Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv.

 An RFLP-based map consisting of 160 loci was constructed in an intervarietal cross of foxtail millet [Setaria italica (L.) P. Beauv.], Longgu 25×Pagoda Flower Green. The map comprises nine linkage groups, which were aligned with the nine foxtail millet chromosomes using trisomic lines, and spans 964 cM. The intraspecific map was compared to an interspecific map, constructed in a S. italica×S. viridis cross. Both the order of the markers and the genetic distances between the loci were highly conserved. Deviations from the expected 1 : 2 : 1 Mendelian segregation ratios were observed in both the intra- and inter-specific populations. The segregation data indicate that chromosome VIII in the Longgu 25×Pagoda Flower Green cross carries a gene that strongly affects gamete fertility. Received: 18 December 1996 / Accepted: 4 August 1997     

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F₂ population, i.e. “B100” of cultivated S. italica and “A10” of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces’ grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic variability of foxtail millet (Setaria italica P. Beauv.)

Summary The genetic diversity of a world collection of foxtail millet strains (Setaria italica) and some samples of wild populations (Setaria viridis) was studied by means of electrophoresis on five enzymes (10 loci) Est, Acph, Got, Mdh, Pgd. In spite of an overall limited polymorphism, the diversity appeared to be clearly regionalized. The wild populations collected in France and China introduced new genetic variability to the cultivated forms. However, the interregional diversity within both species was greater than the between species (S. viridis/S. italica) diversity.     

Late Neolithic agriculture in eastern Austria: archaeobotanical results from sites of the Baden and Jevišovice cultures (3600–2800 b.c.)

The article presents archaeobotanical results from six late Neolithic excavation sites in eastern Austria. Two of the sites belong to the Jevišovice culture (3200–2800 cal b.c.), the remaining four to the Baden culture (3600–2900 cal b.c.). Results show that farmers around 3000 cal b.c. were relying on the use of Triticum monococcum and Hordeum vulgare as principal cereals, with Triticum dicoccum and Panicum miliaceum as additional crops. Common millet was found in quantity at one of the Jevišovice sites and shows the remarkably early westward spread of this species. Single records of Triticum spelta are discussed in the light of the recently proposed ideas about an independent central European origin of spelt. Another record concerns the “new-type” glume wheat, providing further evidence for the once widespread occurrence of this cultivar. Triticum aestivum (hexaploid naked wheat) and Setaria italica (foxtail millet) were found as rare admixtures at the Jevišovice settlements. Pulses were represented by Pisum sativum and Lens culinaris, oil plants by Papaver somniferum and Linum usitatissimum. One of the Jevišovice sites offered a good opportunity for a study of the undisturbed spatial distribution of charred plant remains within a burnt house. Among wild plants, the occurrence of Stipa sp., Teucrium chamaedrys, Asperula cynanchica and Plantago media point to the presence of dry steppe grassland in the vicinity of the settlements, which was probably used for grazing. Woodland plants were mainly represented by fruit-bearing plants growing in clearings and forest edges, reflecting both the deliberate collection of wild fruits and the growing human impact on the vegetation.     

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.]

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar ‘Prasad’, 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F₂ mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30–0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.     

Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P. Beauv., and a survey of variation from Europe and Asia

 Restriction fragment length polymorphism (RFLP) and the structure of ribosomal RNA genes (rDNA) were investigated in 117 landraces of foxtail millet, Setaria italica (L.) P. Beauv. Five RFLP phenotypes were found when the genomic DNA was digested with BamHI; these were named types I–V. Of these types I, II and III were the most frequent. Type I was mainly distributed in the temperature zone, type II in the Taiwan-Philippines Islands and type III in South Asia. Restriction mapping of the cloned rDNA and comparison with RFLP phenotypes showed that the different types originated from a polymorphism in the length within the intergenic spacer (IGS) and BamHI site changes within the IGS. Received: 28 August 1996 / Accepted: 28 February 1997     

Inheritance of some marker genes in Setaria italica (L.) P. Beauv.

Summary A study on a series of genetic markers was run on five hybrids of foxtail millet, Setaria italica, and on one interspecific hybrid S. viridisxS. italica (S. viridis is the wild relative of S. italica). Seven enzymatic systems were investigated using starch gel electrophoresis (esterase, alcohol dehydrogenase, glutamate oxaloacetate transaminase, acid phosphatase, malate dehydrogenase, 6-phosphogluconate dehydrogenase, cathodic peroxidase). This genetic analysis of the 6 F2 has allowed us to define 12 polymorphic loci: Est-1, -2 and -3, Adh-1, Got-1 and -2, Acph-1, Mdh-1 and -2, Pgd-1 and -2, and Pox-1. All of them behaved like dimers, except Est-1 and Est-2 which showed monomeric structures. Two other markers were examined: waxy endosperm, which appeared to be controlled by one locus, and anthocyanic pigmentation of the collar, for which at least two loci are responsible. Studies of linkage carried out on three F2 showed two linkage groups: Mdh-1, Pox-1, Wx, Est-3, and a locus for collar colour, and Est-2, and one or two other loci of colouring.     

Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa)

 A foxtail millet-rice comparative genetic map was constructed using mapped rice RFLP markers and wheat genomic and cDNA clones with known map position in rice. About 74% and 37% of the cDNA and genomic clones, respectively, were transferable to foxtail millet, confirming that conservation at the DNA level is greatest in genic regions. A high degree of conserved colinearity was observed between the two genomes. Five entire foxtail millet chromosomes appear to be colinear with five entire rice chromosomes. The remaining four foxtail millet linkage groups each show colinearity with segments of two rice chromosomes. The rearrangements of rice chromosomes 3 and 10 to form foxtail millet chromosome IX, and 7 and 9 to form chromosome II are very similar to those required to form maize chromosomes 1 and 7 and sorghum linkage groups C and B, indicating Setaria’s clear taxonomic position within the subfamily of the Panicoideae. Received: 18 December 1996 / Accepted: 4 August 1997     

A new acuariid nematode, <Emphasis Type="Italic">Syncuaria mackoi</Emphasis> n. sp. (Spirurida), from <Emphasis Type="Italic">Ciconia nigra</Emphasis> (L.) (Ciconiiformes: Ciconiidae) in Europe

Syncuaria mackoi n. sp. is described, based on light and scanning electron microscopy, from the stomach of the black stork Ciconia nigra in Bulgaria. The new species is characterised by: body length 7.18–8.30 mm (males) and 10.13–11.40 mm (females); cordons anastomosing about the level of the middle of the muscular oesophagus and consisting of delicate cuticular plates; bifurcate deirids 7–9 μm long; lateral longitudinal cuticular band-like swellings; nine pairs of pedunculate caudal papillae, i.e. four precloacal and five postcloacal, the latter forming two groups (2 + 3); sixth pair of postcloacal papillae sessile; left spicule 854–907 μm long; right spicule 138–154 μm in length, with a curved distal end resembling a horn and a short lateral projection at some distance from its tip; and vagina vera provided with an anteriorly-directed blind appendix. The specimens identified as S. ciconiae (Gil’bert, 1927) by Macko (1964) from C. nigra in Slovakia are considered as belonging to S. mackoi. A pair of small cupolae situated dorsally and ventrally between bases of cordons of the new species is described for the first time in this genus; they are recognised as homologous to the pair of spines in the same position previously described in S. diacantha Petter, 1961 and S. plegadisi Digiani, 1999.     

Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica×Setaria viridis

Drought tolerance is an important breeding target for enhancing the yields of grain crop species in arid and semi-arid regions of the world. Two species of Setaria, domesticated foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis) are becoming widely adopted as models for functional genomics studies in the Panicoid grasses. In this study, the genomic regions controlling germination and early seedling drought tolerance in Setaria were identified using 190 F₇ lines derived from a cross between Yugu1, a S. italica cultivar developed in China, and a wild S. viridis genotype collected from Uzbekistan. Quantitative trait loci were identified which contribute to a number of traits including promptness index, radical root length, coleoptile length and lateral root number at germinating stage and seedling survival rate was characterized by the ability of desiccated seedlings to revive after rehydration. A genetic map with 128 SSR markers which spans 1293.9 cM with an average of 14 markers per linkage group of the 9 linkage groups was constructed. A total of eighteen QTLs were detected which included nine that explained over 10% of the phenotypic variance for a given trait. Both the wild green foxtail genotype and the foxtail millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtail millet breeding.     

Reproductive biology of Setaria magna Griseb. (Poaceae: Panicoideae: Paniceae)

The genus Setaria is economically important because many species are cultivated for grains or forage. Setaria magna is an American species, native to North America and introduced in South America. The morphological aspect of this species is similar to S. italica (foxtail millet), suggesting its potential value as a crop. The purpose of this work was to understand the breeding system (self-pollination vs. open pollination) of S. magna; additionally, the floral development was described. The results of the breeding system analysis indicated that S. magna is mainly autogamous and does not appear to have a self-incompatibility mechanism. The floral development observed was similar to that described for other Paniceae; in most of the spikelets only the upper anthecium developed fruit, but a small number of spikelets presented bisexual lower florets. These spikelets produced two caryopses per spikelet. Thus, S. magna can produced two types of dispersal units; a few whitish naked caryopses from the lower anthecium that fall without their lemma and palea at maturity; and a high number of brown caryopses protected by the lemma and palea from the upper anthecium. The presence of a normal embryo sac in the upper anthecium suggests that S. magna would present normal sexual reproduction, although we can not reject the formation of apomitic seeds in the lower anthecium.     

