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.     

Genetic analysis of <Emphasis Type="Italic">NEKODE1</Emphasis> gene involved in panicle branching of foxtail millet, <Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv., and mapping by using QTL-seq

We carried out genetic analysis and mapping of a gene for the tip-branched panicle (Nekode or Neko-ashi in Japanese) in foxtail millet. We revealed that this trait is controlled by a single dominant gene by using two F₂ populations and designated the gene as NEKODE1. By using an F₂ population between closely related Taiwanese landraces with a new method based on next-generation sequencing (NGS), QTL-seq, we successfully and rapidly mapped the responsible gene (NEKODE1) on chromosome 9. We also mapped the gene by using SSR markers to verify that this gene is located at the position on chromosome 9, suggested by QTL-seq, and we obtained SSR markers closely linked to the gene and found several candidate genes for this trait in a foxtail millet genome sequence database. The use of a foxtail millet genome sequence and NGS enables rapid mapping of a gene(s) by using a segregation population derived from a cross even between closely related foxtail millet landraces.     

Experiments on the effects of charring on <Emphasis Type="Italic">Setaria italica</Emphasis> (foxtail millet)

This study aims to better understand taphonomical effects relevant to Setaria italica (foxtail millet), particularly the deformation caused by charring in fully-formed grains, and the potential preservation of underdeveloped seeds. Foxtail millet is a staple grain commonly found in Neolithic and later sites across Eurasia after initial domestication in northern China. Precise control of atmospheric conditions enabled determination of ideal parameters for charring without seed destruction. These experiments were able to produce charred seeds that strongly resemble archaeological specimens, making three key findings: (1) lateral expansion found in many ancient foxtail millet seeds indicates that charring occurred with the seeds in the husks. (2) Oxidizing conditions produced far better results in terms of seed preservation and retention of identifiable characteristics. (3) Smaller and less developed or ‘filled’ seeds survived in the same conditions as larger, plump seeds. These results allow for better interpretation of depositional context of millet seeds, and point to heat treatment during the de-husking process as a common way for seeds to enter the archaeological record.     

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.     

Mapping of <Emphasis Type="Italic">Sihc1</Emphasis>, which controls hull color,using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet [<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.]

Hull color (HC) in foxtail millet appears to be a major indicator of nutritional quality. To attempt to identify and characterize the gene or quantitative trait locus (QTL) related to HC and to provide a basis for quality and yield breeding of foxtail millet, a restriction site-associated DNA sequencing (RAD-seq) analysis was employed to reveal genome-wide single nucleotide polymorphisms (SNPs) and to genotype the F₂ progeny from a cross between two cultivars: Heizhigu with green HC and Changnong 35 with yellow HC. A high-density linkage map spanning 1542.87 cM was constructed using 1694 bin markers, consisting of 46,256 SNP markers, and a QTL locus controlling HC was identified and temporarily named as Sihc1 (Setaria italica hull color). Results showed that Sihc1 was located in the interval between markers M33926512 and M34281352 on the end of chromosome 6, and explained 80.26% of the phenotypic variation with a logarithm of odds ratio of 93.46. The additive and dominant effects of Sihc1 were 1.0025 and ?0.9991, respectively. Sihc1 was narrowed to a 354.84 kb physical region, inclusive of 30 open reading frames, and further analysis suggested that Seita.6G226500, Seita.6G226800, Seita.6G228300, and Seita.6G228600 might be the key candidates of Sihc1.     

Antioxidative responses and their relation to salt tolerance in <Emphasis Type="Italic">Echinochloa oryzicola</Emphasis> Vasing and <Emphasis Type="Italic">Setaria virdis</Emphasis> (L.) Beauv.

