Transcript 19 082804
Chapter 19 Genomics and Agriculture Applications of genomics approaches to agriculture © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Contents Background Agriculturally related sequencing projects Crop plant Farm animal Pathogen Genomics applied to trait improvement Breeding Transgenics and clones © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Background Agriculture looks to genomics for the next “green revolution” Reasons: Pace of traditional breeding Identify genes for useful traits Relate genetic and physical maps Protect food chain © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics applied to agriculture Approaches Similar for plants and animals Relating traits to genes Relating genetic maps to physical maps QTL analysis DNA sequence Problem of genome size Syntenic relationships ESTs © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Sequencing of plant genomes Reference plant: Arabidopsis thaliana No agricultural value Related to cabbage and mustard Reference for all plants First plant genome sequenced (Dec. 2000) Size: 130 Mbp Number of genes: 28,000 Segmental duplications Evidence for past increase in ploidy © 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 Demand likely to increase dramatically © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Rice genome Smallest grass genome Few repetitive elements Synteny with other grasses Genetic and physical maps Genomic resources ESTs Efficient transformation © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Efforts to sequence the rice genome Different efforts Public: IRGSP/Beijing Genomics Institute Private: Monsanto/Syngenta Public performed 10x coverage Two strains: Indica and Japonica Gold standard for other cereal genomes Microarray of rice used on maize RNA © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Facts about the rice genome Size: 430 Mbp Number of genes: approximately 60,000 Repetitive elements: Most in intergenic regions © 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 Only 50% of rice genes have homologs in Arabidopsis Rice Arabidopsis © 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 islands in sea of retroposons © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Sequencing strategies for grass genomes Alternative approaches to genome sequencing Methylation based Hybridization based EST collections © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics of other crop plants Tomato, potato, soybean EST collections Woody species Poplar and pine Genome organization No genic islands Candidate-gene approach © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics of farm animals Livestock farming = 30–40% of world agriculture Poultry and livestock sales in United States > $70 billion Disadvantages of genomics Large sizes of farm-animal genomes Long gestation times Difficulty of doing genetics © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics of farm mammals Pig, cow, sheep Draft sequencing Compare to mouse, rat, and human BAC libraries Physical maps EST libraries © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics of poultry No reference genome BAC libraries > 300,000 ESTs Microarrays © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Sequencing of agricultural pathogens Animal pathogens Brucella suis Infects animals, but can affect humans Genome revealed to be similar to plant pathogen Plant pathogens Problem: large size of genomes © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Bioterrorism issues Intensive agriculture raises risks of disease spread Example: outbreak of foot-and-mouth disease Knowledge of pathogen genomes Helps identify disease agent Could be used in rapiddetection technologies © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Breeding Domestication of plants and animals selected for valuable traits e.g., temperament Later, other traits selected for e.g., milk production Traits controlled by several genes For each gene, different alleles © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Quantitative traits Major traits in continuous gradient Controlled by QTLs Infinitesimal model Many genes, each with small effect Major-gene model A few genes, each with large effect Genomic nature of QTLs © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 QTL analysis QTL analysis requires genetic and physical maps Similar to association mapping in humans Relate traits to markers Or cross two subspecies with different traits Both domesticated Wild plus domesticated © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genome scan for QTLs Genome scan for QTLs in progeny Relate trait to markers Identifies interval on chromosome © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 QTL for tomato fruit size © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Marker-assisted breeding Once a QTL is found, it can be used to assist breeding Even if the nature of gene is unknown Markers on either side of the QTL can be followed during the breeding program Introgress the QTL from one subspecies into another Markers have to be very closely linked © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 QTL to gene If genome sequenced: Candidate genes in interval If genome not sequenced: Find syntenic region in sequenced genome To confirm identity: Look for mutations Microarrays and 2-D gels Transfer gene and determine consequences © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Genomics tools for breeding Polymorphic markers Microsatellites SNPs Expression approaches Microarrays 2-D gels Bioinformatics Databases © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Improvement of plant traits Stress resistance Abiotic Salinity Drought Biotic Pathogens Increased yield Decreased fertilizer utilization Improved value-added traits © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Examples of plant breeding Hybrid vigor Corn with improved yield Compare inbred parental lines with hybrids Size of tomato fruit Comparisons of wild relatives with crop plants and a QuickTime™QuickTime™ and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Improvement of animal traits Growth rate Meat quality Disease resistance Reproductive performance Behavior © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Example of animal breeding Meat quality in pigs Meat-to-fat ratio Cross Chinese Meishan pigs with European Large White pigs Meishan much fatter than European variety Identified QTL for lean meat © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Transgenic technologies Goal: rapid modification of genes responsible for traits in plants and animals Gain of function: Overexpression Ectopic expression Loss of function: Homologous recombination Antisense or RNAi © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Transgenic plant technology Tumor production Agrobacteriummediated transformation Gene inserted into Ti plasmid Agrobacterium cocultivated with plant Ti plasmid transferred into plant genome Selection with antibiotics Nopaline synthesis T-DNA T-DNA Transfer functions Ti plasmid Nopaline utilization Origin of replication Agrobacterium gall on a cherry tree © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Transformation of rice © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Transgenic animal technologies Introduction of genes directly into nucleus Microinjection Used to produce transgenic pigs, cattle, and sheep Problems: inefficiency, chromosomal insertion © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Gene knockout techniques Homologous recombination RNAi Can be combined with nuclear transfer Deleted in KO AGL5 wt genomic AGL5 KO construct agl5 KO genomic KanR KanR © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Nuclear transfer “Nuclear transfer” or “cell nuclear replacement” better than “cloning” Transfer of nucleus from adult cell to unfertilized egg with nucleus removed Or fusion of adult cell with enucleated egg Problem: abnormal development © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Animal cloning Scottish Blackface Finn Dorset Udder cell Egg cell Fuse cells with electric shock Remove nucleus from egg cell Fused cell grows into an embryo Embryo is placed in foster mother Cloned lamb is born Dolly Finn Dorset © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Pharmaceutical proteins Alpha-1-antitrypsin Applications in emphysema and cystic fibrosis Problems in isolating from humans, yeast, or bacteria Target in cell and then perform nuclear transfer © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Summary I Need for genomics approaches in agriculture Genomic sequencing Crop plant Rice Farm animal Livestock and poultry Pathogens Bioterrorism © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Summary II Genomics and breeding QTLs Traits Transgenic technologies Plant Animal © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458