Plant Breeding and Genomics News

One of the major concerns of the general public about transgenic crops relates to the mixing of genetic materials between species that cannot hybridize by natural means. To meet this concern, the two transformation concepts cisgenesis and intragenesis were developed as alternatives to transgenesis. Both concepts imply that plants must only be transformed with genetic material derived from the species itself or from closely related species capable of sexual hybridization. Furthermore, foreign sequences such as selection genes and vector-backbone sequences should be absent. Intragenesis differs from cisgenesis by allowing use of new gene combinations created by in vitrorearrangements of functional genetic elements. Several surveys show higher public acceptance of intragenic/cisgenic crops compared to transgenic crops. Thus, although the intragenic and cisgenic concepts were introduced internationally only 9 and 7 years ago, several different traits in a variety of crops have currently been modified according to these concepts. Five of these crops are now in field trials and two have pending applications for deregulation. Currently, intragenic/cisgenic plants are regulated as transgenic plants worldwide. However, as the gene pool exploited by intragenesis and cisgenesis are identical to the gene pool available for conventional breeding, less comprehensive regulatory measures are expected. The regulation of intragenic/cisgenic crops is presently under evaluation in the EU and in the US regulators are considering if a subgroup of these crops should be exempted from regulation. It is accordingly possible that the intragenic/cisgenic route will be of major significance for future plant breeding.

Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to deconstruct complex traits such as those involved in growth responses to the environment. Still, only a few facilities are known to handle individual plants of small stature for non-destructive, real-time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high-throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It automatically adjusts watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, with automatic image analysis allowing manual correction. When applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro-environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large proportion of the micro-environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large-scale experiments that would not be possible or reproducible by hand. When applied to a typical quantitative trait loci (QTL) mapping experiment, we show that mapping power is more limited by genetic complexity than phenotyping accuracy. This will help to draw a more general picture as to how genetic diversity shapes phenotypic variation.

Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted the sequence-based Whole Genome Profiling (WGP ) technology to gain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between Nicotiana sylvestris and Nicotiana tomentosiformis about 200,000 years ago. This resulted in tobacco having a haploid genome size of 4,500 million base pairs, about four times larger than the related tomato and potato genomes. In this study a physical map containing 9,750 contigs of bacterial artificial chromosomes (BACs) was constructed. The average contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated will be an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology with tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance. This article is protected by copyright. All rights reserved.

SummaryOaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses.We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum.Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated.In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.

To develop genetic improvement strategies to modulate raffinose family oligosaccharides (RFO) concentration in chickpea (Cicer arietinum L.) seeds, RFO and their precursor concentrations were analyzed in 171 chickpea genotypes from diverse geographical origins. The genotypes were grown in replicated trials over two years in the field (Patancheru, India) and in the greenhouse (Saskatoon, Canada). Analysis of variance revealed a significant impact of genotype, environment, and their interaction on RFO concentration in chickpea seeds. Total RFO concentration ranged from 1.58 to 5.31 mmol/100 g and from 2.11 to 5.83 mmol/100 g in desi and kabuli genotypes, respectively. Sucrose (0.60–3.59 g/100 g) and stachyose (0.18–2.38 g/100 g) were distinguished as the major soluble sugar and RFO, respectively. Correlation analysis revealed a significant positive correlation between substrate and product concentration in RFO biosynthesis. In chickpea seeds, raffinose, stachyose, and verbascose showed a moderate broad sense heritability (0.25–0.56), suggesting the use of a multilocation trials based approach in chickpea seed quality improvement programs.

This is a really exciting time for phytochemistry research. Plant scientists studying specialized plant metabolism (previously often known as ‘secondary metabolism’) can foresee tremendous advances in their understanding of the mechanisms underlying the production and function of an enormous variety of plant metabolites, and of their regulation and evolution. Such remarkable progress would never have been expected 10 years ago and has taken place in just the last few years (Yonekura-Sakakibara and Saito 2009).

