Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses

Foxtail millet is one of the oldest domesticated diploid C₄ Panicoid crops having a comparatively small genome size of approximately 515?Mb, short life cycle, and inbreeding nature. Its two species, Setaria italica (domesticated) and Setaria viridis (wild progenitor), have characteristics that classify them as excellent model systems to examine several aspects of architectural, evolutionary, and physiological importance in Panicoid grasses especially the biofuel crops such as switchgrass and napiergrass. Foxtail millet is a staple crop used extensively for food and fodder in parts of Asia and Africa. In its long history of cultivation, it has been adapted to arid and semi-arid areas of Asia, North Africa, South and North America. Foxtail millet has one of the largest collections of cultivated as well as wild-type germplasm rich with phenotypic variations and hence provides prospects for association mapping and allele-mining of elite and novel variants to be incorporated in crop improvement programs. Most of the foxtail millet accessions can be primarily abiotic stress tolerant particularly to drought and salinity, and therefore exploiting these agronomic traits can enhance its efficacy in marker-aided breeding as well as in genetic engineering for abiotic stress tolerance. In addition, the release of draft genome sequence of foxtail millet would be useful to the researchers worldwide in not only discerning the molecular basis of biomass production in biofuel crops and the methods to improve it, but also for the introgression of beneficial agronomically important characteristics in foxtail millet as well as in related Panicoid bioenergy grasses.     

增强UV-B辐射和氮对谷子叶光合色素及非酶促保护物质的影响

以谷子(Setaria italica(L)Beauv.)为对象,从拔节期开始持续给予低氮(1.875 mmol/L)和高氮(15 mmol/L)两种氮供应条件并从抽穗期开始进行26 d两种强度(4.29、7.12 kJ·m-2·d-1)的增强UV-B辐射处理,研究了谷子叶中光合色素含量、类黄酮含量和苯丙氨酸解氨酶(PAL)活性的变化.结果表明:与高氮供应条件相比,低氮供应条件明显降低了谷子叶中光合色素含量但提高了类胡萝卜素/叶绿素含量比值;在开花期中段和灌浆期中段,高氮供应条件下谷子叶中光合色素含量对增强UV-B辐射比低氮供应条件下的谷子更敏感.从灌浆期开始到处理结束,两种影响因子对谷子叶中类黄酮含量均有显著影响,增强UV-B辐射导致谷子叶中类黄酮含量逐渐升高,且相同增强UV-B辐射强度下低氮供应条件下的谷子叶中类黄酮含量明显高于高氮供应条件下的谷子.谷子叶中PAL活性对两种影响因子的响应较类黄酮含量更加敏感,低氮供应条件使谷子叶中PAL活性明显提高.结合上述指标的相关性分析结果可知,低氮供应条件加强了处于繁殖期主要阶段的谷子叶中类黄酮的积累,并使谷子叶中的类胡萝卜素/叶绿素含量比值明显提高,进而有助于维持谷子叶中光合色素含量在增强UV-B辐射条件下的相对稳定性,对植株抵抗UV-B辐射伤害有利.     

The wild-weed-crop complex in Setaria: a hybridization study

Evidence is given of spontaneous hybridizations between cultivated foxtail millet (Setaria italica) and its wild relative the green foxtail (S. viridis). Such a cross produces F₂ plants similar to the giant wild variant S. viridis var. major found as a weed in cultivated areas. S. viridis major was also crossed to the same cultivar and the two F₂s were compared on the basis of 19 morphological characters. This study indicates that S. viridis major is more closely related to S. italica than S. viridis sensu stricto and indeed could have resulted from a wild x crop hybridization.     

Isolation of gametes and zygotes from Setaria viridis

Setaria viridis, the wild ancestor of foxtail millet (Setaria italica), is an effective model plant for larger C₄ crops because S. viridis has several desirable traits, such as short generation time, prolific seed production and a small genome size. These advantages are well suited for investigating molecular mechanisms in angiosperms, especially C₄ crop species. Here, we report a procedure for isolating gametes and zygotes from S. viridis flowers. To isolate egg cells, ovaries were harvested from unpollinated mature flowers and cut transversely, which allowed direct access to the embryo sac. Thereafter, an egg cell was released from the cut end of the basal portion of the dissected ovary. To isolate sperm cells, pollen grains released from anthers were immersed in a mannitol solution, resulting in pollen-grain bursting, which released sperm cells. Additionally, S. viridis zygotes were successfully isolated from freshly pollinated flowers. Isolated zygotes cultured in a liquid medium developed into globular-like embryos and cell masses. Thus, isolated S. viridis gametes, zygotes and embryos are attainable for detailed observations and investigations of fertilization and developmental events in angiosperms.

