Higher expression of induced defenses in teosintes (Zea spp.) is correlated with greater resistance to fall armyworm,Spodoptera frugiperda

Selection for plant traits important for agriculture can come at a high cost to plant defenses. While selecting for increased growth rate and yield, domestication and subsequent breeding may lead to weakened defenses and greater susceptibility of plants to herbivores. We tested whether expression of defense genes differed among maize, Zea mays ssp. mays L. (Poaceae), and its wild relatives Zea mays ssp. parviglumis Iltis & Doebley and Zea diploperennis Iltis et al. We used two populations of Z. mays ssp. parviglumis: one expected to express high levels of an herbivore resistance gene, wound‐inducible protein (wip1), and another expected to have low expression of wip1. To test whether maize and wild Zea differed in induction of defenses against Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), we quantified expression of several genes involved in plant defense: wip1, maize protease inhibitor (mpi), pathogenesis‐related protein (PR‐1), and chitinase. Moreover, we compared growth, development, and survival of caterpillars on maize and wild Zea plants. We found that maize expressed low levels of all but one of the genes when attacked by caterpillars, whereas the wild relatives of maize expressed induced defense genes at high levels. Expression of wip1, in particular, was much greater in the Z. mays ssp. parviglumis population that we expected to naturally express high levels of wip1, with expression levels 29‐fold higher than in herbivore‐free plants. Elevated expression of defenses in wild plants was correlated with higher resistance to caterpillars. Larvae were 15–20% smaller on wild Zea compared with maize, developed 20% slower, and only 22% of them survived to pupation on Z. mays ssp. parviglumis with high levels of wip1. Our results suggest that domestication has inadvertently reduced the resistance of maize, and it is likely that expression of wip1 and other genes associated with defenses play an important role in this reduction in resistance.     

Allelopathic effects of Sorghum vulgare Pers.

Summary Sorghum vulgare Pers. a tropical fodder crop significantly reduced the vertical growth and drymass of Sorghum vulgare, Pennisetum americanum, Zea mays and Setaria italica. Aqueous extracts of various plant parts, field soils and decaying mulch significantly reduced germination, radicle growth and water contents of all test species. The toxicity levels were depending upon the plant parts used in the biossay experiments and the sensitivity of the test species. It is suggested that the Sorghum fields be rotated with other crops to maximize the crop productivity.     

Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA

The phylogenetic relationships of the genus Sorghum and related genera were studied by sequencing the nuclear ribosomal DNA (rDNA) internal transcribed spacer region (ITS). DNA was extracted from 15 Sorghum accessions, including one accession from each of the sections Chaetosorghum and Heterosorghum, four accessions from Parasorghum, two accessions from Stiposorghum, and seven representatives from three species of the section Sorghum (one accession from each of S. propinquum and S. halepense, and five races of S. bicolor). The maize (Zea mays) line, H95, and an accession from Cleistachne sorghoides were also included in the study. Variable nucleotides were used to construct a strict consensus phylogenetic tree. The analyses indicate that S. propinquum, S. halepense and S. bicolor subsp. arundinaceum race aethiopicum may be the closest wild relatives of cultivated sorghum; Sorghum nitidum may be the closest 2n=10 relative to S. bicolor, the sections Chaetosorghum and Heterosorghum appear closely related to each other and more closely related to the section Sorghum than Parasorghum; and the section Parasorghum is not monophyletic. The results also indicate that the genus Sorghum is a very ancient and diverse group.This research was partially supported by a Third Country Scholarship from Pioneer Hi-Bred International Incorporated Contribution 94-182-J from Kansas Agricultural Experiment Station     

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ‘domestication syndrome’. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non‐orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ‘classic’ domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non‐overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.     

The use of ribosomal ITS to determine phylogenetic relationships within Sorghum

 For the first time, a combined analysis of the ITS1 regions of all twenty-five Sorghum species has been undertaken. Parsimony analysis revealed a distinct lineage of Sorghum consisting of the cultivated species and their progenitors plus S. angustum, S. brachypodum, S. ecarinatum, S. macrospermum, S. laxiflorum and Saccharum officinarum. A second unsupported lineage consists of the Parasorghum and Stiposorghum species S. grande, S. leiocladum, S. nitidum, S. purpureosericeum, S. timorense, S. versicolor, S. amplum, S. bulbosum, S. interjectum, S. plumosum, S. stipoideum and the African grass Cleistachne sorghoides. Three Australian endemic species, S. angustum, S. brachypodum and S. ecarinatum, are closely related to S. bicolor, with S. angustum showing no difference to S. bicolor in ITS1 sequence. Sorghum macrospermum and S. laxiflorum form a strong clade within the Eusorghum branch indicating closer relationships to this group than to any of the Parasorghum or Stiposorghum species. Saccharum officinarum has shown closer relationships to Sorghum than to Zea mays, while the close relationship of Cleistachne sorghoides to Sorghum has been confirmed. These relationships between Sorghum species provide an important guide for plant breeders to exploit the wider Sorghum genepool through crosses between wild and cultivated species in an effort to improve sorghum production. Received April 30, 2001 Accepted July 10, 2001     

