QTL mapping of agronomic traits in tef [<Emphasis Type="Italic">Eragrostis tef</Emphasis>(Zucc) Trotter]

Background  

Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5).     

A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. Ninety-four F₉ recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis tef cv. Kaye Murri × Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST–SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

RFLP linkage map of the Ethiopian cereal tef [Eragrostis tef (Zucc) Trotter]

Tef [Eragrostis tef (Zucc)Trotter] is one of the most important cereal crops in Ethiopia. It is an allotetraploid species with a genome size of 720 Mbp. In this paper we report results of genetic linkage-map construction for E. tef using tef and heterologous cDNA probes for the first time. One hundred and sixteen F₈ recombinant inbred lines (RILs) from the cross E. tef cv Kaye Murri×Eragrostis pilosa (accession30–5) were used for mapping. Parental lines were digested with nine restriction enzymes and screened using 159 tef cDNA and 162 heterologous probes including the grass genome anchor probes. The polymorphism level between parental lines was 66.9%. One hundred and thirty nine polymorphic probes were hybridized against 116 RILs. Both the tef and the heterologous probes hybridized well against tef genomic DNA. The linkage map defined 1,489 cM of the tef genome comprising 149 marker loci distributed among 20 linkage groups. The average interval between markers was 9.99 cM. A fraction (14.8%) of the markers deviated significantly from the expected segregation. Such a genetic linkage map is useful for tagging economically useful genes in tef because a wide range of agronomically important traits is segregating within this population. This would enable the use of a marker assisted breeding strategy which, in turn, will enhance breeding efficiency. Alignment of the tef RFLP map with the rice RFLP map indicates that a number of syntenic chromosomal fragments exist between tef and rice in which the gene order was for the most part collinear. The comparative mapping information should enable tef scientists to take advantage of whatever genetic progress is made on the cereal model species rice. Received: 9 June 2000 / Accepted: 31 August 2000     

Literature review and numerical taxonomy ofEragrostis tef (T’ef)

Eragrostis tef (Zucc.) Trotter is a native Ethiopian cereal. It was recently classified into 35 cultivars which are united into 6 complexes based on inflorescence morphology, grain color, time to maturity and uses. These complexes do not show ecogeographic unity, and they cross ethnological boundaries. Thirty-nine collections of t’ef were studied in biosystematic detail, and compared withE. aethiopica Chiov. andE. pilosa (L.) Beauv., two putative ancestors of the cereal. The latter species is morphologically variable but closely allied to E. tef. Three morphologically distinct complexes are recognized within the cereal. The ethnological significance of these complexes of t’ef is not clear.     

Gynogenic plant regeneration from unpollinated flower explants of Eragrostis tef (Zuccagni) Trotter

Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal in Ethiopia. In its wild relative E. mexicana, regeneration of six green plants resulted from culture of 121 non-pollinated immature pistils. In the allotetraploid crop species tef, however, only callus and root formation was obtained by this method. By contrast, immature spikelets and panicle segments of E. tef proved amenable to gynogenic plant regeneration. Upon step-wise optimization of the protocol, efficient plant formation was achieved in all three cultivars tested. In cv. DZ-01-196, culture of 1305 immature spikelets resulted in formation of 159 green plants. Flow cytometric analysis revealed (di)haploid, triploid, tetraploid and octoploid regenerants, from which the vast majority was tetraploid. Tef-breeding programs will likely benefit substantially from efficient generation of true-breeding plants.     

DNA amount, latitude, and crop plant distribution

Avdulov and Stebbins noted a tendency for species with large chromosomes in several angiosperm groups or families (including the Gramineae, Commelinaceae, Liliales, Polemoniales and the Leguminosae) to be localized in distribution to temperate latitudes. As chromosome size and DNA content are closely correlated, the distribution of species with large DNA amounts per chromosome, or per diploid genome, might expected to be similarly localized. This hypothesis was tested using samples of crop species with large ranges of DNA amounts from the Gramineae and the Leguminosae. For instance, the mean DNA amount per chromosome for the sample of cereal grain species showed about a 36-fold range from 0·033 picograms (pg) in Eragrostis tef to 1·186 pg in Secale cereale, while for the sample of pulse crops the range was about 70-fold from 0·032 pg in Lablab niger to 2·225 pg in Vicia faba. The results for cereal grain crops, cultivated pasture grasses and pulse crops show that cultivation of species with high DNA amounts per diploid genome tends to be localized in temperate latitudes, or to seasons and regions at lower latitudes where the conditions approximate to those normally found in temperate latitudes. Moreover, man has shown a strong tendency to choose species for cultivation with increasingly lower DNA amounts at successively lower latitudes. Thus, there is a cline for DNA amount and latitude. This cline is exhibited independently by both C₃ and C₄ crop species, and by both annuals and perennials and hence is independent of life cycle type and the taxonomic distribution of C₃ and C₄ photosynthesis. The cline is apparently a natural phenomenon which man has modified and exaggerated in agriculture. It is suggested, therefore, that interspecific variation in DNA amount between angiosperm species may have adaptive significance affecting the distribution of both crop and non-crop species. The cline might be caused either by variation in DNA amount per se, or by variation in some factor(s) correlated with DNA amount. The factor(s) causally responsible for the cline, and their mode of action should be investigated since they may have implications for agriculture and plant breeding.     

