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.     

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.     

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.     

Cytogenetics of double cross hybrids between Pennisetum americanum — P. purpureum amphiploids and P. americanum x Pennisetum squamulatum interspecific hybrids

Summary Pearl millet, Pennisetum americanum L. Leeke-napiergrass, Pennisetum purpureum Schum. amphiploids (2n=42) were crossed with pearl millet X Pennisetum squamulatum Fresen. interspecific hybrids (2n=41) to study the potential of germplasm transfer from wild Pennisetum species to pearl millet. These two interspecific hybrids were highly cross-compatible and more than two thousand trispecific progenies were produced from 17 double crosses. All doublecross hybrids were perennial and showed a wide range of morphological variations intermediate to both parents in vegetative and inflorescence characteristics. Some crosses resulted in sublethal progenies. Chromosomes paired mainly as bivalents (¯x15.88) or remained as univalents. At metaphase I, trivalents, quadrivalents, an occasional hexavalent and a high frequency of bivalents indicated some homeology among the genomes of the three species. Delayed separation of bivalents, unequal segregation of multivalents, lagging chromosomes, and chromatin bridges were observed at anaphase I. Although approximately 93% of the double-cross hybrids were male-sterile, pollen stainability in male-fertile plants ranged up to 94%. Seed set ranged from 0 to 37 seed per inflorescence in 71 plants under open-pollinated conditions. Apomictic embryo sac development was observed in double-cross progenies when crosses involved a pearl millet x P. squamulatum apomictic hybrid as pollen parent. These new double-cross hybrids may serve as bridging hybrids to transfer genes controlling apomixis and other plant characteristics from the wild Pennisetum species to pearl millet.     

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.     

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.     

The effect of genome and sex on recombination rates in Pennisetum species

The effects of homoeology and sex on recombination frequency were studied in crosses between cultivated pearl millet, Pennisetum glaucum, and two wild subspecies, P. violaceum and P. mollissimum. For the two wild x cultivated crosses, reciprocal three-way crosses were made between the F₁ hybrid and an inbred line (Tift 23DB₁). The three-way cross populations were mapped to produce a female map of each wide cross (where the F₁ was the female) and a male map (where the F₁ was the male). Total genetic map lengths of the two inter-subspecies crosses were broadly similar and around 85 % of a comparable intervarietal map. In the P. glaucumxP. mollissimum crosses, the map was further shortened by a large (40 cM) inversion in linkage group 1. Comparison of the recovered recombinants from male and female meiocytes showed an overall trend for the genetic maps to be longer in the male (10%) in both inter-subspecific crosses; however, analysis of individual linkage intervals showed no significant differences. Gametophytic selection was prevalent, and sometimes extreme, for example 121 in favour of wild alleles in the P. glaucumxP. mollissimum male recombinant population. One of the loci which determines panicle type in cultivated pearl millet and wild relatives, H, was mapped 9 cM from Xpsm812 on linkage group 7 in the P. violaceum cross.     

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.     

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.     

Inheritance of chloroplast and mitochondrial DNA in alloplasmic forms of the genus Daucus

The inheritance of mitochondrial (mt) and chloroplast (ct) DNA in the progeny from interspecific crosses between the cultivated carrot (Daucus carota sativus) and wild forms of the genus Daucus was investigated by analysis of mt and ct RFLPs in single plants of the parental and filial generations. We observed a strict maternal inheritance of the organellar DNAs in all interspecific crosses examined. Previous studies on putative F₂ plants from a cross between Daucus muricatus x D. carota sativus suggested paternal inheritance of ctDNA. Our reinvestigation of this material revealed that the mtDNA of the putative F₂ plants differed from the mtDNA of both putative parents. Therefore, our data suggest that the investigated material originated from other, not yet identified, parents. Consequently, the analysis of this material cannot provide evidence for a paternal inheritance of ctDNA.     

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     

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     

The occurrence and identification of <Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv. (foxtail millet) grains from the Chengtoushan site (ca. 5800 cal B.P.) in central China,with reference to the domestication centre in Asia

Archaeobotanical remains of Setaria grains and chaff were found at the Chengtoushan site in south-central China (ca. 5800 cal b.p.). Grain shape was determined, using length to breadth ratios, and morphological variation in the upper lemma of modern domesticated and wild Setaria species were examined using scanning electron microscopy as a basis for identifying archaeobotanical remains. Grains of S. viridis, S. yunnanensis, and S.×pycnocoma are slender, whereas S. italica, S. italica var. germinica, S. lutescenes, S. faberi, S. glauca, S. pallidefusca and S. intermedia are round in shape. The papillae distributed on the upper lemma of S. italica are small (8–15 μm) with a non-ridged base, while other Setaria species have large papillae (15–20 μm) with a widely ridged base. The remains of the Setaria from the Neolithic layers at Chengtoushan included S. italica, based on these identification characters. These new finds of foxtail millet are the earliest discoveries from the Yangtze River basin of southern China and are also the earliest evidence for co-cultivation of foxtail millet with rice. The implications of these findings for understanding foxtail millet domestication centres are discussed.     