TAXONOMY OF ZEA (GRAMINEAE). II. SUBSPECIFIC CATEGORIES IN THE ZEA MAYS COMPLEX AND A GENERIC SYNOPSIS

A compromise classification of the genus Zea, reflecting both phylogeny and practical needs, recognizes six taxa, as follows: Section Luxuriantes : Zea perennis. Zea diploperennis, Zea luxurians. Section Zea : Zea mays ssp. mexicana (Neo-volcanic Plateau), Zea mays ssp. parviglumis Iltis & Doebley ssp. n. var. parviglumis (Rio Balsas drainage, Pacific slope from Guerrero to Jalisco), Zea mexicana ssp. parviglumis var. huehuetenangensis Iltis & Doebley var. n. (Pacific slope, western Guatemala, Prov. Huehuetenango), Zea mays ssp. mays. The new subspecies is distinguished by smaller spikelets and rachis joints, the varieties by different habitats, blooming dates and their genetic behavior in relation to cultivated Zea mays. Zea mays ssp. mexicana is the ancestor of corn.     

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.     

Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley

The barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. Towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cM interval in a “cold spot” of recombination of the proximal region of the short arm of barley chromosome 2H. Extensive synteny between the barley Sdw3 locus (Hvu_sdw3) and the orthologous regions (Osa_sdw3, Sbi_sdw3, Bsy_sdw3) of three other grass species (Oryza sativa, Sorghum bicolor, Brachypodium sylvaticum) allowed for efficient synteny-based marker saturation in the target interval. Comparative sequence analysis revealed colinearity for 23 out of the 38, 35, and 29 genes identified in Brachypodium, rice, and Sorghum, respectively. Markers co-segregating with Hvu_sdw3 were generated from two of these genes. Initial attempts at chromosome walking in barley were performed with seven orthologous gene probes which were delimiting physical distances of 223, 123, and 127 kb in Brachypodium, rice, and Sorghum, respectively. Six non-overlapping small bacterial artificial chromosome (BAC) clone contigs (cumulative length of 670 kb) were obtained, which indicated a considerably larger physical size of Hvu_sdw3. Low-pass sequencing of selected BAC clones from these barley contigs exhibited a substantially lower gene frequency per physical distance and the presence of additional non-colinear genes. Four candidate genes for sdw3 were identified within barley BAC sequences that either co-segregated with the gene sdw3 or were located adjacent to these co-segregating genes. Identification of genic sequences in the sdw3 context provides tools for marker-assisted selection. Eventual identification of the actual gene will contribute new information for a basic understanding of the mechanisms underlying growth regulation in barley.     

Sorghum resolved as a distinct genus based on combined ITS1, ndhF and Adh1 analyses

Recent studies on Sorghum have attempted to determine the genetic relationships between the 17 Australian native Sorghum species and the cultivated species, with several studies contradictory in their findings. To resolve these issues within Sorghum, a detailed investigation of the phylogenetic relationships was made. The alcohol dehydrogenase 1 gene (Adh1) from 25 Sorghum species and Cleistachne sorghoides was sequenced. Independent analyses of the Adh1 data, and combined analyses of the Adh1, ITS1 and ndhF data were carried out. All Sorghum species were resolved to a distinct clade with 100% support. Within Sorghum, the Eu-sorghum species were resolved to a strongly supported lineage that included the Australian native species S. macrospermum and S. laxiflorum. All other Australian species were resolved to a second strongly supported lineage. Sorghum laxiflorum and S. macrospermum have again been identified as the Australian species most closely related to cultivated sorghum. Analysis based on three genes has shown that the 25 Sorghum species form a distinct monophyletic group, and that there is little evidence to support the recent taxonomic revision of these species into three separate genera.     

Chromosome localization and characterization of a family of long interspersed repetitive DNA elements from the genus Zea

This paper describes the characterization and chromosomal distribution of new long repetitive sequences present in all species of the genus Zea. These sequences constitute a family of moderately repetitive elements ranging approximately from 1350 to 1700 copies per haploid genome in modern maize (Zea mays ssp. mays) and teosinte (Zea diploperennis), respectively. The elements are long, probably larger than 9 kb, and they show a highly conserved internal organization among Zea subspecies and species. The elements are present in all maize chromosomes in an interspersed pattern of distribution, are absent from centromeric and pericentric heterochromatin, and with some clustering in the distal regions of chromosome arms.     

Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping

Abstract

Background

Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9–11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear.

Results

About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea.

Conclusions

The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1025) contains supplementary material, which is available to authorized users.     

