and west Mexico (recently grouped into the Balsas race) grouped together but separately from other teosintes. The latter teosintes may merit special designation in a racial taxonomic system. Only the Central Plateau teosintes consistently overlapped with maize OTU's for the first few principal components. Even in that case there was no consistent association between the Central Plateau teosintes and any specific race of maize.     

Inheritance,intracellular localization,and genetic variation of phosphoglucomutase isozymes in maize (Zea mays L.)

Phosphoglucomutase (PGM; EC 2.7.5.1) isozyme variants were studied in a large number of inbred lines, crosses, and races of maize (Zea mays L.). Patterns of Mendelian inheritance demonstrated for PGM isozyme variants indicated that they are encoded by nuclear genes. Two unlinked loci, Pgm1 and Pgm2, located on the long arm of chromosome 1 and the short arm of chromosome 5, respectively, specify the observed electrophoretic variation on starch gels. No intra- or interlocus hybrid bands were found, suggesting that each isozyme band consists of a single polypeptide. PGM isozymes were present in all plant parts studied and the activity specified by both loci appears to reside in the cytoplasm. In studies of 520 racial collections of maize from Latin America, a single allele at each locus predominated in most collections. Likewise, the same alleles predominated in a set of 406 inbred lines of maize from the United States and Canada.This work was supported in part by NIH Research Grant GM 11546.Paper No. 8496 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, North Carolina.     

A Bird in the Hand Versus Two in the Bush? The Specialist Leafhopper <Emphasis Type="Italic">Dalbulus maidis</Emphasis> (Hemiptera: Cicadellidae) Does Not Discriminate Against Sub-optimal Host Plants (<Emphasis Type="Italic">Zea</Emphasis> spp.)

The corn leafhopper [Dalbulus maidis (DeLong & Wolcott)] is a specialist on Zea (Poaceae) that coevolved with maize (Zea mays mays) and its teosinte (Zea spp.) relatives. This study tested the hypothesis that host acceptance by females varies among Zea hosts, and is correlated with variation in defensive levels across those hosts. Prior studies revealed differences in plant defenses among Zea hosts and corresponding differences in corn leafhopper performance. Thus, host acceptance was expected to be correlated with defensive levels and offspring performance across Zea hosts, following the hypothesis that offspring performance mediates host preference. In parallel, host acceptance was expected to be correlated with transitions in life history strategy (perennial to annual life cycle), domestication status (wild to domesticated), and breeding intensity (landrace to hybrid variety) in Zea because variation in defensive levels and corn leafhopper performance were shown in prior studies to be correlated with those transitions. The study’s hypotheses were tested by comparing, under no-choice conditions, host acceptance by corn leafhopper of a suite of Zea hosts encompassing those transitions: perennial teosinte (Zea diploperennis), Balsas teosinte (Zea mays parviglumis), and landrace and commercial hybrid maize. The results did not show differences in host acceptance for oviposition or feeding among the hosts. Thus, under no-choice conditions, all Zea hosts may be similarly acceptable for feeding and oviposition, despite marked ovipositional preferences under choice conditions and poorer offspring performance on teosintes relative to maize shown previously. The results suggested also that oviposition frequency per plant by females was not correlated with their offspring’s performance.     

Different mechanisms generating sequence variability are revealed in distinct regions of the hydroxyproline-rich glycoprotein gene from maize and related specie*

Summary The sequences of the genes coding for a hydroxyproline-rich glycoprotein from two varieties of maize (Zea mays, Ac1503 and W22), a teosinte (Zea diploperennis) and sorghum (Sorghum vulgare) have been obtained and compared. Distinct patterns of variability have been observed along their sequences. The 500 by region immediately upstream of the TATA box is highly conserved in theZea species and contains stretches of sequences also found in the sorghum gene. Further upstream, significant rearrangements are observed, even between the two maize varieties. These observations allow definition of a 5 region, which is common to the four genes and is probably essential for their expression. The 3 end shows variability, mostly due to small duplications and single nucleotide substitutions. There is an intron present in this region showing a high degree of sequence conservation among the four genes analyzed. The coding region is the most divergent, but variability arises from duplications of fragments coding for similar protein blocks and from single nucleotide substitutions. These results indicate that a number of distinct mechanisms (probably point mutation, transposon insertion and excision, homologous recombination and unequal crossing-over) are active in the production of sequence variability in maize and related species. They are revealed in different parts of the gene, probably as the result of the different types of functional constraints acting on them, and of the specific nature of the sequence in each region.The sequences reported in this paper have been deposited in the EMBL/GenBank Database (Bolt, Beranek, and Newman Laboratories, Cambridge, Mass., and EMBL, Heidelberg), accession nos. M36635 (maize Ac1503), X63134 (maize W22), X64173 (teosinte) and X56010 (sorghum)     

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.     

Inflorescence development in a perennial teosinte: Zea perennis (Poaceae)

The ontogeny of tassels and ears in a perennial Mexican teosinte, Zea perennis (Hitchc.) Reeves and Mangelsdorf, was examined using scanning electron microscopy and light microscopy. Ear development follows a pattern previously described for two annual teosintes, Z. mays subsp. mexicana and Z. mays subsp. parviglumis var. parviglumis (race Balsas), and for the bisexual mixed inflorescence in a diploperennial teosinte, Z. diploperennis; it differs from that described for the ear of Z. diploperennis plants grown at the latitudes of Iowa and Wisconsin. Common bud primordia of the ear are initiated in the axil of distichously arranged bracts along the ear axis. These common primordia bifurcate to form paired pedicellate and sessile spikelet primordia. Development of the pedicellate spikelets in the ear is arrested leaving the sessile spikelets, along with the adjoining rachis segment, to form solitary grains enclosed within cupulate fruitcases. The organogenesis of the central spike of the tassel is similar to that previously described in other Zea taxa. This developmental study supports the hypothesis that both femaleness and maleness are derived from and expressed on a common background; it is consistent with the view that the maize ear was derived from the central spike of a male inflorescence terminating a primary branch of the main axis of the inflorescence.