PLANT BREEDING: CAN METABOLOMICS HELP?

Transcription

1 PLANT BREEDING: CAN METABOLOMICS HELP? Carlos Muñoz Schick Ingeniero Agrónomo, M.S., Ph.D. UNIVERSIDAD DE CHILE Facultad de Ciencias Agronómicas

2 OUTLINE OF THE PRESENTATION Origin of Plant Breeding Domestication of crops Importance of Plant Breeding A little bit of history Clasical method of genetic improvement Mendelian vs quantitative traits Bottlenecks in plant breeding Emergence of modern biotechology Metabolomics from the breeder's view Is metabolomics a new breeding tool? Conclusions 22/03/2012 2

3 PLANT BREEDING CAN BE TRACED BACK TO THE ORIGIN OF AGRICULTURE Agriculture probably started to years ago when man realized that he can no longer rely on hunted animals or plants gathered from the wild. Agriculture started in the most advanced ancient cultures, located in the tropical and subtropical regions of Asia, Africa and America. 22/03/2012 3

4 DOMESTICATION From the Latin domesticus, that comes from domus = house. Process by which wild animals or plants are subjected to the domain of man to transform them into useful. Species were domesticated to: produce food (cereals, legumes, fruits, vegetables, meat, milk, egg). Produce raw materials (cotton, wool, silk). Produce working animals (traction, transport, scientific research or enjoyment). Produce ornamental plants. and... many other uses. Domestication is a permanent endeavor that continues to this days. 22/03/2012 4

5 PERIOD OF DOMESTICATION OF SOME CULTIVATED SPECIES ESPECIES ORIGIN PERIOD Fig West Asia years BC Rice Southeast Asia years BC Potatoes South America years BC Corn Central America years BC Wheat West Asia years BC Avocado Central America years BC Olive West Asia years BC Sunflower Northamérica years BC Eggplant Asia 100 years BC Blueberries Northamérica 1900 years AC Kiwifruit China 1950 years AC 22/03/2012 5

6 NUMBER OF DOMESTICATED SPECIES Of over 300,000 species of vascular plants on Earth, only 300 have been domesticated and less than 30 are the basis of human food. Only 12 per cent of the plant families contain domesticated species. A few families (Gramineae, Leguminosae, Solanaceae, Rosaceae) provide the bulk of the species of agricultural interest. 22/03/2012 6

7 IMPORTANCE OF DOMESTICATED SPECIES Only 30 crops provide 95% of the energy (calories) and proteins of the human diet. Only wheat, rice and maize provide more than 50% of the global energy intake, and other 6 crops (sorghum, millet, potatoes, sweet potato, soybean and sugar cane) carries the total energy intake to 75%. These figures show the enormous potential that exists to domesticate new species for use by man. 22/03/2012 7

8 GENETIC IMPROVEMENT IS RESPONSIBLE FOR, AT LEAST, 50% OF INCREASE IN CROP YIELDS Source: FAO 22/03/2012 8

9 THIS IS WHAT HAS BEEN ACHIEVED IN MAIZE 22/03/2012 9

10 DEFINITION OF BREEDING OR GENETIC IMPROVEMENT Genetic improvement is the acceleration of the natural evolution of the species, to create new varieties that have advantages for their cultivation, use and/or consumption by humans and/or domestic animals. This acceleration of evolution is achieved by applying the laws of genetics, evolution and the probabilistic. When the genetic improvement is applied to plants, it is called plant breeding. 22/03/

11 HISTORY OF GENETIC IMPROVEMENT Initially, breeding was intuitive. The primitive man just selected the best plants from where they were naturally growing. This system of improving was used by almost 10,000 years, and resulted in the domestication of most of the cultivated species. Only by the end of the 19 th Century, when sexuality was discovered in plants, modern breeding begun. 22/03/