Silicon Deposition in the Inflorescence Bristles and Macrohairs of Setaria italica (L.) Beauv.

Silicon deposits in the inflorescence bristles subtending eachspikelet, and in the macrohairs of foxtail millet (Setaria italica(L.) Beauv.) were investigated using scanning electron microscopyand electron-probe microanalysis. High concentrations of silicon were detected in the pricklehairs which covered the bristles. In the unicellular macrohairscovering the inflorescence axis and its branches, silicon wasdeposited along the whole length of the hairs. The mechanisms by which silicification may have taken place,and the possibility that the bristles and macrohairs are involvedin the aetiology of oesophageal cancer in N. China are discussed. Setaria italica (L.) Beauv., foxtail millet, millet, silicon deposits, silicification, prickle hairs, scanning electron microscopy, electron-probe microanalysis     

Infraspecific variation and systematics of cultivatedSetaria italica,foxtail millet (Poaceae)

Foxtail millet (Setaria italica,) is grown as a cereal in southern Europe and in temperate, subtropical, and tropical Asia. Its closest wild relative isS. italica ssp.viridis (green foxtail). Green foxtail is native to temperate Eurasia, but was introduced and became widely established as a weed in temperate and warmer parts of the Americas. Spontaneous and cultivatedS. italica cross to produce fertile hybrids. Derivatives of such crosses, resembling foxtail millet in some inflorescence traits but with efficient natural seed dispersal, accompany the cereal across its range of cultivation. Giant green foxtail of Europe and the American corn belt is a weed of hybrid origin. Foxtail millet was domesticated in the highlands of central China; remains of cultivated foxtail millet are known from the Yang-shao culture period dating back some 5,000 yrs. Comparative morphology suggests that foxtail millet spread to Europe and India as a cereal soon after its domestication. Three cultivated races are recognized. Moharia, from Europe and southwestern Asia, includes cultivars with 5–52 culms, each bearing several, small, more or less erect inflorescences. Cultivars in race maxima are characterized by plants with 1–8 usually unbranched culms that bear large inflorescences; they occur in Transcaucasian Russia and the Far East. Race indica is intermediate in culm number (ave. 6.6) and inflorescence size between races moharia and maxima, and is cultivated in southern Asia.     

First and second millennium a.d. agriculture in Rwanda: archaeobotanical finds and radiocarbon dates from seven sites

This article presents the results from a programme of bulk soil sampling and flotation of first and second millennium a.d. early farming, ‘Iron Age’, archaeological sites in Rwanda conducted in 2006–2007 alongside a new set of associated radiocarbon dates, which contribute toward the development of a chronology of plant use for the region. This research has identified the earliest examples of pearl millet (Pennisetum glaucum), finger millet (Eleusine coracana) and sorghum (Sorghum bicolor) in Great Lakes Africa and thus this article also discusses the significance of these finds within the later archaeology of the region and presents a brief synthesis of the direct archaeological evidence for finger millet in sub-Saharan Africa.     

A Ser–Gly substitution in plastid-encoded photosystem II D1 protein is responsible for atrazine resistance in foxtail millet (<Emphasis Type="Italic">Setaria italica</Emphasis>)

A foxtail millet (Setaria italica L. Beauv.) line resistant to atrazine was obtained through interspecific hybridization between wild S. viridis L. Beauv. and cultivated S. italica. The resistance was proved to be controlled by a chloroplast-inherited gene and it has further been utilized in foxtail millet production. However, the sequence information of the putative atrazine resistance gene, psbA in foxtail millet’s chloroplast genome encoding photosystem II D1 protein (32 kDa thylakoid membrane protein) (photosystem Q_B protein) and the mutation site responsible for the resistance are not known. In this paper the psbA sequences of six atrazine susceptible/resistant foxtail millet varieties were obtained and compared. The results indicated that there was only one amino acid difference between susceptible and resistance gene, resulting from a single base substitution. It was concluded that a mutant allele of photosystem II protein D1 encoding a Gly residue instead of a Ser residue at position 264 is a major gene of resistance to atrazine. Moreover, the phylogenetic tree based on the psbA coding region of thirty-five plant species was carried out. The phylogenetic relationship between S. italica and other plants and the related evolutionary issues were discussed and it was suggested that psbA sequences could be used in phylogenetic studies in plants. Xiaoping Jia and Jincheng Yuan have equal contribution.     