Effects on Growth and Development of Individual Chromosomes from Slow-growing Lophopyrum elongatum Love when Incorporated into Bread Wheat (Triticum aestivum L.)

Aspects of growth and development were evaluated in the fast-developingannual Triticum aestivum L. ‘Chinese Spring’, theslow-developing perennial Lophopyrum elongatum Löve, theiramphiploid, and chromosome addition and substitution lines ofL. elongatum into ‘Chinese Spring’. Relative growthrates (RGR) of shoots of L. elongatum and the amphiploid werelower than those of ‘Chinese Spring’ (34 and 13%respectively) and main stem development was also slower. Therewas no difference in shoot RGR of any of the chromosome additionor substitution lines and that of ‘Chinese Spring’when assessed between Haun stages 2.0 and 5.0. In contrast,several aspects of plant development were observed to differin the chromosome addition and substitution lines. SubstitutingE genome chromosomes (with the exceptions of 3E and 4E) forD genome chromosomes, or adding E genome chromosomes, slowedthe rate of main stem development, at least up to Haun stage5.0. Despite these differences in the rate of main stem development,the appearance of adventitious roots commenced at approximatelyHaun stage 2.0 in all genotypes. However, the numbers of adventitiousroots and tillers at the 5.0 Haun stage differed between someof the lines when compared to ‘Chinese Spring’.Although incorporation of some L. elongatum chromosomes alteredaspects of plant development, all lines showed more similarityto bread wheat than to L. elongatum, reflecting, in part, thegreater genetic contribution made by bread wheat to these lines.Copyright 2001 Annals of Botany Company Adventitious roots, chromosome addition and substitution lines, Haun stage, Lophopyrum elongatum, relative growth rate (RGR), Triticum aestivum(wheat)     

Key Features of Cereal Genome Organization as Revealed by the Use of Cytosine Methylation-Sensitive Restriction Endonucleases

Unlike mammalian genomes, cereal (Gramineae) genomes exhibit little suppression of CpG dinucleotides. In cereal genomes, however, most of the numerous potential recognition sites for CpG methylation-sensitive restriction enzymes are methylated. Analysis of cereal genomic libraries and of regions flanking genes indicates that unmethylated NotI sites are useful landmarks for regions containing genes/single-copy sequences. Studies of a rye chromosome arm indicate that its pericentromeric region has a reduced density of unmethylated NotI (and MluI) sites and therefore of genes. Unmethylated MluI and NruI sites are distributed nonrandomly in the genomes of wheat, barley, and rice. Analysis of the genomic blocks defined by these sites in wheat and barley indicates that they are most likely to have arisen by amplification. These observations form the basis of a proposed model for the organization and evolution of the wheat, barley, and rice genomes.     

Spatial Separation of Ancestral Genomes in the Wild Grass Milium montianum Parl.

Previous work showed a strong tendency for genomes from twodifferent parents to be spatially separated in cell nuclei ofseveral man-made F₁ hybrids between grass species. An importantquestion therefore is whether similar nonrandom genome dispositionoccurs in wild species. Milium montianum Parl. (2n = 22) isa naturally occurring allopolyploid grass combining two geneticallydissimilar chromosome sets (V and M genomes), each originatingfrom a different ancestral species. These two ancestral genomeswere easily discriminated as all V genome chromosomes were largerthan all M genome chromosomes. In two-dimensional spread preparations,the V genome derived from M. vernale Bieb. (2n = 8), and theM genome (of different but uncertain origin) showed a highlysignificant tendency to lie apart. Generally, the V chromosomestended to surround the M chromosomes in both mitotic and meioticnuclei suggesting that this arrangement persists throughoutplant development. Such nuclear organization is probably undergenetic control and may facilitate some independent behaviourof ancestral genomes in allopolyploids. Indeed it may play asignificant role in plant evolution and speciation, especiallyif different intranuclear positions (e.g. central or peripheral)are correlated with preferential phenotypic expression of ancestralgenes. Milium montianum Parl., Gramineae, allopolyploid, spatial chromosome disposition, ancestral genome separation, plant speciation and evolution     

