Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery

Sequencing and analysing of the Arabidopsis thaliana genome, the first plant kingdom genome to be unraveled, will always remain a scientific landmark. International initiatives to sequence rice, the most important cereal in Asia, are underway. However as functional information piles up in Arabidopsis and rice, researchers working in other crops will benefit from this new knowledge and apply it to their studied plants or crop species. The increasing role of public databases of model organisms and bio-informatics in data mining, presents a new opportunity as well as a challenge to researchers to develop more focused molecular tools for gene discovery and deployment. The work presented in here describes how such an approach has benefited sorghum, a rainfed semi-arid troprical cereal.

[1]  S. Tanksley,et al.  RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. , 1988, Genetics.

[2]  J. Bennetzen,et al.  Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[3]  J. Doebley,et al.  Comparative genome mapping of Sorghum and maize. , 1992, Genetics.

[4]  S. Briggs,et al.  Reductase activity encoded by the HM1 disease resistance gene in maize. , 1992, Science.

[5]  N. Young,et al.  Evidence for orthologous seed weight genes in cowpea and mung bean based on RFLP mapping. , 1992, Genetics.

[6]  J. Doebley,et al.  Construction of an RFLP map in sorghum and comparative mapping in maize. , 1994, Genome.

[7]  R. Ragab,et al.  Construction of a sorghum RFLP linkage map using sorghum and maize DNA probes. , 1994, Genome.

[8]  A. Paterson,et al.  Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. , 1995, Genetics.

[9]  Andrew H. Paterson,et al.  Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci , 1995, Science.

[10]  T. Helentjaris,et al.  Was there a single ancestral cereal chromosome? , 1995, Trends in genetics : TIG.

[11]  J. Bennetzen,et al.  The unified grass genome: synergy in synteny. , 1997, Genome research.

[12]  B. Sobral,et al.  Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[13]  P. Dufour,et al.  Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid , 1997, Theoretical and Applied Genetics.

[14]  K. Devos,et al.  Comparative genetics in the grasses. , 1998, Plant molecular biology.

[15]  J. Bennetzen,et al.  Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Toward a successful multinational crop plant genome initiative. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[17]  S McCouch,et al.  Toward a plant genomics initiative: thoughts on the value of cross-species and cross-genera comparisons in the grasses. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Ronald L. Phillips,et al.  Relationships of cereal crops and other grasses , 1998 .

[19]  S. Lin,et al.  A high-density rice genetic linkage map with 2275 markers using a single F2 population. , 1998, Genetics.

[20]  C. Mcintyre,et al.  Construction of a genetic map in a sorghum recombinant inbred line using probes from different sources and its comparison with other sorghum maps (vol 49, pg 729, 1998) , 1998 .

[21]  S. C. Liu,et al.  Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. , 1998, Genetics.

[22]  M. Yano,et al.  Rapid reorganization of resistance gene homologues in cereal genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Bennetzen,et al.  Grass genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  G. E. Hart,et al.  Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines , 1999 .

[25]  K. Boivin,et al.  Towards a saturated sorghum map using RFLP and AFLP markers , 1999, Theoretical and Applied Genetics.

[26]  D. Adam.  Now for the hard ones , 2000, Nature.

[27]  A. Paterson,et al.  Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. , 2001, Plant physiology.

[28]  J Quackenbush,et al.  Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. , 2001, Plant physiology.

[29]  B. Staskawicz.  Genetics of plant-pathogen interactions specifying plant disease resistance. , 2001, Plant physiology.

[30]  S R McCouch,et al.  Genomics and synteny. , 2001, Plant physiology.

[31]  G. F. Barry.  The use of the Monsanto draft rice genome sequence in research. , 2001, Plant physiology.