Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction–denaturing gradient gel electrophoresis. The bacterial communities’ richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community

GMOs: Prospects for Increased Crop Productivity in Developing Countries

Genetically Modified Crops (GMO foods) have been widely available to farmers since 1996. The Gene Revolution, based on recombinant DNA (rDNA) genetic engineering techniques, is seen by proponents as both supplanting Green Revolution varieties, based on conventional plant breeding techniques, and potentially enabling "disadvantaged" production environments, unreached by Green Revolution varieties to achieve productivity improvements. This paper argues that the private firms supplying GM crop products have generally had little interest in selling products in disadvantaged production environments. The paper also argues that present rDNA techniques allow only static gains from specific "trait" improvements. But these GM products can be installed on Green Revolution varieties where continued dynamic varietal improvement is possible. As a consequence, the Gene Revolution complements the Green Revolution, and because trait incorporation expands area planted to Green Revolution varieties, there is potential for productivity improvement in disadvantaged environments.Genetically Modified Foods, Genetic Engineering

Genetic diversity of Myanmar rice and their implementation on management methods

Myanmar has diverse agronomic landscape and potentially preserves high level of genetic resources for important crop species. However, little study on rice landrace diversity in Myanmar has been done. Genetic and phenotypic variation to characterize rice genetic resource in Myanmar was analyzed using molecular markers as well as common garden experiments. Two populations of rice landraces, a seedbank population maintained by seed-propagation in a genebank for several generations and an “onfarm” population collected from agricultural lands were used. A functional (cytochrome P450 related PBA) and neutral (SSR) markers were used in this study. Phenotypic characteristics of representative agronomic traits in rice, such as culm length, panicle length, number of tillers and days to heading, were measured in both populations. Multivariate analysis suggested that the seed-bank and on-farm population had different genetic bases with both functional and neutral markers. There was no significant relationship between the functional and neutral markers based on Mantel test. In addition, PCA analyses of agronomic traits showed that a variation in the seed-bank population had narrower genetic bases than the on-farm population. Genetic bias caused by ‘unconscious selection’ during the genebank management processes may have occurred in the landraces. The importance of the conservation on on-farm landraces of Oryza sativa and its wild relatives was proposed in order to ensure the genetic resources for further breeding and conserve biological diversity.Key words: Oryza sativa, rice, landrace, on-farm, diversity, conservation

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

Background Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. Results We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. Conclusions This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach

Molecular approaches for characterization and use of natural disease resistance in wheat

Wheat production is threatened by a constantly changing population of pathogen species and races. Given the rapid ability of many pathogens to overcome genetic resistance, the identification and practical implementation of new sources of resistance is essential. Landraces and wild relatives of wheat have played an important role as genetic resources for the improvement of disease resistance. The use of molecular approaches, particularly molecular markers, has allowed better characterization of the genetic diversity in wheat germplasm. In addition, the molecular cloning of major resistance (R) genes has recently been achieved in the large, polyploid wheat genome. For the first time this allows the study and analysis of the genetic variability of wheat R loci at the molecular level and therefore, to screen for allelic variation at such loci in the gene pool. Thus, strategies such as allele mining and ecotilling are now possible for characterization of wheat disease resistance. Here, we discuss the approaches, resources and potential tools to characterize and utilize the naturally occurring resistance diversity in wheat. We also report a first step in allele mining, where we characterize the occurrence of known resistance alleles at the wheat Pm3 powdery mildew resistance locus in a set of 1,320 landraces assembled on the basis of eco-geographical criteria. From known Pm3 R alleles, only Pm3b was frequently identified (3% of the tested accessions). In the same set of landraces, we found a high frequency of a Pm3 haplotype carrying a susceptible allele of Pm3. This analysis allowed the identification of a set of resistant lines where new potentially functional alleles would be present. Newly identified resistance alleles will enrich the genetic basis of resistance in breeding programmes and contribute to wheat improvemen

Dispersal of transgenes through maize seed systems in Mexico.

ObjectivesCurrent models of transgene dispersal focus on gene flow via pollen while neglecting seed, a vital vehicle for gene flow in centers of crop origin and diversity. We analyze the dispersal of maize transgenes via seeds in Mexico, the crop's cradle.MethodsWe use immunoassays (ELISA) to screen for the activity of recombinant proteins in a nationwide sample of farmer seed stocks. We estimate critical parameters of seed population dynamics using household survey data and combine these estimates with analytical results to examine presumed sources and mechanisms of dispersal.ResultsRecombinant proteins Cry1Ab/Ac and CP4/EPSPS were found in 3.1% and 1.8% of samples, respectively. They are most abundant in southeast Mexico but also present in the west-central region. Diffusion of seed and grain imported from the United States might explain the frequency and distribution of transgenes in west-central Mexico but not in the southeast.ConclusionsUnderstanding the potential for transgene survival and dispersal should help design methods to regulate the diffusion of germplasm into local seed stocks. Further research is needed on the interactions between formal and informal seed systems and grain markets in centers of crop origin and diversification

Assessment relationship between agro-morphological traits and grain yield in bread wheat genotypes under drought stress condition

To evaluate the genetic diversity in bread wheat landraces along with six controls (Azar2, Fankang, Trakia, Siosson, Gaspard and Gascogne), an experiment based on randomized complete block design with three replications was carried out under drought stress condition in the Agricultural Research Station of Islamic Azad University, Ardabil, Iran. Analysis of variance indicated that there were highly significant differences among the genotypes in all of the traits. There were significant correlations between yield and all of the studied traits. Principal components (PC) analysis showed that five components explained 69.3% of the total variation among traits. The first PC assigned 29% and the second PC assigned 15% and of total variation between traits. The first PC was more related to tiller numbers, fertile tillers, biological yield, grain yield and volume of seed plants. Therefore, selection based on first component is helpful for a good hybridization breeding program. A principal component biplot showed low distance between grain yield and biological yield, volume of seed, plant height and hectoliter. From this study, it was concluded that a good hybridization breeding program can be initiated by the selection of genotypes from the PC1.Keywords: Bread wheat, biplot, landrace, drought stress, agronomic trait

Awn Reduction and the Domestication of Asian Rice: A Syndrome or Crop Improvement Trait?

International audienc