Two gramineous species among wild plants, Echinochloa oryzicola Vasing and Setaria viridis (L.) Beauv., and Oryza sativa L. cv. Nipponbare were subjected to salt stress. The relative growth rate (RGR), Na content, photosynthetic rate, antioxidant enzymes activity (superoxide disumutase (SOD), catalase (CAT), ascorbate peroxidase (APx) and glutathione reductase (GR)), and malondialdehyde (MDA) content in leaves after NaCl treatment were studied. RGR significantly decreased in O. sativa more than in E. oryzicola and S. viridis. Comparatively salt-tolerant S. viridis showed higher growth rate, lower Na accumulation rate in leaves, higher photosynthetic rate, and induced more SOD, CAT, APx, and GR activity and lower increase of MDA content as compared to the salt-sensitive O. sativa. At the same time, the comparatively salt-tolerant E. oryzicola also showed higher growth rate, much lower Na accumulation and no observable increase of MDA content, even though the CAT and APx activities were not induced by salinity. These results suggested that the scavenging system induced by H₂O₂-mediated oxidative damage might, at least in part, play an important role in the mechanism of salt tolerance against cell toxicity of NaCl in some gramineous plants     

<Emphasis Type="Italic">In vitro</Emphasis> morphogenesis and micropropagation of <Emphasis Type="Italic">Aechmea ramosa</Emphasis> var. <Emphasis Type="Italic">ramosa</Emphasis> Mart. ex Schult. f. (Bromeliaceae) from leaf explants

Aechmea ramosa Mart. ex Schult. f. is an endemic bromeliad of the Brazilian Atlantic Forest. The current habitat degradation of this hotspot biome threatens this species, which besides having an important ecological role, is also of invaluable ornamental interest. Plant tissue culture has been used in mass propagation and conservation of various bromeliads. We have established a micropropagation protocol for A. ramosa var. ramosa using leaf explants grown in MS medium supplemented with 2 μM of 1-naphthaleneacetic acid (NAA) and 2 μM of 6-benzylaminopurine (BAP) that showed higher values of shoot induction. NAA and BAP are associated with the production of proteins involved in stress response modulation, metabolic activity, and cell division, the latter being involved in inducing the differentiation of competent cells. After 120 d of culture, each explant presented 28.9 shoots with an average size of 27.8 mm, with no variation in either Stomatal Index or density of the regenerated shoots. Plantlets measuring above 15-mm height were successfully acclimatized, presenting 100% survival rate. Thus, this protocol can be used for mass propagation of A. ramosa, and to supply demand for the market of ornamental plants. Furthermore, it represents an important tool for the conservation of this species and maintenance of an in vitro germplasm.     

Factors affecting <Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation in <Emphasis Type="Italic">Hybanthus</Emphasis><Emphasis Type="Italic">enneaspermus</Emphasis> (L.) F. Muell.

Agrobacterium tumefaciens-mediated transformation system was established for Hybanthus enneaspermus using leaf explants with the strain LBA4404 harbouring pCAMBIA 2301 carrying the nptII and gusA genes. Sensitivity of leaf explants to kanamycin was standardized (100 mg/l) for screening the transgenic plants. Transformation parameters (OD, virulence inducer, infection time, co-cultivation period, bactericidal antibiotics, etc.) influencing the gene transfer and integration were assessed in the present investigation. Fourteen-day pre-cultured explants were subjected with Agrobacterium strain LBA4404. Optimized parameters such as culture density of 0.5 OD₆₀₀, infection time of 6 min, AS concentration of 150 µM with 3 days co-cultivation revealed maximum transformation efficiency based on GUS expression assay. The presence of gusA in transgenics was confirmed by polymerase chain reaction and Southern blotting analysis. The present transformation experiment yielded 20 shoots/explant with higher transformation efficiency (28 %). The protocol could be used to introduce genes for trait improvement as well as for altering metabolic pathway for secondary metabolites production.     

Ectopic expression of cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) <Emphasis Type="Italic">CsTIR</Emphasis>/<Emphasis Type="Italic">AFB</Emphasis> genes enhance salt tolerance in transgenic <Emphasis Type="Italic">Arabidopsis</Emphasis>

Auxin receptors TIR1/AFBs play an essential role in a series of signaling network cascades. These F-box proteins have also been identified to participate in different stress responses via the auxin signaling pathway in Arabidopsis. Cucumber (Cucumis sativus L.) is one of the most important crops worldwide, which is also a model plant for research. In the study herein, two cucumber homologous auxin receptor F-box genes CsTIR and CsAFB were cloned and studied for the first time. The deduced amino acid sequences showed a 78% identity between CsTIR and AtTIR1 and 76% between CsAFB and AtAFB2. All these proteins share similar characteristics of an F-box domain near the N-terminus, and several Leucine-rich repeat regions in the middle. Arabidopsis plants ectopically overexpressing CsTIR or CsAFB were obtained and verified. Shorter primary roots and more lateral roots were found in these transgenic lines with auxin signaling amplified. Results showed that expression of CsTIR/AFB genes in Arabidopsis could lead to higher seeds germination rates and plant survival rates than wild-type under salt stress. The enhanced salt tolerance in transgenic plants is probably caused by maintaining root growth and controlling water loss in seedlings, and by stabilizing life-sustaining substances as well as accumulating endogenous osmoregulation substances. We proposed that CsTIR/AFB-involved auxin signal regulation might trigger auxin mediated stress adaptation response and enhance the plant salt stress resistance by osmoregulation.     

