Arable Agriculture and the Genomics Revolution
JOHN W. SNAPE. B.Sc. Ph.D.
Journal of the Royal Agricultural Society of England, Volume 163, 2002 (p12-20)

Professor John Snape is Head of Department of Crop Genetics at the John Innes Centre, Norwich, and is an international expert on cereal genetics and biotechnology, and was winner of the 2001 RASE research medal.

What is the Genomics Revolution?  

In the nucleus of each cell of each species of plant and animal is the hereditary material, the DNA, which determines the structure and function of the organism. The DNA is packaged into structures, the chromosomes. Each chromosome is, essentially, one long molecule of DNA protected and packed into a coherent structure by proteins. All the chromosomes, and hence, DNA. together make up the GENOME of that organism. The sequence of four bases, adenine, thiamine, cytosine and guanine, which make up the DNA of each chromosome, provide a code for the genes (Figure 1). This code is interpreted by the cellular mechanisms to produce proteins which govern all cellular structures and functions. GENOMICS is the science of understanding the structure and function of each of the tens of thousands of genes that are coded for by all the DNA.....

..... However, this will take years and even decades to complete because of the numbers of genes (30,000 or so in man, for example)! ....When applied to the study of arable crops....knowledge of gene function means that we have the potential to understand the genetic makeup of all of our crop species, and relate the structure of genes to variation between varieties in yield, quality, disease resistance, or any trait. The challenge is now to develop this knowledge base and then to think through how to use this information to adapt to the changing face of agriculture....

The recent developments in tissue culture and molecular biology, as well as genetics and genomics, means that plant breeding now has the potential to follow two directions. First, the conventional route, as practised by plant breeders for well over a century, but now aided by molecular approaches, using the genetical variation that already exists within a species. Central to this will be the use of molecular markers to 'tag' genes, so that selection can be practised in the laboratory for specific genes associated with desirable traits. This requires a much greater understanding of the inheritance of agronomic traits, which is now possible because of the development of genetic maps (see below).

Second is the genetic modification approach, which allows the introduction of isolated individual genes from any biological source....Undoubtedly, the [GM] technology has promise, but there are still, obviously, barriers to be overcome in terms of public acceptability... Our understanding of genomics will contribute to this [GM technology] by producing a library of 'useful' genes from a range of crop species that can be introduced into any another....

However, genomic science's biggest contribution is likely to be through providing markers and understanding to conventional plant breeding. For most arable crops, conventional plant breeding is still, and will be the mainstay for the production of new arable crop varieties for the near future. This, of course, involves creating variation through making crosses between established varieties with complementary characteristics..... to date, very few breeders can quantify the genetic advances they have made in terms of known genes for any complex trait. The current advances in our knowledge of genomics and genetics of our crops has the potential to dramatically change this situation, and, ultimately, to change the plant breeder's 'art' into an objectively based plant breeding science!

One of the most immediate and ongoing uses of genomics is in the development of genetic maps of major crop species. Genetic maps define the locations of genes on the individual chromosomes relative to landmarks, - see Figure 1, for example, for a diagrammatic representation of the genetic maps of wheat. These landmarks, termed molecular markers, are anonymous pieces of DNA which differ in sequence between varieties visualised by various molecular techniques. These genetic maps provide the 'road maps' of the genome of any one plant species, and are one of the major starting points for isolating genes. Good genetic maps, based on molecular marker technologies are now available for all major, and for many minor, species.

The major use of genetic maps is to locate genes of interest so that the maps can be fully annotated with the locations of genes, be it for quality, agronomic performance, disease resistance, adaptability, or any other trait. For many traits, this is complicated by the fact that the variation is quantitative in nature determined by many genes acting in unison. Nevertheless, major progress in developing statistical as well as genetical tools to locate such genes, so called quantitative trait loci, QTL, is taking place.

.... The full genomic sequencing of crop plants is not a realistic strategy in most cases because of the high amount of 'junk' DNA (for example, 80% of the wheat genome is junk DNA)... there are many genes of unknown function in cereals........ Probably in the next five years, all expressed genes will be captured..... Again, however, as in whole genome sequencing, the challenge will be to ascribe function to these genes.

As the functions of individual genes are identified, the relationships between different genes in common metabolic pathways can also be understood, so that the 'circuitry' of particular traits of interest will be elucidated...

So, although a start has already been made on developing a battery of genomic tools to understand the biology of key traits, there is still many years of research and technology development to complete the picture.

In this millennium, genomics research has the potential to define the total extent of the genetic variation for simple and complex characters within our crop plants. This will allow our plant breeders, using high-through-put molecular marker systems, to produce 'designer' varieties. Also there is the capacity to modify metabolic pathways by genetic engineering.... Much of this research is 'big science', for example, sequencing of the rice genome is estimated to have cost at least $40 million US.... As well as leading to economic prosperity, this research can also make an important contribution to world food security through development of varieties much more resistant to pest and diseases both in major crops, and in 'orphan' crops of the less developing world through comparative approaches. Clearly we have only just started to see the fruits of this genomics revolution leading, hopefully, to the evolution of a new Green Revolution."

'Will GM Crops Deliver Benefits To Farmers?'
www.nlpwessex.org/docs/gmagric.htm

USDA Report Exposes GM Crop Economics Myth
www.nlpwessex.org/docs/usdagmeconomics.htm

More USDA Data On Rising Pesticide Applications On GM Crops
www.nlpwessex.org/docs/benbrook.htm

The Fundamental Scientific Error
Of Pursuing Transgenics Before Competency In Genomics
www.nlpwessex.org/docs/genomicsparadigm.htm

Moving GM Food Debate Towards A Solution
www.nlpwessex.org/docs/monsantomaspossibilities.htm

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