Geometric morphometric analysis of <Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv. (foxtail millet) and <Emphasis Type="Italic">Brachiaria ramosa</Emphasis> (L.) Stapf. (browntop millet) and its implications for understanding the biogeography of small millets

Setaria italica (L.) P. Beauv. (foxtail millet) was originally domesticated in northern China. The time and route of its introduction into South Asia is currently unclear due to the possible confusion with autochthonous Brachiaria ramosa (L.) Stapf. (browntop millet). Geometric morphometrics (GM) offer an alternative to traditional archaeobotanical methods to distinguish between these two small millet species. This study aims at finding a method to securely distinguish among charred caryopses of S. italica and B. ramosa, testing its validity on archaeobotanical assemblages and proposing a new approach for studying the dispersion of S. italica throughout Eurasia. Modern S. italica (n = 35) and B. ramosa (n = 34) caryopses and 15 archaeological specimens from a 5th millennium bp archaeological occupation site in northwestern India were analysed. Archaeological and modern caryopses (before and after charring) were photographed with a Leica EZ4D stereoscope, and TPSdig software was used to scale the photographs and manually apply a configuration of three landmarks and six semi-landmarks onto the contours of the embryos. Multivariate statistics were carried out to analyse the shape differences between modern S. italica and B. ramosa and to classify the archaeological specimens. The results show that the shape of the embryo of both species can be clearly distinguished using a GM-approach, both before and after charring. However, charring tends to smooth the shape differences between the two groups, which may affect the interpretation of archaeobotanical assemblages. The comparison between modern and archaeological caryopses suggests that S. italica was not present in northwestern India during the 5th millennium bp.     

Somatic embryogenesis and in vitro rosmarinic acid accumulation in Salvia officinalis and S. fruticosa leaf callus cultures

The effect of explant age, plant growth regulators and culture conditions on somatic embryogenesis and rosmarinic acid production from leaf explants of Salvia officinalis and S. fruticosa plants collected in Greece was investigated. Embryogenic callus with numerous spherical somatic embryos could be induced on explants derived from both species and cultured for 3 weeks on a Murashige and Skoog (MS) medium supplemented with 1.8–18 μm 2,4-dichlorophenoxyacetic acid (2,4-D) and kinetin (Kin) or 10.5–21 μm 1-naphthalenacetic acid and 6-benzyladenine. Only explants from young plants (with six to eight leaves) responded to the culture treatments and, in general, low light intensities (50 μmol m^–2 s^–1) favoured callus formation and induction of somatic embryos. Somatic embryos were further developed on the same medium. Heart- and torpedo-shaped embryos (1–2 mm long) were subcultured on a growth-regulator-free MS medium for maturation. Maximum rosmarinic acid accumulation in S. officinalis and S. fruticosa callus cultured on 4.5 μm 2,4-D and 4.5 μm Kin was 25.9 and 29.0 g/l, respectively. Received: 17 January 1997 / Revision received: 26 May 1997 / Accepted: 30 June 1997     

Agrobacterium-mediated transformation of finger millet (Eleusine coracana (L.) Gaertn.) using shoot apex explants

A new Agrobacterium-mediated transformation system was developed for finger millet using shoot apex explants. The Agrobacterium strain LBA4404 harboring binary vector pCAMBIA1301, which contained hygromycin phosphotransferase (hptII) as selectable marker gene and β-glucuronidase (GUS) as reporter gene, was used for optimization of transformation conditions. Two finger millet genotypes, GPU 45 and CO 14, were used in this study. The optimal conditions for the Agrobacterium-mediated transformation of finger millet were found to be the co-cultivation of explants obtained on the 16th day after callus induction (DACI), exposure of explants for 30 min to agrobacterial inoculum and 3 days of co-cultivation on filter paper placed on medium supplemented with 100 μM acetosyringone (AS). Addition of 100 μM l-cysteine in the selection medium enhanced the frequency of transformation and transgenic plant recovery. Both finger millet genotypes were transformed by Agrobacterium. A frequency of 19% transient expression with 3.8% stable transformation was achieved in genotype GPU 45 using optimal conditions. Five stably transformed plants were fully characterized by Southern blot analysis. A segregation analysis was also performed in four R₁ progenies, which showed normal Mendelian pattern of transgene segregation. The inheritance of transgenes in R₁ progenies was also confirmed by Southern blot analysis. This is the first report on Agrobacterium-mediated transformation of finger millet. This study underpins the introduction of numerous agronomically important genes into the genome of finger millet in the future.