Acetyl-CoA Carboxylase in Higher Plants: Most Plants Other Than Gramineae Have Both the Prokaryotic and the Eukaryotic Forms of This Enzyme

The presence and the absence of a prokaryote type and a eukaryotetype of acetyl-CoA carboxylase (EC 6.4.1.2 [EC] ; ACCase) were examinedin members of 28 plant families by two distinct methods: thedetection of biotinylated subunits of ACCase with a streptavidinprobe, and the detection of the accD gene, which encodes a subunitof the prokaryotic ACCase, by Southern hybridization analysis.The protein extracts of all the plants studied contained a biotinylatedpolypeptide of 220 kDa, which was probably the eukaryotic ACCase.All the plants but those belonging to Gramineae also containeda biotinylated polypeptide of ca. 35 kDa, which is a putativesubunit of the prokaryotic ACCase. In all plants but those inGramineae, the ca. 35 kDa polypeptide was found in the proteinextracts of plastids, while the 220 kDa polypeptide was absentfrom these plastid extracts. The plastid extracts of the plantsin Gramineae contained the 220 kDa polypeptide, as did the homogenatesof the leaves. Southern hybridization analysis demonstratedthat all the plants but those in the Gramineae contained theaccD gene. These findings suggest that most higher plants havethe prokaryotic ACCase in the plastids and the eukaryotic ACCasein the cytosol. Only Gramineae plants might contain the eukaryoticACCases both in the plastids and in the cytosol. The originof the plastid-located eukaryotic ACCase in Gramineae is discussedas the first possible example of substitution of a plastid geneby a nuclear gene for a non-ribosomal component. ⁴Present address: Plant-Growth Regulation Laboratory, The Instituteof Physical and Chemical Research (RIKEN), Hirosawa 2-1, Wako,351-01 Japan ⁵Present address: Laboratory of Plant Molecular Biology, Schoolof Agricultural Sciences, Nagoya University, Chikusa-ku, Nagoya,464-01 Japan     

SYSTEMATIC REVISION OF THE EPIMENIIDAE (MOLLUSCA: SOLENOGASTRES)

The species of Epimeniidae (Solenogastres: Cavi-belonia) arecompared and revised according to available type material. Structuresof particular interest include the differentiation of the foregut,the pharyngo-buccal nervous system and the blood cells. Sevenspecies are recognized in the family. Of these, six are placedin the genus Epimenia: E. australis (Thiele) (synonym Dinomeniaverrucosa Nierstrasz), E. ohshimai Baba, E. arabica Salvini-Plawen& Benayahu, and the three new species E. babai from offKyushu, Japan (synonym E. verrucosa in Baba 1939–1951),E. allohaemata from off Korea and E.indica from the Maldives. E. vixinsignis Salvini-Plawen is transferred to Epiherpia gen.nov. (Received 2 February 1996; accepted 19 September 1996)     

Leaf Abscission Zones in Molinia caerulea (L.) Moench, the Purple Moor Grass

Leaf separation and loss in the grass Molinia caerulea (L.)Moench was investigated using scanning electron microscopy.Leaf senescence and subsequent shedding of leaves was precededby the formation of a leaf abscission zone. The zone containscells which have more than doubled their wall thickness to greaterthan 0-4 µm. The line of fracture associated with thezone principally followed the middle lamellae, leaving intactcells on the fracture faces. Molinia should prove an interestingmodel in which to study abscission processes in the Gramineae. Molinia caerulea, leaf abscission zone, electron microscopy     

Somatic Embryogenesis and Plant Regeneration from Suspension Cultures of Pearl Millet (Pennisetum americanum)

