Nuclear ribosomal DNA diversity of a cotton pest (Rotylenchulus reniformis) in the United States

The reniform nematode (Rotylenchulus reniformis) has emerged as a major cotton pest in the United States. A recent analysis of over 20 amphimictic populations of this pest from the US and three othercountries has shown no sequence variation at the nuclear ribosomal internal transcribed spacer (ITS) despite the region’s usual variability. We investigated this unexpected outcome by amplifying, cloningand sequencing two regions of the nuclear ribosomal DNA (18S, ITS1) to ascertain whether any variation occurred within and among populations of reniform nematodes in Alabama, US. Both thenrITS1 and the relatively conserved 18S region showed a fairly substantial amount of variation among populations. The identity among ITS sequences ranged from 1.00 to 0.86, while sequence identity at the18S ranged from 1.00 to 0.948. We conclude that variation does exist in these sequences in reniform nematodes, and the earlier report showing no ribosomal ITS variation in this pest might have beencaused by preferential amplification of a conserved ITS paralog. Current and future application towards resistance in cotton varieties to this pest requires reliable information on the molecular variability of thenematode in cotton-growing areas

Conservation value of the native Hungarian wild grape (Vitis sylvestris Gmel.) evaluated by microsatellite markers

Wild grape (Vitis sylvestris GMEL.) has became a highly threatened species in Europe because of habitat loss, competition with alien grape species and intensive forest exploitation. Twenty-three Vitis spp. samples were analysed at 8 microsatellite loci to estimate the genetic diversity of the natural Vitis sylvestris specimens. In order to analyse the morphological traits and to perform molecular analysis, 11 native individuals were sampled from 6 remnant Hungarian habitats of the wild grape. To compare the genetic relationships among the wild specimens, samples from Turkish habitats, as well as cultivars of Vitis vinifera, Vitis labrusca and Vitis riparia were also included. Genetic diversity was higher within the Hungarian wild grape locations, with a mean of He = 0.74, which was higher that of samples originating from a larger area of Turkey, He = 0.69. Most of the Hungarian samples formed a well-defined, separate branch on the NJ tree. Based on the morphological traits and molecular analysis on the territory of Szentendre Island, formerly considered to be one of the largest native locations of wild grape, interspecific hybrids of Vitis sylvestris and Vitis riparia were identified. It can be concluded from the results that most of the Hungarian habitats studied could be valuable for the conservation. This paper reports on Hungarian Vitis sylvestris habitats, providing the first genetic study on diversity and on the relationship of Vitis sylvestris to other Vitis specimens, wild or cultivated, in the central part of the Carpathian Basin

Fermions and Loops on Graphs. I. Loop Calculus for Determinant

This paper is the first in the series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the Loop Calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassman variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called BP (Bethe-Peierls or Belief Propagation) gauge, yields the desired loop representation. The set of gauge-fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix.Comment: 11 pages, 1 figure; misprints correcte

Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats

Global agricultural intensification during climate change: A role for genomics

Summary: Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change. &gt

Application of genomicsassisted breeding for generation of climate resilient crops: progress and prospects

CCAFS Climat

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change

Identification of antibody neutralization epitopes on the fusion protein of human metapneumovirus

Human metapneumovirus (hMPV) is genetically related to respiratory syncytial virus (RSV); both cause respiratory tract illnesses ranging from a mild cough to bronchiolitis and pneumonia. The F protein-directed monoclonal antibody (mAb) palivizumab has been shown to prevent severe lower respiratory tract RSV infection in animals and humans. We have previously reported on a panel of mAbs against the hMPV F protein that neutralize hMPV in vitro and, in two cases, in vivo. Here we describe the generation of hMPV mAb-resistant mutants (MARMs) to these neutralizing antibodies. Sequencing the F proteins of the hMPV MARMs identified several neutralizing epitopes. Interestingly, some of the epitopes mapped on the hMPV F protein coincide with homologous regions mapped previously on the RSV F protein, including the site against which the broadly protective mAb palivizumab is directed. This suggests that these homologous regions play important, conserved functions in both viruses

Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security

Volatile emissions of scented Alstroemeria genotypes are dominated by terpenes, and a myrcene synthase gene is highly expressed in scented Alstroemeria flowers

Native to South America, Alstroemeria flowers are known for their colourful tepals, and Alstroemeria hybrids are an important cut flower. However, in common with many commercial cut flowers, virtually all the commercial Alstroemeria hybrids are not scented. The cultivar ‘Sweet Laura’ is one of very few scented commercial Alstroemeria hybrids. Characterization of the volatile emission profile of these cut flowers revealed three major terpene compounds: (E)-caryophyllene, humulene (also known as α-caryophyllene), an ocimene-like compound, and several minor peaks, one of which was identified as myrcene. The profile is completely different from that of the parental scented species A. caryophyllaea. Volatile emission peaked at anthesis in both scented genotypes, coincident in cv. ‘Sweet Laura’ with the maximal expression of a putative terpene synthase gene AlstroTPS. This gene was preferentially expressed in floral tissues of both cv. ‘Sweet Laura’ and A. caryophyllaea. Characterization of the AlstroTPS gene structure from cv. ‘Sweet Laura’ placed it as a member of the class III terpene synthases, and the predicted 567 amino acid sequence placed it into the subfamily TPS-b. The conserved sequences R28(R)X8W and D321DXXD are the putative Mg2+-binding sites, and in vitro assay of AlstroTPS expressed in Escherichia coli revealed that the encoded enzyme possesses myrcene synthase activity, consistent with a role for AlstroTPS in scent production in Alstroemeria cv. ‘Sweet Laura’ flowers