Cytogenetic characterization of <Emphasis Type="Italic">Amaranthus caudatus</Emphasis> L. and <Emphasis Type="Italic">Amaranthus hybridus</Emphasis> subsp<Emphasis Type="Italic">. cruentus</Emphasis> (L.) Thell.

The present study is aimed to identify genetic variability between two species of Amaranthus viz., A. caudatus and A. hybridus subsp. cruentus, two economically important species, cultivated mainly for grain production. Karyomorphological studies in Amaranthus are scarce, probably due to higher number of small sized chromosomes. Karyomorphological studies were conducted using mitotic squash preparation of young healthy root tips. Karyological parameters and karyotypic formula were established using various software programs and tabulated the karyomorphometric and asymmetry indices viz., Disparity index, Variation coefficient, Total forma percentage, Karyotype asymmetry index, Syi index, Rec index, Interchromosomal and Intrachromosomal asymmetry index and Degree of asymmetry of karyotypes. The mitotic chromosome number observed for A. caudatus was 2n = 32 with a gametic number n = 16 and A. hybridus subsp. cruentus was 2n = 34 with a gametic number n = 17. In A. caudatus the chromosome length during somatic metaphase ranged from 0.8698 to 1.7722 μm with a total length of 39.1412 μm. In A. hybridus subsp. cruentus the length of chromosome ranged from 0.7756 to 1.9421 μm with a total length of 44.9922 μm. Various karyomorphometry and asymmetry indices analyzed revealed the extend of interspecific variation and their evolutionary status.     

Determining the Fertility Status of Setaria Infecting <Emphasis Type="Italic">Magnaporthe grisea</Emphasis> Isolates with Standard Testers and Identification of Tolerant Cultivar of <Emphasis Type="Italic">Setaria italica</Emphasis>

A total of 128 isolates of Setaria-infecting Magnaporthe grisea strains were obtained from different states of South India which includes sampling sites from Tamil Nadu, two from Karnataka, one from Andhra Pradesh and Kerala. Out of the selected 128 isolates 30 strains were tested with MAT1-1 and MAT1-2 fertile standard testers to determine their mating type. None of the 30 Setaria isolates produced perithecia with fertile testers. However, when monoconidial isolates were mated among themselves, isolates from the same field produced only barren perithecia and the tester isolates were able to mate readily with finger millet isolates. This is the first report of the mating-type studies on Setaria infecting Magnaporthe grisea with standard testers. This result indicates that the Setaria infecting population is infertile. In pathogenicity assay, it was found that 9 out of the 22 Setaria accessions were highly susceptible to Setaria strains of the blast fungus and seven cultivars/accessions were resistant to blast pathogen. Various virulence reactions were scored according to Standard Evaluation System.     

Genetics and fine mapping of a yellow-green leaf gene (<Emphasis Type="Italic">ygl</Emphasis>-<Emphasis Type="Italic">1</Emphasis>) in cabbage (<Emphasis Type="Italic">Brassica oleracea</Emphasis> var. <Emphasis Type="Italic">capitata</Emphasis> L.)