12 SOME MILESTONES IN GENETIC IMPROVEMENT 1694 Camerarius discovers the existence of separate sexes in plants (Monoecious) and suggests interbreeding for hybrids Mather noted natural crosses in maize Kohlreuter showed that the offspring of hybrids showed characteristics of both parents, and he developed the first hybrids in tobacco Darwin published "The origin of the species" where he postulates his theories on natural selection and evolution Mendel makes first scientific experiments through hybridization, which later made the "laws of Mendel Borlaug received the Nobel Peace Prize by the green revolution 22/03/

13 TRAITS MOST COMMONLY MANIPULATED THROUGH GENETIC IMPROVEMENT Characters of interest to farmers Resistance to diseases and pests Use of water and fertilizer Adaptation to conditions of climate and soil Yield Characters of interest to consumers shape, size, color and flavor Food composition Contents of proteins, fats, sugars, etc. Contents of vitamins or other factors associated with the health of persons Non-food uses Biofuels Bioremediation drugs and other molecules of high value 22/03/

14 CLASICAL PLANT BREEDING METHODOLOGY Discovery (and creation) of genetic variability Genebanks Induced mutagenesis Combination of available variability interspecific crosses Crosses between species The role played by the Law of Probabilities, Mendel s Laws and quantitative genetics Selection of individuals with characters of interest Darwin s Laws of natural selection The role of experimental designs and Biostatistics Multiplication of selected varieties Seed multiplication and its technologies Cloning (grafting, rooting of cuttings, etc.) Distribution and marketing of the created varieties The new role of intellectual property rights. 22/03/

15 CONTROLED CROSSES 1. Gets the parent pollen. 2. Deposit the pollen on the pistil of the mother. 3. Allowed for seed formation and harvesting the seed 4. Sowing the seed for segregant generation. 22/03/

16 RECURRENT SELECTION: HOW IT WORKS X 0 S X s Select best 10% of C X 1 R /03/

17 MENDELIAN VS QUANTITATIVE TRAITS Quite early R.A. Fisher (1930) realized that most agronomic traits (yield) do not exhibit mendelian hinreritance He proposed that some traits result from the action of many genes with small effects This moved the focus from the effect of single genes to the cumulative effects of many genes on phenotypes But breeding methods continued to rely on phenotypes for selection His hypotesis resulted in the development of what is now called quantitative genetic 22/03/2012 CMM/Biosigma Workshop: Insights on metabolomics and its applications 17

18 SOME COMPLICATING FACTORS IN SELECTION Genotype-by-environment interaction Use of proper experimental design and analyses of the experiments Need for trails at different locations and in different years Life cycle of the species Generation intervals Juvenility Traits that are difficult to evaluate Plant architecture Chilling requirement 22/03/

19 PREDICTING GENETIC PERFORMANCE A longtime goal for breeders has been to have tools to predict the behavior of the segregants that are generated from particular parents or group of parents. These predictions would be very useful to improve the efficiency of breeding programs. The advent of genomics raised great hopes, because markers based on DNA and mrna were free of genotype-environment interaction 22/03/

20 THE EMERGENCE OF MODERN BIOTECHNOLOGY Break the limits for gene transfer (appears the transgenics). Significantly increases the capacity to make more effective genetic improvement and efficient (molecular markers appear). Enhances the ability to identify useful genes (Genomics appears). Provide us with tools to fully understand biological systems (other Omics appear). 22/03/

21 TRANSFORMATION USING Agrobacterium A. tumefaciens causes a disease in Dicot species (Crown Gall). It has a plasmid (Ti) that inserts part of it on the chromosome of the host cell. Agrobacterium Plásmido Ti inductor de tumores contiene oncogenes (genes onc) T-ADN Núcleo Cromosoma cromosoma célula vegetal tumores Proliferación de hormonas del crecimiento. Se forman tumores en las zonas de la lesión 22/03/

22 CONVENTIONAL BREEDING DNA is a chain of genes which combine randomly Donor Plant Comercial Variety New variety Gene of interest X = Cross Gene of interest BREEDING USING TRANSGENICS Biotechnology enables the aggregation of specific genes Gene of interest Commercial variety New variety = Transgenic s Gene of interest 22/03/