Immature embryos of Pennisetum americanum (pearl millet), culturedin the presence of 2,4-dichlorophenoxy acetic acid (2,4-D) produceda pale-yellow and compact callus tissue by proliferation ofthe scutellum. Teased pieces of the compact callus were placedin a liquid medium on a gyrotory shaker to establish suspensioncultures. The cultures were composed of large, elongated andhigly vacuolated cells, and a population of richly cytoplasmiccells. The latter, here termed embryogenic cells, containednumerous plastids with starch, and occurred in tight groupsof four or more cells, and occasionally as single cells. Structuresresembling various stages of embryogenic development were foundin the suspension cultures. When the cultures were plated ina 2,4-D-free agar medium containing abscisic acid, embryoidswith the typical organization of cereal embryos were produced.The embryoids ‘germinated’ in vitro to give riseto plantlets, which were successfully transferred to soil. Theregenerated plants showed the normal diploid chromosome numberof 14. Embryoids apparently arose from single embryogenic cells,either directly or after the formation of a proembryonal massof cells. embryogenesis, pearl millet, Pennisetum americanum, regeneration, suspension culture     

An 8 kb Nucleotide Sequence at the 3' Flanking Region of the sspC Gene (184{degrees}) on the Bacillus subtilis 168 Chromosome Containing an Intein and an Intron

As part of the Bacillus subtilis genome sequencing project,we determined the complete nucleotide sequence of an 8000-bpfragment downstream of the sspC gene (184°) of the B. subtilis168 chromosome. The sequence analysis shows that the sspC geneis located inside of the SPß region, which differsfrom the current genetic map of B. subtilis 168. This regioncontains 12 putative ORFs (yojQ through yojZ and sspC). A homologysearch for the deduced products of the ORFs shows signi.cantsimilarities to enzymes involved in deoxyribonucleotide metabolism:ribonucleotide reductase (Nrd) E, NrdF, thioredoxinand dUTPase.Interestingly, this DNA fragment includes two split genes, yojPcontaining conserved motifs of an intein and yojQ and yojS withan 808-bp intervening sequence for a putative intron structure.In addition, the yojR gene includes a putative new DNA replicationterminator.     

Epidermal Structure in the Ligule of Rice (Oryza sativa L.)

The structure of the abaxial epidermis of the ligule of rice(Oryza sativa L.) as seen in the light and scanning electronmicroscope is described. Long cells, silica cells, cork cells,prickle hairs, microhairs and stomata-like structures were found.Reasons for considering these latter structures to be true stomataare given. Results of an X-ray analysis for silicon are presentedand the distribution of silica discussed in relation to itsfunctional role in the ligule. Oryza sativa L, rice, Gramineae, ligule, epidermis, scanning electron microscopy, X-ray analysis, silica, stomata     

Karyotype diversification and evolution in diploid and polyploid South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data

Background and Aims: Changes in chromosome structure and number play an importantrole in plant evolution. A system well-suited to studying differentmodes of chromosome evolution is the genus Hypochaeris (Asteraceae)with its centre of species' diversity in South America. AllSouth American species uniformly have a chromosome base numberof x = 4 combined with variation in rDNA number and distribution,and a high frequency of polyploidy. The aim of this paper isto assess directions and mechanisms of karyotype evolution inSouth American species by interpreting both newly obtained andprevious data concerning rDNA localization in a phylogeneticcontext. Methods: Eleven Hypochaeris species from 18 populations were studiedusing fluorescence in situ hybridization (FISH) with 35S and5S rDNA probes. A phylogenetic framework was established fromneighbour-net analysis of amplified fragment length polymorphism(AFLP) fingerprint data. Key Results: A single 5S rDNA locus is invariably found on the short armof chromosome 2. Using 35S rDNA loci, based on number (one ortwo) and localization (interstitial on the long arm of chromosome2, but sometimes lacking, and terminal or interstitial on theshort arm of chromosome 3, only very rarely lacking), sevenkaryotype groups can be distinguished; five of these includepolyploids. Karyotype groups with more than one species do notform monophyletic groups. Conclusions: Early evolution of Hypochaeris in South America was characterizedby considerable karyotype differentiation resulting from independentderivations from an ancestral karyotype. There was marked diversificationwith respect to the position and evolution of the 35S rDNA locuson chromosome 3, probably involving inversions and/or transpositions,and on chromosome 2 (rarely 3) concerning inactivation and loss.Among these different karyotype assemblages, the apargioidesgroup and its derivatives constitute by far the majority ofspecies.     

