Genomic insights into the evolution of Echinochloa species as weed and orphan crop.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Vanillin extracted from proso and barnyard millets induces cell cycle inhibition and apoptotic cell death in MCF-7 cell line.

CONTEXT: Consuming whole grain food has been motivated due to numerous health benefits arising from their bioactive components. AIMS: This study aims to study whether the active compound extracted from Proso and Barnyard millets inhibits cell proliferation and induces apoptotic cell death in MCF-7 cell line. MATERIALS AND METHODS: Cell proliferative effect was assessed by 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay using MCF-7 cell line. Cytotoxicity was determined by release of lactate dehydrogenase (LDH) enzyme from cells. Apoptotic morphological changes in MCF-7 cells were observe under fluorescence microscope using double staining of Hoeschst 33342/propidium iodide (PI). Induction of apoptosis was analyzed using Annexin V-fluorescein isothiocyanate/PI through flow cytometry. RESULTS: In this study, cell proliferative effect of the bioactive compounds from proso millet (Compound 1) and barnyard millet (Compound 2) was evaluated using MCF-7 cell line. Both the compounds significantly inhibited the proliferation of MCF-7 cells after treated with 250 µg/ml and 1000 µg/ml concentration for 48 h. Cytotoxic activity of compounds was assessed by the release of LDH showed that these extracted compounds were not toxic to the cells. Apoptosis was confirmed by Hoechst 33,342/PI dual-staining, Annexin V-FTIC/PI staining, and flow cytometry results of cell cycle analysis shows that there was a significant cell arrest in the G0/G1 phase and increased the apoptotic cells in sub-G0 phase in a dose-dependent manner. CONCLUSIONS: This study suggests that the extracted vanillin compound from these millets have effectively induced apoptotic cell death in breast cancer cell line.

Target-Site Mutations and Expression of ALS Gene Copies Vary According to Echinochloa Species.

The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid Echinochloa spp. resistant to ALS inhibitors. Better knowledge of the Echinochloa species present in Italian rice fields and the study of ALS genes involved in target-site resistance could significantly contribute to a better understanding of resistance evolution and management. Using a CAPS-rbcL molecular marker, two species, E. crus-galli (L.) P. Beauv. and E. oryzicola (Vasinger) Vasing., were identified as the most common species in rice in Italy. Mutations involved in ALS inhibitor resistance in the different species were identified and associated with the ALS homoeologs. The relative expression of the ALS gene copies was evaluated. Molecular characterization led to the identification of three ALS genes in E. crus-galli and two in E. oryzicola. The two species also carried different point mutations conferring resistance: Ala122Asn in E. crus-galli and Trp574Leu in E. oryzicola. Mutations were carried in the same gene copy (ALS1), which was significantly more expressed than the other copies (ALS2 and ALS3) in both species. These results explain the high resistance level of these populations and why mutations in the other ALS copies are not involved in herbicide resistance.

[Effects of different baynyardgrass varieties on grain yield formation of rice at different nitrogen application levels.] / 不同氮水平下不同种稗草对水稻产量形成的影响.

This study aimed to investigate the effects of different barnyardgrass varieties on yield formation of rice. A Japonica rice cultivar, Nanjing 9108, was used and co-cultured with three barnyardgrass varieties from transplanting to maturity under different nitrogen (N) levels of 0, 120, 240, and 360 kg N·hm-2, taking baynyardgrass free as control. The three barnyardgrass varieties were Echinochloa crusgalli var. mitis, E. crusgali var. zelayensis and E. colonum. The results showed that, at the same N level, the plant height of the three barnyardgrass varieties was E. crusgali var. zelayensis > E. crusgalli var. mitis > E. colonum, and the growth duration was E. crusgalli var. mitis > E. crusgali var. zelayensis > E. colonum. The biomass of baynyardgrass increased with the increase of N application rates and reached a peak at the N rate of 240 kg N·hm-2, and it decreased at 360 kg N·hm-2. The biomass of either E. crusgalli var. mitis or E. crusgali var. zelayensis was significantly higher than that of E. colonum. At the 0 kg N· hm-2 level, all barnyardgrass varieties showed no significant effect on rice yield. At the 120 kg N· hm-2 level, rice yield was not significantly different among the three treatments of barnyardgrass free, co-cultured with E. crusgalli var. mitis, and co-cultured with E. colonum, but it was significantly decreased when co-cultured with E. crusgali var. zelayensis. At the 240 kg N·hm-2 level, all treatments of co-cultured with barnyardgrass significantly decreased the rice yield. At the 360 kg N·hm-2 level, rice yield was significantly decreased under the treatments of co-cultured with E. crusgali var. zelayensis or with E. crusgalli var. mitis, and showed no significant difference between barnyardgrass free and co-cultured with E. colonum. All these data indicated an interaction between barnyardgrass and N fertilizer, which mediated the formation of grain yield of rice. Furthermore, at the 120 kg N· hm-2 level, the co-cultured E. crusgali var. zelayensis treatment significantly reduced leaf nitrate reductase activity and photosynthetic rate and root oxidation activity during the grain filling period, and decreased nitrogen accumulation and dry matter accumulation at the maturity stage, but other two treatments showed no significant effect when compared with barnyardgrass free treatment. These physiological indices of rice were significantly reduced by both E. crusgalli var. mitis and E. crusgali var. zelayensis treatments at either 240 or 360 kg N·hm-2 level, and showed no significant difference among all treatments at the 0 kg N·hm-2 level. Regression analysis showed that the order of effects of barnyardgrass phenotypes on rice grain yield was biomass, plant height, growth duration and tiller number. All these results suggested that the coexistence with large biomass of barnyardgrass inhibited the leaf photosynthetic rate, nitrate reductase activity, root oxidation activity, nitrogen accumulation and dry matter accumulation of rice, and consequently, reduced the rice grain yield.

Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species.

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.

Chiral response of Oryzeae and Paniceae plants in alpha-methylbenzyl-3-p-tolyl urea agar medium.

The results presented here support the hypothesis that plants of the tribe Oryzeae respond enantioselectively and homogeneously to optically active 1-alpha-methylbenzyl-3-p-tolylurea (MBTU) in root growth inhibition, in contrast to Echinochloa species. The Oryzeae plants tested in this study belong to different genera (Oryza, Leersia, Chikusichloa and Zizania), to different species (O sativa, O glaberrima, O alta, O coarctata, O latifolia, O minuta, O rufipogon), to various ecospecies of Oryza (japonica, indica, japonica x indica, javanica) and to different levels of evolution [cultivated rice (O sativa and O glaberrima) and ancestral wild rice species]. In spite of their different phylogenic status and diverse sensitivity, the root growth of all members of the genus Oryza was inhibited more by R-MBTU than by S-MBTU. Zizania palustris, Z latifolia, Leersia oryzoides and Chikusichloa aquatica belonging to the tribe Oryzeae exhibited similar chiral recognition to the Oryza plants, suggesting that Oryzeae have a common chiral recognition mechanism in their response to optically active MBTUs. In contrast, Echinochloa plants (E crus-galli (L) Beauv var crus-galli and E colonum (L) Link), belonging into subfamily Panicoideae tribe Paniceae, responded in a different way, where their root growth was more sensitive to S-MBTU than to the antipodal R-MBTU. A reverse chiral response between the tribe Oryzeae and the genus Echinochloa was clearly indicated in this study. This diverse response may be relevant to Gramineae classification.

Is it possible to detect Echinochloa spp. tolerance to ACCase-inhibiting herbicides using a simple quick tolerance test?

The objective of this work was to evaluate the reliability of one quick tolerance test that would enable us, in only six days, to quantify tolerance levels of one biotype to one or more herbicides. For this purpose, we evaluated tolerance levels to cyhalofop-butyl of five Echinochloa spp. biotypes: muricata, crus-galli, crus-pavonis, oryzicola and utilis, with unknown records of herbicide treatment. Moreover, two biotypes of Echinochloa phyllopogon were tested, one of them resistant (R) to fenoxaprop-P-ethyl and the other one susceptible (S). The Oryza sativa Puntal var. and Oryza sativa var. (wild rice) were also checked in order to demonstrate cyhalofop-butyl selectivity profiles. The assays were conducted with petri-dishes where, over the following increasing doses, fifty seeds per biotype and dose, were placed in each one: 0, 3, 6, 12, 18, 24, 48 and 60 ppm of cyhalofop-butyl and codacide oil adjuvant. Six days later, the following parameters were evaluated: plumule length, root length, germination (%) and fresh weight reduction (%). E. muricata germination was reduced by 50% with a 6 ppm dose. A non linear relation dose-germination was observed in the rest of the biotypes. The plumule length permitted the ranking of the biotypes into three groups: (1) resistant (E. phyllopogon R) or very tolerant (Oryza sativa Puntal var. and wild rice), those with a reduction of less than 30%, (2) tolerant, between 30 and 60% (E. oryzicola), and (3) susceptible, with a reduction of over 80% (E. muricata, E. crus-galli, E. crus-pavonis, E. utilis and E. phyllopogon S). Only Oryzo sativa and E. phyllopogon R had a minimal reduction of fresh weight (less than 15%). The assays were repeated with whole plants and we checked the accuracy of this test that indicated the resistance level of one biotype in a quick, reliable and economic way.

Botanical identification of several Echinochloa biotypes collected in Spanish rice fields with control failures of cyhalofop-butyl.

There is some disagreement about the species that constitute Echinochloa. Correct identification is agronomically and economically important because Echinochloa spp. are aggressive invaders and difficult to control. The identification of Echinochloa spp. is complicated because of the morphological diversity shown by the genus. This work was initiated because of the differential response to cyhalofop-butyl treatment shown by some populations of Echinochloa spp. Four biotypes were selected for botanical identification: two biotypes collected in the Seville area, one of them susceptible to cyhalofop-butyl (ED50 = 64 g a.i.ha(-1)) and the other one tolerant (ED50 = 560 g a.i.ha(-1)), one tolerant biotype collected in the Badajoz area (ED50 = 420 g a.i.ha(-1)) and one tolerant biotype collected in the Valencia area (ED50 = 860 g a.i.ha(-1)). Botanical identification was carried out following Carretero's Keys (1981) on plants grown at the site of origin. The main distinguishable character of the species was the length of the upper glume. The following results were obtained: the susceptible biotype collected in the Seville area and the tolerant biotype collected in the Valencia area were characterized as Echinochloa oryzoides, the tolerant biotype collected in Badajoz was characterized as E. oryzicola and the tolerant biotype collected in Seville area as E. hispidula.