Discriminative flavonoid patterns within a preliminary collection of the Setaria italica specific complex

One hundred and eighty individuals of Setaria italica ssp. italica, reflecting the worldwide variability of cultivated foxtail millet, and 40 individuals of wild S. i. ssp. viridis, were analysed for their flavonoid content. S. i. spp. italica accumulates native or acylated O-glycosyl derivatives of 8-Cglycosylflavones and O-glycosylfiavones, showing a large qualitative as well as quantitative inter-varietal diversity. The subspecies is strongly organized into seven chemotypes clearly defined by the presence or absence of O-pentosylation and acylation, and by the balance between apigenin and luteolin derivatives. This organization only partly corroborates a previous classification based on morphological and electrophoretical data, chemotypes affording an additional discriminative criterion in most cases. Flavonoid patterns of S. i. ssp. viridis fall in the chemotypes defined from the cereal, and underlines the conspecific nature of the two taxa. Similarities between wild and cultivated foxtail millet from same geographical origin suggest independent domestication from already differentiated gene pools.     

Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane

Modern sugarcane cultivars (Saccharum spp., 2n = 100–120) are complex polyploids derived from interspecific hybridization performed a century ago between the sugar-producing species S. officinarum L. and the wild species S. spontaneum L. Using genomic in situ hybridization, we revealed that between 15 and 27.5% of the genome of modern cultivars is derived from S. spontaneum, including 10–23% of entire chromosomes from this wild species and 8–13% chromosomes derived from interspecific recombination. We confirmed the occurrence of 2n + n transmission in crosses and first backcrosses between these two species and demonstrated that this also can occur in crosses between S. officinarum and modern cultivars. We analysed five S. officinarum clones with more than 80 chromosomes and demonstrated that they were derived from interspecific hybridization supporting the classical view that this species is characterized by 2n = 80. We also illustrated the complementarities between molecular cytogenetics and genetic mapping approaches for analysing complex genomes.     

Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transposable element insertions

The naturally occurring waxy and low-amylose variants of foxtail millet and other cereals, like rice and barley, originated in East and Southeast Asia under human selection for sticky foods. Mutations in the GBSS1 gene for granule-bound starch synthase 1 are known to be associated with these traits. We have analyzed the gene in foxtail millet, and found that, in this species, these traits were originated by multiple independent insertions of transposable elements and by subsequent secondary insertions into these elements or deletion of parts of the elements. The structural analysis of transposable elements inserted in the GBSS1 gene revealed that the non-waxy was converted to the low-amylose phenotype once, while shifts from non-waxy to waxy occurred three times, from low amylose to waxy once and from waxy to low amylose once. The present results, and the geographical distribution of different waxy molecular types, strongly suggest that these types originated independently and were dispersed into their current distribution areas. The patterns of GBSS1 variation revealed here suggest that foxtail millet may serve as a key to solving the mystery of the origin of waxy-type cereals in Asia. The GBSS1 gene in foxtail millet provides a new example of the evolution of a gene involved in the processes of domestication and its post-domestication fate under the influence of human selection. Electronic Supplementary Material Supplementary material is available for this article at     

Heterospecific sperm reduction in interspecific crosses between two closely related phytophagous ladybird beetles,Henosepilachna vigintioctomaculata and H. pustulosa (Coleoptera: Coccinellidae)

In interspecific crosses, a mismatch in internal physiological conditions between two species can reduce sperm viability in the interval from insemination to fertilization, leading to gametic isolation. Two closely related Japanese phytophagous ladybird beetles, Henosepilachna vigintioctomaculata and H. pustulosa, show several isolating barriers, including reduction in the number of heterospecific sperm in the female reproductive tract and low egg‐hatching rates in interspecific matings. However, the mechanisms of these two potential isolating barriers and the association between them are unknown. Here we investigated temporal changes in the number of sperm stored in the female reproductive tract and egg‐hatching rates in inter‐ and intraspecific crosses between these species. Although the number of sperm decreased after both inter‐ and intraspecific crosses, the reduction was more drastic in inter‐ than in intraspecific crosses for females of both species. Most of the sperm reduction occurred early on, during sperm transfer from the bursa copulatrix to the paired ampullae of the common oviduct (the sperm storage organs). These two species also demonstrated stably low egg‐hatching rates in interspecific crosses. Since the degree and timing of the sperm reduction did not correlate with egg‐hatching rates, the reduction in heterospecific sperm in interspecific crosses may not directly cause the low hatching rates. These two isolating barriers could be different expressions of the physiological mismatch and/or genetic incompatibility between gametes of these species.     

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.     

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     

Recombination around the Tm2a and Mi resistance genes in different crosses of Lycopersicon peruvianum

The amount of recombination in three different intraspecific crosses of the wild tomato species Lycopersicon peruvianum was investigated for the short arm of chromosome 6 that harbors the Mi nematode resistance gene and the centromeric region of chromosome 9 that contains the Tm2a virus resistance gene. These two genes have been introgressed into the cultivated tomato and are associated with a significant reduction in recombination in the respective region when crossed to other L. esculentum lines. For both regions and all crosses within L. peruvianum significantly more recombination (up to more than ten fold) was observed in the gametes derived from the female parent than in those from the male parent. In general, the differences were more pronounced for chromosome 6 than for chromosome 9. The amount of recombination in the three intraspecific L. peruvianum crosses was compared with the amount of recombination observed in the standard interspecific cross used for the construction of a saturated genetic map of tomato (L. esculentum x L. pennellii). In two of three cases for each region, more recombination was observed in the intraspecific crosses and in one case for each region significantly less recombination was found in the intraspecific cross when compared to the interspecific cross. Specifically for the Mi-carrying region, crosses within L. peruvianum exhibited up to 15-fold more recombination than crosses between resistant and susceptible L. esculentum lines, and such crosses will allow the fine mapping of this gene for the purpose of map-based cloning.