Variation in response of accessions of minor millets,Pennisetum americanum (L.) Leeke (pearl millet) and Eleusine coracana (L.) Gaertn (finger millet), and Eragrostis tef (Zucc.) Trotter (tef) to salinity in early seedling growth

The response to increasing NaCl concentration of seedlings of 25 accessions of Ethiopian land races of each of Pennisetum americanum (L.) Leeke (pearl millet) and Eleusine coracana (L.) Gaertn (finger millet), and 15 accessions of Eragrostis tef (Zucc.) Trotter (tef), was examined after two week's growth in NaCl solution culture. Although increasing NaCl concentration significantly reduced seedling root lengths, there was considerable variation within, and between accessions within each species.Analysis based upon a non-linear least square inversion method, using root length data, revealed significant differences in accessions of P. americanum and E. tef on the basis of the estimated salinity threshold, C _t , the NaCl concentrations at which root length begins to decrease. C _t did not differ significantly between E. coracana accessions. Estimates of C₅₀ and C₀, mininum concentrations causing a 50% decrease in root length, and zero root growth respectively, revealed differences between and within accessions for all three species. Overall, finger millet was more tolerant than tef, which was more tolerant than pearl millet. There is clear evidence that differences in tolerance are genetically based from broad sense heritability estimates.     

Confirmation of Ancient Polyploidy in Dahlia (Asteraceae) Species using Genomic In Situ Hybridization

The successful production of interspecific hybrids between membersof the dysploid chromosome series inDahlia offers a unique opportunityto investigate chromosome evolution. Analysis of meiotic metaphaseI in these hybrids using genomic in situ hybridization (GISH)has shown that pairing occurs both between and within parentalgenomes. These results have provided clear evidence for theallotetraploid origin of Dahlia species with 2n=32 and suggeststhat species with 2n=34 and 2n=36 have also arisen via allopolyploidy.A bivalent promoting mechanism proposed for species with 2n=32also appears to be present in Dahlia species with 2n=34 and2n=36 .Copyright 1999 Annals of Botany Company Dahlia , GISH, dysploidy, chromosome pairing, karyotype analysis, polyploidy.     

Structure and Function in the Grass Ligule: the Endomembrane System of the Adaxial Epidermis of the Membranous Ligule of Lolium temulentum L. (Poaceae)

The endomembrane system of the adaxial epidermal cells of themembranous ligule of the grass Lolium temulentum L. has beenstudied by conventional transmission electron microscopy, andby using zinc iodide-osmium tetroxide impregnation with examinationof thick sections at 100 kV. The components of the endomembranesystem are the nuclear membranes, rough endoplasmic reticulum(present in both cisternal and tubular forms), dictyosomes,dictyosome-derived vesicles, coated vesicles, plasma membraneand tonoplast. Direct continuity between tubular endoplasmicreticulum and the cis face of dictyosomes is demonstrated andthe applicability of the endomembrane concept to this putativesecretory tissue is discussed. The presence of vesicle-likeprofiles apparently within the outer tangential walls is reported.Copyright1995, 1999 Academic Press Ligule, Lolium temulentum L., darnel, grasses, Poaceae, Gramineae, endomembrane concept, ultrastructure, zinc-iodide-osmium tetroxide impregnation     

Cloning and Sequencing of a 36-kb Region of the Bacillus subtilis Genome between the gnt and iol Operons

Within the framework of an international project for the sequencingof the entire Bacillus subtilis genome, a 36-kb chromosome segment,which covers the region between the gnt and iol operons, hasbeen cloned and sequenced. This region (36447 bp) contains 33complete open reading frames (ORFs; genes) including the fourgnt genes and one partial gene. A homology search for the productsof the 33 complete ORFs revealed significant homology to knownproteins in 16 of them such as tetracycline resistance protein(Clostridium perfringens), asparagine synthetase (Arabidopsisthaliana), aldehyde dehydrogenase (Pseudomonas oleovorans),2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (P. paucimobilis),heat shock protein HtpG (Escherichia coli), galactose-protonsymporter (E. coli), auxin-induced protein (common tobacco),glucitol operon repressor (E. coli) and methylmalonate-semialdehydedehydrogenase (P. aeruginosa). Unlike the regions we sequencedso far, this region contained two short sequence multiplications:one was a tandem sequence duplication (409 and 410 bp), andthe other a triplication consisting of two highly conserved118-bp tandem sequences preceded by a less conserved similarsequence (129 bp). The reasons for the presence of these sequencemultiplications in the gnt to iol region were deduced.