ScienceWeek

PLANT BIOLOGY: ON HORMONES AND GENETIC IMPROVEMENT OF CROPS

The following points are made by Francesco Salamini (Science 2003 302:71):

1) In his famous 1840 manifesto, Justus Liebig (1803-1873) advocated a more rational approach to agronomic research. He proposed integrating physiological and chemical principles to improve the yield of crop plants. However, it was not until after World War II (1939-1945) that agronomists, searching for better herbicides and insecticides (1), took a rational approach to boosting crop yields.

2) The creation of genetically improved crop varieties, in particular dwarf cultivars of wheat and rice, resulted in the doubling of food grain production within a few decades, a success dubbed the "green revolution" (2). The short stature and sturdy stalks of the dwarf varieties of wheat and rice rendered them resistant to flattening by wind, rain, or high densities (lodging), and more effective in converting fertilizer input into higher yields. For example, short semi-dwarf wheat varieties exhibit a 100% greater yield than earlier, taller cultivars (3).

3) The genes responsible for the rice and wheat green revolution dwarf varieties have been identified. They encode proteins that either regulate synthesis of the plant growth hormone gibberellin or modulate its signaling pathway. Multani et al. (4) have identified a new mechanism controlling plant height in maize and sorghum dwarf mutants of agronomic importance. They have demonstrated that the mutant gene in the brachytic2 (br2) maize mutant and the dwarf3 (dw3) sorghum mutant encodes a protein responsible for the transport of auxin, the first plant growth hormone to be discovered.

4) A rational approach to improving crop varieties depends on a better understanding of plant biology. Of the tens of thousands of genes in plant genomes, one needs to know not only which genes control complex traits like size or yield but also how these genes limit successful plant-breeding programs. There are several strategies for elucidating how genes affect the phenotypes of plants. One approach is to analyze quantitative trait loci (QTL), which reveal allelic variations that can be exploited in plant breeding (5). Another approach is to screen plant genomes for a genetic signature, which indicates strong selection for a specific set of genes that generates modified and agronomically beneficial alleles. Such an approach uses statistical methods to reveal significant nucleotide diversity between wild plants and their domesticated counterparts, enabling researchers to identify genes of agronomic importance. A third approach, and the one exploited by Multani et al (4), is to analyze plant mutants that exhibit improved growth characteristics and then to identify the responsible gene mutation.

References (abridged):

1. I. Ishaaya, Ed., Biochemical Sites of Insecticide Action and Resistance (Springer-Verlag, Berlin, 2001)

2. G. S. Khush, Nature Rev. Genet. 2, 815 (2001)

3. N. E. Borlaug, Science 219, 689 (1983)

4. D. S. Multani et al., Science 302, 81 (2003)

5. M. Morgante, F. Salamini, Curr. Opin. Biotechnol. 14, 214 (2003)

Science http://www.sciencemag.org

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ON RICE GENOMES

The following points are made by K. Livingstone and L.H. Rieseberg (Current Biology 2002 12:R470):

1) Although completion of the heavily anticipated human genome sequence project will provide information needed to combat inherited maladies, the recent completion of two sequences of the rice genome [1,2] may be a far greater gift to humanity. After all, as the Byzantine proverb states, "He who has bread has many problems, he who has no bread has only one problem". Because of the importance of rice and its status as a model for all grasses, these sequences will provide a basis for future genetic improvement of all the cereal grains, our most important food resource. Beyond the obvious agricultural benefit, these sequences may also provide unparalleled views of the processes operating on DNA sequences that change the function and organization of genes, leading to the formation of new species.

2) The two rice sequences are from subspecies that represent the major cultivated gene pools of rice, Oryza sativa L. ssp. indica and O. sativa ssp. japonica. The indica type is primarily grown in China, and the Beijing Genomics Institute (BGI) determined its sequence [1]. The japonica subspecies is preferred in Japan, and Syngenta AG's Torrey Mesa Research Institute (TMRI) determined its sequence [2]. These are both draft sequences, produced by randomly sequencing small genomic bits and relying on multiple, offset sequences to assemble the larger pieces.

3) From a functional standpoint, while each draft should contain nearly all the genes in rice, many of the sequences identified as genes are only predicted on the basis of different gene detection algorithms. It will take a long time to validate the expression of the putative genes biologically and take full advantage of these efforts. Structurally, both drafts cover the majority of the rice genome, but many of the intergenic regions are missing. Consequently, each draft resembles a puzzle with tens of thousands of pieces on the table, but only a few joined to start to form a picture of the twelve rice chromosomes.

4) Even in a draft state, however, these sequences provide enormous agricultural benefits. Rice is a crucial staple for much of the world's population, and rice is also the compact key to other grass genomes [3] . The main differences between rice and maize, wheat, barley, and so on are that, while the same genes are found in each species, they are in different arrangements, amid various amounts of species-specific "junk" DNA. The compactness of the rice genome, coupled with a known sequence, will make identification of important genes easier. In addition, the rice sequence provides a means for directing searches in other grasses to the genes in a particular chromosomal region. The TMRI group [2] has already demonstrated the power of a focused search approach to define candidates for a subset of agronomically important traits mapped in maize [4,5].

References (abridged):

1. Yu J., Hu S., Wang J., Wong G.K.-S., Li S., Liu B., Deng Y., Dai L., Zhou Y. and Zhang X. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Indica) Science, 296:79-92

2. Goff S.A., Ricke D., Lan T.H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P. and Varma H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Japonica) Science, 296:92-100

3. Devos K.M. and Gale M.D. (2000) Genome relationships: the grass model in current research. Plant Cell, 12:637-646

4. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature, 408:796-815

5. Brendel V., Kurtz S. and Walbot V. (2002) Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol, 3:1005

Current Biology http://www.current-biology.com

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