Nonstop Selection for High and Stable Crop Yield by Two Prognostic Equations to Reduce Yield Losses

Yield losses occurring at the field level, whether due to plant diseases or abiotic stresses, reveal reduced stability of the crop yield potential. The paper argues that the stability of crop yield potential is a trait with a clear genetic component, which can be successfully selected for at the single-plant level and incorporated into high-yielding cultivars. Two novel selection equations with prognostic power are presented, capable to objectively phenotype and evaluate individual plants in real field conditions in the absence of the masking effects of interplant competition and soil heterogeneity. The equations predict performance at the crop stand through the key concept of coefficient of homeostasis and are equally useful for early generation selection and for nonstop selection within finished cultivars in order to continuously incorporate the adaptive (genetic or epigenetic) responses of plants. Exploitation of adaptive responses acquires particular importance in view of the climate change effects on crop productivity and the changing biotic or abiotic micro-environments. Cotton is used as a case study to highlight the potential of nonstop selection for increasing crop yield and for the gradual build-up of disease resistance. In addition, the paper envisions and proposes the formation of international networks of researchers focusing on specific diseases as, for example, the cereal root-rot or the cotton Verticillium wilt that will concurrently use the proposed strategy in their respective environments to select for resistant genotypes, while gaining a deeper understanding of the nature of the genetic or epigenetic changes at the phenotypic and genomic levels

Studies on 4-vinyl protochlorophyllide reductase and the biological significance of the divinyl and monovinyl monocarboxylic chlorophyll a biosynthetic routes

Monovinyl chlorophyll a is the end product of chlorophyll a biosynthesis in higher plants. Most of the monovinyl chlorophyll a is formed via two major biosynthetic routes, the divinyl and monovinyl monocarboxylic routes which appear to be linked at various levels of chlorophyll precursors. The enzymes responsible for the conversion of the divinyl to monovinyl route are 4-vinyl reductases. The 4-vinyl protochlorophyllide a reductase converts divinyl protochlorophyllide to monovinyl protochlorophyllide.In this thesis, the biological significance of the two monovinyl chlorophyll a biosynthetic routes is investigated. Studies involve a comparison of various physical-electronic properties of the divinyl and monovinyl protochlorophyllide a via three-dimensional molecular modelling and in vitro work with the enzyme 4-vinyl protochlorophyllide reductase. It appears that the reduction occurring at the level of protochlorophyllide is not the prominent point linking the two routes. Studies are extended to investigation of the differential incorporation of the monovinyl chlorophyll a that forms via either of the two routes into pigment-protein complexes in the thylakoid membranes. The relationship of the two routes with increased field yield of various species is also investigated and is shown that selection for yield in wheat and corn favors the monovinyl monocarboxylic chlorophyll a biosynthetic route at the end of the dark phase of the photoperiod. It is proposed that the monovinyl route represents a biosynthetic shortcut favorable to plants.U of I OnlyETDs are only available to UIUC Users without author permissio

On the prediction of non-CG DNA methylation using machine learning

DNA methylation can be detected and measured using sequencing instruments after sodium bisulfite conversion, but experiments can be expensive for large eukaryotic genomes. Sequencing nonuniformity and mapping biases can leave parts of the genome with low or no coverage, thus hampering the ability of obtaining DNA methylation levels for all cytosines. To address these limitations, several computational methods have been proposed that can predict DNA methylation from the DNA sequence around the cytosine or from the methylation level of nearby cytosines. However, most of these methods are entirely focused on CG methylation in humans and other mammals. In this work, we study, for the first time, the problem of predicting cytosine methylation for CG, CHG and CHH contexts on six plant species, either from the DNA primary sequence around the cytosine or from the methylation levels of neighboring cytosines. In this framework, we also study the cross-species prediction problem and the cross-context prediction problem (within the same species). Finally, we show that providing gene and repeat annotations allows existing classifiers to significantly improve their prediction accuracy. We introduce a new classifier called AMPS (annotation-based methylation prediction from sequence) that takes advantage of genomic annotations to achieve higher accuracy

Image based remote sensing method for modeling black-eyed beans (Vigna unguiculata) Leaf Area Index (LAI) and Crop Height (CH) over Cyprus

