Arabidopsis thaliana genome. Now for the hard ones

Now for the hard ones: is there a limit on CRISPR genome editing in crops?

This article comments on the following paper: Martín-Pizarro C, Triviño JC, Posé D. 2019. Functional analysis of the TM6 MADS-box gene in the octoploid strawberry by CRISPR/Cas9-directed mutagenesis. Journal of Experimental Botany 70, 885–895.

QUANTITATIVE DETECTION OF TRANSGENIC AND ENDOGENOUS DNA SEQUENCES IN SEEDS AFTER AUTOMATED DNA PREPARATION

In applied transgenic research as well as in agriculture there is an increasing need for high-throughput analyses of plants for genotypic selection or to identify the purity of seed stocks, e.g. for transgenic contaminations or the identification of pathogens. We developed and optimised conditions for the isolation of DNA from single seeds using an automated high-throughput protocol. Our results show that the system provided is capable of isolating DNA from any tested seed source. Furthermore, seeds remain capable of germinating during the homogenisation procedure. Quantification of endogenous and transgenic sequences by Real-Time PCR revealed that the prepared DNA is suitable in quality and quantity for multiple PCR analyses with both SYBR Green and hybridisation probe detection. The described method will be a useful tool for routine analyses like screening of large populations or the specific detection of genetically modified organisms (GMO).

A high-throughput genome-walking method and its use for cloning unknown flanking sequences

We developed a PCR-based high-throughput genome-walking protocol. The novelty of this protocol is in the random introduction of unique walker primer binding sites into different regions of the genome efficiently by taking advantage of the rolling circle mode of DNA synthesis by Phi29 DNA polymerase after annealing the partially degenerate primers to the denatured genomic DNA. The inherent strand-displacement activity of the Phi29 DNA polymerase displaces the 5' ends of downstream strands and DNA synthesis continues, resulting in a large number of overlapping fragments that cover the whole genome with the unique walker adapter attached to the 5' end of all the genomic DNA fragments. The directional genome walking can be performed using a locus-specific primer and the walker primer and Phi29 DNA polymerase-amplified genomic DNA fragments as template. The locus-specific primer will determine the position and direction of the genome walk. Two rounds of successive PCR amplifications by locus-specific and walker primers and their corresponding nested primers effectively amplify the flanking DNA fragments. The desired PCR fragment can be either cloned or sequenced directly using another nested, locus-specific primer. We successfully used this protocol to isolate and sequence 5' flanking regions/promoters of selected plant genes.

Proteome analysis of non-model plants: a challenging but powerful approach

Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives.

DNA banking for plant breeding, biotechnology and biodiversity evaluation

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.

Sputnik: a database platform for comparative plant genomics

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics.

Deciding among green plants for whole genome studies

Recent comparative DNA-sequencing studies of chloroplast, mitochondrial and ribosomal genes have produced an evolutionary tree relating the diversity of green-plant lineages. By coupling this phylogenetic framework to the explosion of information on genome content, plant-genomic efforts can and should be extended beyond angiosperm crop and model systems. Including plant species representative of other crucial evolutionary nodes would produce the comparative information necessary to understand fully the organization, function and evolution of plant genomes. The simultaneous development of genomic tools for green algae, bryophytes, 'seed-free' vascular plants and gymnosperms should provide insights into the bases of the complex morphological, physiological, reproductive and biochemical innovations that have characterized the successful transition of green plants to land.

Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology

Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants; however, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight into understanding the evolution of complex traits both in crops and in wild plants.