Infrageneric Phylogeny and Temporal Divergence of Sorghum (Andropogoneae,Poaceae) Based on Low-Copy Nuclear and Plastid Sequences

The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. x drummondii, S. propinquum, and S. virgatum were closely related to S. x almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.     

Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana

To provide a framework for studies to understand the contribution of SALT OVERLY SENSITIVE1 (SOS1) to salt tolerance in Thellungiella halophila, we sequenced and annotated a 193-kb T. halophila BAC containing a putative SOS1 locus (ThSOS1) and compared the sequence to the orthologous 146-kb region of the genome of its salt-sensitive relative, Arabidopsis thaliana. Overall, the two sequences were colinear, but three major expansion/contraction regions in T. halophila were found to contain five Long Terminal Repeat retrotransposons, MuDR DNA transposons and intergenic sequences that contribute to the 47.8-kb size variation in this region of the genome. Twenty-seven genes were annotated in the T. halophila BAC including the putative ThSOS1 locus. ThSOS1 shares gene structure and sequence with A. thaliana SOS1 including 11 predicted transmembrane domains and a cyclic nucleotide-binding domain; however, different patterns of Simple Sequence Repeats were found within a 540-bp region upstream of SOS1 in the two species.     

Duplication and Divergence of Grass Genomes: Integrating the Chloridoids

Expressed Sequence Tags from a variety of plant species have been useful for comparative genomics. The evolution of the Chloridoideae subfamily, previously lacking sequence data, was clarified by analysis of Bermudagrass (Cynodon dactylon) ESTs generated from a normalized cDNA library. Using EST collections, we generated unigene sets and analyzed them to further elucidate the evolutionary history of grass subfamilies. A total of eight grasses (C. dactylon, Sorghum bicolor, Saccharum officinarum, Zea mays, Oryza sativa, Hordeum vulgare, Festuca arundinacea, and Triticum aestivum) in four subfamilies and five tribes were analyzed using two different approaches—synonymous substitution rates (Ks) and phylogenetic trees. Ks distributions of paralogous genes suggested several duplication events in C. dactylon, S. bicolor, H. vulgare, and T. aestivum. Phylogenetic analysis with the unigene sets indicated that the analyzed grasses diverged from a common ancestor after a shared ancient polyploidization (ca. 50.0?~?67.8 million years ago). Ks distributions of orthologous genes suggested that the Chloridoideae and Panicoideae subfamilies diverged about 34.6?~?38.5 million years ago. With the evidence described in this study, we found traces of genomic changes in some grass subfamilies after the divergence of the PACC and BEP clades as well as divergence of Chloridoideae subfamily.     

Inoculated Host Range and Effect of Host on Morphology and Size of Macroconidia Produced by Claviceps africana and Claviceps sorghi

Twenty graminaceous plant species were evaluated for their susceptibility to the two sorghum ergot pathogens Claviceps sorghi and Claviceps africana. Five species viz., Sorghum arundinaceum, Sorghum halepense, Sorghum versicolor, Sorghum virgatum and Pennisetum glaucum were found to become infected by both pathogens via inoculation with 10⁶ conidia/ml. Species which did not become infected under these conditions included Pennisetum pedicellatum, Zea mays, and species of Panicum, Brachiaria, Cenchrus, Andropogon, Dichanthium, Chrysopogon, Iseilema, Bothriochloa and Chloris. Honeydew secretions were observed from infected flowers of susceptible plant species. There was marked variation in size of macroconidia of both C. sorghi and C. africana on different hosts on which the pathogens were able to establish symptoms. Dimorphism was observed for macroconidia produced on P. glaucum, as elliptical and spindle shaped macroconidia were observed. Based on inoculation under greenhouse conditions, we conclude that C. sorghi and C. africana may have similar host ranges.     

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)     

高粱属植物的地理分布

为探讨高粱属(Sorghum Moench)的系统发育关系,通过野外调查及查阅标本和文献资料,对高粱属植物的地理分布进行了整理和研究。高粱属植物约有29种,分布于全世界热带到温带地区,其中澳大利亚22种,亚洲15种,非洲9种,欧洲3种,地中海2种,美洲6种。中国有5种,分布在东北、西南到华南各省(区)。高粱属有5亚属,仅高粱亚属(subgen.Sorghum)延伸至新世界,其他亚属均分布在旧世界,高粱亚属覆盖非洲并扩散到全世界热带到温带地区;拟高粱亚属(subgen.Parasorghum)分布在非洲、亚洲、澳大利亚;有柄高粱亚属(subgen.Stiposorghum)主要分布在澳大利亚,个别种分布到亚洲;多毛高粱亚属(subgen.Chaetosorghum)分布在澳大利亚;异高粱亚属(subgen.Heterosorghum)分布在澳大利亚和亚洲。这表明澳大利亚东北部是高粱属的现代分布中心和多样化中心,非洲东北部和热带亚洲是否是高粱属的起源地尚需确证。     

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.