     

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.     

Induced mutations in foxtail millet (Setaria italica Beauv.)

Summary Chlorophyll mutations induced by gamma rays, EMS and DES were studied in foxtail millet (Setaria italica), using two cultures, MU-1 (bristled) and MU-2 (non-bristled). No major differences in the mutagenic response of the two cultures were observed. The treatments included four doses of gamma rays (10Kr, 20Kr, 30Kr, 40Kr) and four durations (6 hrs, 12 hrs, 18 hrs, 24 hrs) each of EMS (0.1%) and DES (0.1%). The combined treatments of gamma rays + EMS and gamma rays + DES were also given.Frequencies of chlorophyll mutations were recorded by three different methods, viz. (a) mutations per cent M₁ plants, (b) mutations per cent M₁ spikes and (c) mutants per cent M₂ plants. No significant differences in the results obtained by these three methods were observed. The frequencies and spectrum of mutations are discussed.Chlorina type were most frequent andviridoalbina least frequent.Striata and virescens were also quite common.Albinos, reported frequently in other crops, were found to be less frequent in foxtail millet during the present study. Number of sectors per spike were also determined from segregation ratios and only one sector per spike was found at all doses. Efficiency and effectiveness of mutagens were also determined and discussed. The results are also discussed with respect to mutagen specificity.     

Photosynthetic and physiological responses of foxtail millet (<Emphasis Type="Italic">Setaria italica</Emphasis> L.) to low-light stress during grain-filling stage

Two foxtail millet (Setaria italica L.) varieties were subjected to different shading intensity treatments during a grain-filling stage in a field experiment in order to clarify physiological mechanisms of low-light effects on the yield. Our results showed that the grain fresh mass per panicle, yield, photosynthetic pigment contents, net photosynthetic rate, stomatal conductance, effective quantum yield of PSII photochemistry, and electron transport rate decreased with the increase of shading intensity, whereas the intercellular CO₂ concentration increased in both varieties. In addition, shading changed a double-peak diurnal variation of photosynthesis to a one-peak curve. In conclusion, the lower yield of foxtail millet was caused mainly by a reduction of grain mass assimilated, a decline in chlorophyll content, and the low photosynthetic rate due to low light during the grain-filling stage. Reduced light energy absorption and conversion, restricted electron transfer, and reduced stomatal conductance might cause the decrease in photosynthesis.     

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     

Outcrossing and hybridization in wild and cultivated foxtail millets: consequences for the release of transgenic crops

Summary Outcrossing rates within the wild green foxtail, Setaria viridis, and the cultivated foxtail millet, S. italica, are very low. However, spontaneous interspecific hybridizations in the experimental garden occurred in both directions at rates ranging from 0.002% to 0.6% according to plant density and distance between parents. Offtypes found in farmers' fields where foxtail millet is cultivated were shown to have originated from such interspecific crosses. Differences in the EcoR1 patterns of chloroplast DNA between cultivated and wild plants indicated that reciprocal crosses do occur in the field. These findings indicate that even a largely selfing cultivated species may exchange genetic information with wild relatives at rates that may cause problems if transgenic cultivars are released.     

A straight-forward seed production technology system for foxtail millet (Setaria italica)

For autogamous crops, a precondition for using heterosis is to produce sufficient pure male-sterile female parents that can be used to produce hybrid seeds. To date, cytoplasmic male sterility(CMS)and environment-sensitive genic male sterility(EGMS) have been used commercially to exploit heterosis for autogamous species. However, neither CMS nor EGMS has been established for foxtail millet(Setaria italica). Here, we report on the establishment and application of a seed production technology(SPT)...     

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.     

Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers

AFLP markers were used to assess genetic diversity and patterns of geographic variation among 39 accessions of foxtail millet (Setaria italica) and 22 accessions of green foxtail millet (S. viridis), its putative wild progenitor. A high level of polymorphism was revealed. Dendrograms based on Nei and Li distances from a neighbour joining procedure were constructed using 160 polymorphic bands. Bootstrap values revealed that no specific geographic structure can be extracted from these data. The high level of diversity among Chinese accessions was consistent with the hypothesis of a centre of domestication in China. The results also showed that accessions from Eastern Europe and Africa form two distinct clusters. The narrow genetic basis of these two gene pools may be the result of local-adaptation. Received: 1 June 1999 / Accepted: 16 September 1999     

Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass,Setaria

The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F₇ recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C₄ model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture.     

Phytolith analysis for differentiating between foxtail millet (Setaria italica) and green foxtail (Setaria viridis)

Foxtail millet (Setaria italica) is one of the oldest domesticated cereal crops in Eurasia, but identifying foxtail millets, especially in charred grains, and differentiating it from its wild ancestor, green foxtail (Setaria viridis), in the archaeobotanical remains, is still problematic. Phytolithic analysis provides a meaningful method for identifying this important crop. In this paper, the silicon structure patterns in the glumes, lemmas, and paleas from inflorescence bracts in 16 modern plants of foxtail millet and green foxtail from China and Europe are examined using light microscopy with phase-contrast and a microscopic interferometer. Our research shows that the silicon structure of ΩIII from upper lemmas and paleas in foxtail millet and green foxtail can be correspondingly divided into two groups. The size of ΩIII type phytolith of foxtail millet is bigger than that from green foxtail. Discriminant function analysis reveals that 78.4% of data on foxtail millet and 76.9% of data on green foxtail are correctly classified. This means certain morphotypes of phytoliths are relatively reliable tools for distinguishing foxtail millet from green foxtail. Our results also revealed that the husk phytolith morphologies of foxtail millets from China and Eastern Europe are markedly different from those from Western Europe. Our research gives a meaningful method of separating foxtail millet and green foxtail. The implications of these findings for understanding the history of foxtail millet domestication and cultivation in ancient civilizations are significant.     

Development and Harmfulness of the European Corn Borer,Ostrinia nubilalis Hb. (Lepidoptera,Pyralidae), in the Central Chernozem Region

Long-term observations have revealed the factors responsible for periodic rises in abundance of the European corn borer Ostrinia nubilalis Hb. in the Central Chernozem Region of Russia. These factors are sufficient precipitation during several consecutive years and the current decline in agrotechnical soil treatment. The host specialization, biology, and phenology of the corn borer in the region have been clarified. Corn is damaged most intensely among the cultivated plants, and the yellow foxtail Setaria glauca, among the weeds. The effects of precipitation on seasonal development and harmfulness of the corn borer have been demonstrated. Low precipitation during the pest pupation period leads to mass pupal mortality, a shift of the seasonal development onto later dates, and a lower proportion of damaged stems in the crops. Insufficient precipitation during the larval feeding period enhances the effect of pest damage on the plant productivity and results in heavier yield loss. During the corn borer outbreaks the yield loss reached 15% in corn and 11.4% in millet. Depending on the weather conditions, the loss of millet yield due to this pest may be as great as 39% or as low as 3%.

     

Induced accumulation of tyramine,serotonin, and related amines in response to Bipolaris sorokiniana infection in barley

The inducible metabolites were analyzed in barley leaves inoculated with Bipolaris sorokiniana, the causal agent of spot blotch of barley. HPLC analysis revealed that B. sorokiniana-infected leaves accumulated 4 hydrophilic compounds. They were purified by ODS column chromatography and preparative HPLC. Spectroscopic analyses revealed that they were tyramine (1), 3-(2-aminoethyl)-3-hydroxyindolin-2-one (2), serotonin (3), and 5,5′-dihydroxy-2,4′-bitryptamine (4). Among these, 2 and 4 have not been reported as natural products. They showed antifungal activity in an assay of inhibition of B. sorokiniana conidia germination, suggesting that they play a role in the chemical defense of barley as phytoalexins. The accumulation of 1–4 was examined also in the leaves of rice and foxtail millet. Rice leaves accumulated 2, 3, and 4, whereas foxtail millet leaves accumulated 3 and 4 in response to pathogen attack, suggesting the generality of accumulation of 3 and 4 in the Poaceae species.     

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.