In this paper, Leaf Area Index (LAI) and Crop Height (CH) are modeled to the most known spectral vegetation index — NDVI — using remotely sensed data. This approach has advantages compared to the classic approaches based on a theoretical background. A GER-1500 field spectro-radiometer was used in this study in order to retrieve the necessary spectrum data for estimating a spectral vegetation index (NDVI), for establishing a semiempirical relationship between black-eyed beans’ canopy factors and remotely sensed data. Such semi-empirical models can be used then for agricultural and environmental studies. A field campaign was undertaken with measurements of LAI and CH using the Sun-Scan canopy analyzer, acquired simultaneously with the spectroradiometric (GER1500) measurements between May and June of 2010. Field spectroscopy and remotely sensed imagery have been combined and used in order to retrieve and validate the results of this study. The results showed that there are strong statistical relationships between LAI or CH and NDVI which can be used for modeling crop canopy factors (LAI, CH) to remotely sensed data. The model for each case was verified by the factor of determination. Specifically, these models assist to avoid direct measurements of the LAI and CH for all the dates for which satellite images are available and support future users or future studies regarding crop canopy parameters

Report of a Working Group on Barley. Seventh Meeting, 10-12 May 2011, Nicosia, Cyprus

vokpka ks

Developmental stage-and concentration- specific sodium nitroprusside application results in nitrate reductase regulation and the modification of nitrate metabolism in leaves of Medicago truncatula plants

Nitric oxide (NO) is a bioactive molecule involved in numerous biological events that has been reported to display both pro-oxidant and antioxidant properties in plants. Several reports exist which demonstrate the protective action of sodium nitroprusside (SNP), a widely used NO donor, which acts as a signal molecule in plants responsible for the expression regulation of many antioxidant enzymes. This study attempts to provide a novel insight into the effect of application of low (100 μΜ) and high (2.5 mM) concentrations of SNP on the nitrosative status and nitrate metabolism of mature (40 d) and senescing (65 d) Medicago truncatula plants. Higher concentrations of SNP resulted in increased NO content, cellular damage levels and reactive oxygen species (ROS) concentration, further induced in older tissues. Senescing M. truncatula plants demonstrated greater sensitivity to SNP-induced oxidative and nitrosative damage, suggesting a developmental stage-dependent suppression in the plant's capacity to cope with free oxygen and nitrogen radicals. In addition, measurements of the activity of nitrate reductase (NR), a key enzyme involved in the generation of NO in plants, indicated a differential regulation in a dose and time-dependent manner. Furthermore, expression levels of NO-responsive genes (NR, nitrate/nitrite transporters) involved in nitrogen assimilation and NO production revealed significant induction of NR and nitrate transporter during long-term 2.5 mM SNP application in mature plants and overall gene suppression in senescing plants, supporting the differential nitrosative response of M. truncatula plants treated with different concentrations of SN

Molecular characterization of chemical mutagenesis induced diversity in elite maize germplasm

Three classical breeding Iowa Super Stiff Stalk (SSS) inbred lines B37, B73 and B84, one Lancaster inbred Oh43 and mutant lines obtained by chemical mutagenesis followed by mutation breeding as follows: two of B37 and four of Oh43 were selected for molecular characterization. The mutant inbred lines were chosen because in addition to the improved GCA and SCA for grain yield, proven by their predominance in the Bulgarian breeding programs, they showed shifts in the flowering time as compared to the initial inbreds. Molecular markers (micro satellites and other PCR-based DNA markers) were used for characterization of maize genotypes and determination of the induced by chemical mutagenesis genetic variability in maize germplasm. The tested nine SSR markers (umc 1001, umclO14, umcl057, umcll81, umcl0lS, umc 1029. umcl003, umc 1033 and umcl035) can discriminate between the initial classical breeding inbred lines and the originating mutant inbreds. Allelic diversity was also studied by PCR amplification with specifically de-signed primers in the coding regions and flanking sequence of two genes: dwarf8 (d&: chromosome 1, 198.5 cM), and indeterminate l (id1; chromosome 1. 175.0 cM). These are considered candidate genes for variation in plant height and/or flowering time, based on mutant phenotypes and chromosomal locations near major QTLs. Single nucleotide polymorphisms and indels were detected in the region flanking the SH2 domain of dwarf8 gene in some of the mutant inbreds as a result of SSCP and sequencing analyses. However, these polymorphisms could not be associated with the observed variations in flowering time. PCR analysis of the promoter region dwarf8 showed a variant fragment of about 1 kb in the inbred line Oh43 that was not present in any other initial and mutant in-bred lines included in the study. PCR amplification of the 5' end of the Id1 coding sequence revealed polymorphic bands in the mutant lines XM535, XM521, XM250-l, XM98-8 and XM85-105, as well as in the classical breeding line B73. The data, presented here demonstrate the usefulness of chemical mutagenesis for generation of genetic diversity within the elite maize germplasm. Some of this variation may affect the major genes in the QTLs. Our initial data revealed mutagenesis induced polymorphisms in the coding sequences of two important for the determination of flowering time transcription factors. Further molecular analyses of the proposed model systems may complement the trait association efforts and will help to directly identify the major genes in the QTLs