Cabbage (Brassica oleracea var. capitata L.) is one of the most popular cultivated vegetables worldwide. Cabbage has rich phenotypic diversity, including plant height, head shape, head color, leaf shape and leaf color. Leaf color plays an important role in cabbage growth and development. At present, there are few reports on fine mapping of leaf color mutants in B. oleracea. In this study, a naturally occurring yellow-green leaf cabbage mutant (YL-1), derived from the self-pollinated progenies of the hybrid ‘Hosom’, was used for inheritance analysis and gene mapping. Segregation populations including F₂ and BC₁ were generated from the cross of two inbred lines, YL-1 and 01–20. Genetic analysis with the F₂ and BC₁ populations demonstrated that the yellow-green leaf color was controlled by a single recessive nuclear gene, ygl-1. Insertion–deletion (InDel) markers, designed based on the parental re-sequencing data, were used for the preliminary mapping with BSA (bulked segregant analysis) method. A genetic map constructed with 15 InDels indicated that ygl-1 was located on chromosome C01. The ygl-1 gene is flanked by InDel markers ID2 and M8, with genetic distances of 0.4 cM and 0.35 cM, respectively. The interval distance between two markers is 167 kb. Thus, it enables us to locate the ygl-1 gene for the first time in B. oleracea. This study lays the foundation for candidate gene prediction and ygl-1gene cloning.     

<Emphasis Type="Italic">Agrobacterium-</Emphasis>mediated transformation of gypsophila (<Emphasis Type="Italic">Gypsophila paniculata</Emphasis> L.)

As a major contributor to the flower market, Gypsophila paniculata is an important target for the breeding of new varieties. However, gypsophila breeding is strongly hampered by the sterility of this species’ genotypes and the lack of a genetic-transformation procedure for this genus. Here we describe the establishment of a transformation procedure for gypsophila (Gypsophila paniculata L.) based on Agrobacterium inoculation of highly regenerative stem segments. The transformation procedure employs stem explants derived from GA₃-pretreated mother plants and a two-step selection scheme. The GA₃ treatment was crucial for obtaining high gene-transfer frequencies (75–90% GUS-expressing explants out of total inoculated explants), as shown using three different gypsophila varieties. An overall transformation efficiency of five GUS-expressing shoots per 100 stem explants was demonstrated for cv. Arbel. The applicability of the transformation system to gypsophila was further reinforced by the generation of transgenic plants expressing Agrobacterium rhizogenes rolC driven by a CaMV 35S promoter. Transgenic gypsophila plantlets exhibited extensive rooting and branching, traits that could be beneficial to the ornamental industry.     

<Emphasis Type="Italic">Ty</Emphasis>1<Emphasis Type="Italic">/copia</Emphasis>- and <Emphasis Type="Italic">Ty</Emphasis>3<Emphasis Type="Italic">/gypsy</Emphasis>-like DNA sequences in <Emphasis Type="Italic">Helianthus </Emphasis>species

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.     

<Emphasis Type="Italic">Quinua</Emphasis> and Relatives (<Emphasis Type="Italic">Chenopodium</Emphasis> sect.<Emphasis Type="Italic">Chenopodium</Emphasis> subsect.<Emphasis Type="Italic">Celluloid</Emphasis>)

Traditionally viewed as an Andean grain crop,Chenopodium quinoa Willd. includes domesticated populations that are not Andean, and Andean populations that are not domesticated. Comparative analysis of leaf morphology and allozyme frequencies have demonstrated that Andean populations, both domesticated(quinua) and free-living(ajara), represent an exceptionally homogeneous unit that is well differentiated from allied domesticates of coastal Chile(quingua) and freeliving populations of the Argentine lowlands(C. hircinum). This pattern of relationships indicates that Andean populations represent a monophyletic crop/weed system that has possibly developed through cyclic differentiation (natural vs. human selection) and introgressive hybridization. Relative levels of variation suggest that this complex originated in the southern Andes, possibly from wild types allied withC. hircinum, with subsequent dispersal north to Colombia and south to the Chilean coast. Coastal populations were apparently isolated from post-dispersal differentiation and homogenization that occurred in the Andes. Other data point toward a center of origin in the northern Andes with secondary centers of genetic diversity subsequently developing in the southern Andes and the plains of Argentina. Comparative linkage of South American taxa, all tetraploid, with North American tetraploids of the subsection will eventually clarify this problem. While the possibility of a direct phyletic connection betweenC. quinoa and the Mexican domesticate(C. berlandieri subsp. nuttalliae,) cannot be excluded, available evidence indicates that the latter represents an autonomous lineage that is associated with the basal tetraploid, C. b. subsp.berlandieri, through var.sinuatum, whereas South American taxa show possible affinities to either var. zschackei or var.berlandieri. An extinct domesticate of eastern North America,C. b. subsp.jonesianum, represents either another instance of independent domestication, possibly from subsp. b. var.zschackei, or a northeastern outlier of subsp.nuttalliae.