Functional Plant Genomics
Edited by J. F. Morot-Gaudry, P. Lea & J. F. Briat
A global investment in plant genomics is under way, thanks to increasing recognition of the services provided by higher plants to ecosystems. These plants fix the greenhouse gas carbon dioxide, enrich soil constituents and are valuable as a source of food, fuel, fibres and medicines.
We already know the genome sequences of thale grass (Arabidopsis thaliana), rice, the poplar tree and the grapevine, and those of papaya, sorghum and others are in the pipeline. The sequences of most crop genomes will probably be in hand in the next decade. These will seed “the birth of a new plant biology”, a concept that forms the focus of Functional Plant Genomics and promises to expose relationships between DNA sequence and botanical diversity.
The book — edited by former leaders of the plant biology department at INRA, the French agricultural research agency — exceeds the scope of its title. It reaches from the ancestry of genomics, through genome sequencing, annotation and functional dissection, to translation of functional information from botanical models into crop improvement. The section on structural genomics includes results from classical cytogenetics and renaturation kinetics research. The findings have shaped our understanding of genome organization, from cloning and sequencing to the computational techniques that convert sequences into information. Included are intuitive explanations of basic methodologies along with detailed coverage of knowledge and resources.
Complete or exhaustive sequencing is addressed in detail. The authors note that “the cost of a complete sequence ... in the future will have to be balanced against the [pro]portion of specific information”, but coverage of advances in whole-genome shotgun (equated to “partial or draft-type”) sequencing is brief.
The section on functional genomics considers large-scale approaches to quantifying gene function, as reflected by phenotype, expression of messenger RNA, and protein and metabolite levels. It also gives some attention to the statistical methods used to extract signals from these (often noisy) data. Metabolomics features prominently. There is a particularly interesting chapter on the application of in silico metabolic mapping to complement and accelerate the deduction of pathways that are followed by each molecule entering an organism.
A final short section on genomics and technology is an extension of metabolomics. It details metabolic fingerprinting for developmental, genetic and stress-induced variations, as well as the self-assembly (and potential for manipulation) of biopolymers that determine the quality and utility of plant products.
Functional Plant Genomics gives specific attention to the many manifestations of botanical diversity. It evaluates models that range from small genomes such as A. thaliana, with its experimental expediency and extensive infrastructure, to complex large genomes of plants such as sugarcane (dear to my heart), the world's number-one biofuel crop.
How can hard-won functional information best be applied to crop improvement through plant breeding? The book takes on this question by assessing DNA-marker types (including those derived from transposable elements), quantitative trait locus mapping, and approaches based on candidate genes and association with determinants of a trait. There is discussion of progress in utilization of genomics for breeding two very different cereals, maize (corn) and wheat. Maize uses cross-pollination and has two sets of chromosomes; wheat is self-pollinating with six sets of chromosomes.
Minor errors and omissions notwithstanding, Functional Plant Genomics should broaden the perspective of researchers and postgraduate students on the role of genomics in the life sciences. Others will appreciate its glossary in what has become a fast-moving field pervaded by jargon.