Two technological breakthroughs seem to have been the key triggers for this unforeseen progress: metabolomics and mass DNA sequencing. Metabolomics is <15 years old, yet the concept was immediately applied to the plant field as scientists realized its tremendous potential for understanding the capacity of plants for making a huge array of compounds (Bino et al. 2004). Metabolomics now makes possible comprehensive profiling of nearly all the metabolites that accumulate in plant cells (Saito and Matsuda 2010). The second technological breakthrough was ultra-high-throughput DNA sequencing, with so-called ‘next-generation DNA sequencers’ (Wang et al. 2009, Ozsolak and Milos 2011). Until the realization of this technology, no one would have anticipated genomics-based studies of hundreds of medicinal or exotic plant species—genomics was only for model plants or major crops, whose genome sequences could only be revealed by large international research consortia (or by huge …

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Why is cassava important?

Cassava (Manihot esculenta), a major staple crop, is the main source of calories for 500 million people across the globe. No other continent depends on cassava to feed as many people as does Africa. Cassava is indispensable to food security in Africa. It is a widely preferred and consumed staple, as well as a hardy crop that can be stored in the ground as a fall-back source of food that can save lives in times of famine. Despite the importance of cassava for food security on the African continent, it has received relatively little research and development attention compared to other staples such as wheat, rice and maize. The key to unlocking the full potential of cassava lies largely in bringing cassava breeding into the 21st century.

Why genomic selection?

Genomic Selection is a new plant breeding method that uses statistical modeling to predict how a plant will perform, before it is field-tested. Novel statistical models and bioinformatics tools, combined with increasingly abundant genomic information, have enabled the deployment of prediction-based breeding methods such as Genomic Selection in crop breeding programs. Giving breeders the ability to select based on predictions rather than observations will result in much improved genetic gains and efficiency.

 

CassavaBase

Access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.

Hop-derived aroma characteristics in beer are very important for the quality of beer. This study compared the differences of hop aroma characteristics and the compounds contained in beer by changing the variety of hops applying the idea of “food metabolomics” on the GC×GC/TOF-MS analysis data, to clarify which aroma compounds contribute to the differences of hop aroma profiles indicated by sensory descriptors. As a result, by focusing only on hop-derived compounds, 67 compounds were strongly correlated with one or more of the sensory descriptors. Furthermore, the odor descriptions of each key compound corresponded well to each sensory descriptor. Thus, these compounds are likely to be the key compounds explaining the differences of hop aroma characteristics in beer. This study led to the suggestion that understanding the relationship between the comprehensive nontarget analysis by GC×GC-TOF/MS and organoleptic evaluation using PCA is effective in estimating the key compounds.

To coincide with the 2nd International Fascination of Plants Day and contribute by getting as many people as possible around the world fascinated by plants,Taylor & Francis is offering you free access to a definitive list of key articles related to the event.  Simply click on any of the articles below to claim your instant, free access.

Don’t forget that you can still get 20% off Plant-related books at CRC Press by using discount code DWM32.

Terpenoids constitute a large and diverse class of natural products that serve many functions in nature. Most of the tens of thousands of the discovered terpenoids are synthesized by plants, where they function as primary metabolites involved in growth and development, or as secondary metabolites that optimize the interaction between the plant and its environment. Several plant terpenoids are economically important molecules that serve many applications as pharmaceuticals, pesticides, etc. Major challenges for the commercialization of plant-derived terpenoids include their low production levels in planta and the continuous demand of industry for novel molecules with new or superior biological activities. Here, we highlight several synthetic biology methods to enhance and diversify the production of plant terpenoids, with a foresight towards triterpenoid engineering, the least engineered class of bioactive terpenoids. Increased or cheaper production of valuable triterpenoids may be obtained by ‘classic’ metabolic engineering of plants or by heterologous production of the compounds in other plants or microbes. Novel triterpenoid structures can be generated through combinatorial biosynthesis or directed enzyme evolution approaches. In its ultimate form, synthetic biology may lead to the production of large amounts of plant triterpenoids in in vitro systems or custom-designed artificial biological systems.

Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit 'Kranz' anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell-types. Although Kranz evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene thus far implicated in Kranz patterning. To provide a broader oversight into the regulation of Kranz differentiation, we carried out a genome wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages, to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network and elucidates likely components of that network. Furthermore, the data infer a role for additional pathways in the development of Kranz leaves. This article is protected by copyright. All rights reserved.