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Cereal genomics

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Cereal genomics

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Cereal genomics

  1. 1. Cereal crop  FAO's definition of cereals describes these plants as annual plants which generally belong to the gramineous family, producing grains that are used for food, feed, seed and production of industrial products.  Cereal Crops:  Rice  Wheat,  Corn or maize  Barley  Millet  Sorghum  Oat  Rye
  2. 2. introduction  The economic and scientific importance of the cereals has motivated a rich history of research into their genetics, development, and evolution.  The nearly completed sequence of the rice genome is emblematic of a transition to high-throughput genomics and computational biology that has also pervaded study of many other cereals.
  3. 3.  The relatively close (ca. <50 million years old) relationships among morphologically diverse cereals native to environments that sample much of global geographic diversity make the cereals particularly attractive for comparative studies of plant genome evolution.
  4. 4.  Using the rapidly growing capabilities of several informatics resources, genomic data from model cereals are likely to be leveraged tremendously in the study and improvement of a wide range of crop plants that sustain much of the world's population
  5. 5. Japonica and Indica
  6. 6.  The sequence of the japonica cultivar Nipponbare was recently completed by a consortium of 10 countries, which comprised the International Rice Genome Sequencing Project (IRGSP)
  7. 7.  Using the rapidly growing capabilities of several informatics resources, genomic data from model cereals are likely to be leveraged tremendously in the study and improvement of a wide range of crop plants that sustain much of the world's population
  8. 8. Rice:  Rice is considered a model cereal crop because it has a relatively small genome size as compared with other cereals, a vast germplasm collection, an enormous repertoire of molecular genetic resources, and an efficient transformation system.  The scientific value of rice is further enhanced with the elucidation of the genome sequence of the two major subspecies of cultivated rice, Oryza sativa ssp.
  9. 9. Conti…..  For this reason and because of its small size, rice was promoted as a model and was chosen to be the first cereal genome sequenced.  Further, the development of large EST collections and the first inter- and intra-specific comparative studies of BAC sequences from maize, sorghum, rice, wheat and barley have increased the resolution of comparative analyses and have shown that a number of rearrangements disrupting microcolinearity have occurred during the evolution of the cereal genomes in the past 50–70 million years.
  10. 10.  development of molecular markers, and for identifying the region in the model species that might contain candidate genes responsible for a trait of interest. Rice (2n = 24), having a small genome and great economic significance, was the first grass species selected for genome sequencing
  11. 11. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Sequencing of crop-plant genomes  Reasons for sequencing rice first  Importance as crop  Largest food source for poor  Feeds half of world’s population (3 billion)  Demand likely to increase dramatically  80% of daily calories in Asia come from rice  In Asia alone, demand will increase by at least 35%.
  12. 12. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Rice genome  Smallest among grass genomes (Wheat, oat, rye, Barley, corn)  Few repetitive elements  Synteny with other grasses (recent evolution from a common ancestor approximately 50–70 million years ago)  Genetic and physical maps  Genomic resources  Over million ESTs  Efficient transformation
  13. 13. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Facts about the rice genome  Size: 430 Mbp (3.3 X Arabidopsis)  Number of genes: approximately 60,000  Repetitive elements: Most in intergenic regions versus in introns in humans  Animals use alternative splicing and plants gene duplication?
  14. 14. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics of other cereals  Maize: 3,000 Mbp  Wheat: 5,000 Mbp  Barley: 16,000 Mbp  Genome organization  Genic or gene-rich islands in the sea of retroposons
  15. 15. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Rice and Arabidopsis genomes  No large areas of synteny  80% of Arabidopsis genes have homologs in rice  Reverse not true  Only 50% of rice genes have homologs in Arabidopsis  150–200 million years of divergence (Quick change) Rice Arabidopsis
  16. 16. Wheat genome:  A U.S. National Science Foundation-funded wheat expressed sequence tag (EST) project has been studying the structure and function of the expressed portion of the wheat genome by mapping wheat unigenes to individual chromosome regions. Representative ESTs, each belonging to one of the unigenes (http://wheat.pw.usda.gov/NSF/progress_mapping.html) were used for mapping in the wheat genome utilizing 101 wheat deletion stocks, each of which contain a deletion of a defined part of a chromosome (Endo and Gill 1996), referred to as deletion mapping. As of November 2002, over 100,000 ESTs from various tissues of wheat at different stages of development have been sequenced, and 4485 wheat unigenes have been deletion mapped by this project.
  17. 17. Cereal Genome Sizes  Sorghum 1000 Mb  Maize 3000 Mb  Barley 5000 Mb  Wheat 16,000 Mb  Rice 420 Mb
  18. 18. Conti….  The wheat whole genome sequence data provides direct access to all 96,000 genes and represents an essential step towards a systematic understanding of biology and engineering .  The cereal crop for valuable traits. Its implications in cereal genetics and breeding includes the examination of genome variation, association mapping using natural populations.
  19. 19. Maize genome: The 21st century finds maize in the process of being sequenced. With an estimated 2300-2600 Mb of chromosomal DNA (6× rice and 20× Arabidopsis), of which at least 60% is retrotransposon. • the maize genome has initially been “filtered” to enhance its production(Rabinowicz et al. 1999) or low- repeat (Peterson et al. 2002a; Yuan et al. 2003) sequence—before shotgun sequencing (Whitelaw et al. 2003)
  20. 20. Cont…..  Maize (n = 10) is a recent domesticate of the tropical grass (Doebley 2004). The most recent maize whole- genome duplication happened approximately 12 Mya (Gaut and Doebley 1997).
  21. 21. Sorghum genome:  The most detailed sorghum sequence-tagged site (STS)- based map is from a cross between Sorghum bicolor (SB) and S. propinquum (SP), comprising 2512 restriction fragment length polymorphism loci that span 1059.2 cM (Bowers et al. 2003).  A total of 865 heterologous probes link the sorghum map to those of Saccharum (sugarcane: Ming et al. 1998), Zea (maize: Bowers et al. 2003), Oryza (rice: Paterson et al. 1995, 2004), Pennisetum (millet, buffelgrass: Jessup et al. 2003), the Triticeae (wheat, barley, oat, rye), Panicum (switchgrass: Missaoui et al. 2005), and Cynodon (bermudagrass: C. Bethel, E. Sciara, J. Estill, W. Hanna, and A.H. Paterson, in prep.).
  22. 22.  Sorghum was the first plant for which a BAC library was reported (Woo et al. 1994). Physical maps of both SB and SP have been constructed and genetically
  23. 23. The consensus comparative map of seven grass species shows how the genomes can be aligned in terms of "rice linkage blocks" (Gale & Devos, 1998). A radial line starting at rice, the smallest genome and innermost circle, passes through regions of similar gene content in the other species. Therefore a gene in one grass species has a predicted location in a number of other grass species. This observation has driven much sharing among researchers working on the various grass species (Phillips & Freeling, 1998).
  24. 24. Conclusion:  It can help us in comparative genomics.  Itcan also help in crop improvement.  It can also help for maintanace of better quaity crops.  Overall impact on the quality of life on earth.

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