23 COMPARISON BETWEEN TECHNIQUES CONVENTIONAL BREEDING LEVEL Organism Molecule NUMBER OF GENES Thouthand genes Few genes CERTENTY LIMITATIONS PRECISION Gene characterization not needed Gene exchange within species Many genes recombine TRANSGENICS Genes fully characterized No limit to gene exchange Only few genes recombaine 22/03/

24 MARKER-ASSISTED BREEDING (I) It is the process whereby a DNA "marker" is used to select a character of interest, difficult or expensive to measure, indirectly. They are particularly useful in characters which are controlled by many genes (QTLs). Today, the most used markers are based on unique sequences of DNA that are present near the gene or locus of interest. These sequences can be identify using different techniques (RFLPs, RAPD, AFLP, DAF, SCARs, SSR, SNP, etc.). 22/03/

25 MARKER-ASSISTED BREEDING (II) The technique involves construction of genetic maps where pehotypic traits are located along with molecular markers Co-inheritance of phenotype and genotype reveals linked markers These can then be used in fast-track breeding programmes Genotype analysis performed at seedling stage More rapid, and higher throughput than phenotypic selection Plants with correct genotype can then be subjected to phenotypic verification 22/03/

26 GENOMICS AND LINKAGE MAPS 22/03/

27 THE OMICS ERA DNA Genomics mrna Proteins Transcriptomics Proteomics Metabolites Metabolomics Phenotype Phenomics 22/03/

28 THE Arabidopsis GENOME SEQUENCE: A CATALOGUE OF ALL GENES OF THE SPECIES The Arabidopsis Genome Initiative. Nature (2000)

29 A LOT OF WORK YET TO BE DONE POR MOST AGRICULTURAL SPECIES Omics technologies are very useful to build catalogs, but a lot of work is needed to identify cause-effect relationships Linking genes with phenotypic variation is cumbersome and techniques varies depending on the reproduction system of each species (allogamous vs autogamous species) and breeding method used (inbred lines and F1 hybrids vs open pollinated cultivars). 22/03/

30 A VARIETY OF APPROACHES MAS: MARKER-ASSISTED SELECTION Plants are selected for one or more (up to 8-10) alleles MABC: MARKER-ASSISTED BACKCROSSING One or more (up to 6-8) donor alleles are transferred to an elite line MARS: MARKER-ASSISTED RECURRENT SELECTION Selection for several (up to 20-30) mapped QTLs relies on index (genetic) values computed for each individual based on its haplotype at target QTLs GWS: GENOME-WIDE SELECTION Selection of genome-wide several loci that confer tolerance/ resistance/ superiority to traits of interest using Genomic Estimated Breeding Values (GEBVs) based on genome-wide marker profiling 22/03/

31 THE ROLE OF METABOLOMICS (I) Metabolomics, given its early development, have not yet provided new tools that allow us to predict the performance of the progeny based on parental characteristics. Personally, I see it more as a powerful tool for phenotyping, but like with other tools, much effort will be required to find the cause and effect relationships so necessary for selection based on molecular markers. In other words, integration with other genomic tools is still a necessity. This is because the metabolites are subject to strong genotype environment interaction. 22/03/

32 THE ROLE OF METABOLOMICS (II) However, as a formidable phenotyping tool, it will provide new means for the objective measurement of a lot of quality characteristics (flavor, aroma) that are now directly assessed by the breeder or hopefully by trained tasting panels. Also, components of interest (antioxidants) can be more precisely determined than with previous analytical methods. Crop compositional traits. Also, it will provide ways to better understand some characters of the traits and therefore design a better breeding strategies. Better evaluation of Genetic engineered crops. 22/03/

33 THE PROBLEM WITH SOME SPECIES An increasing amounts of information is becoming available on the use of metabolomics for breeding in model plants (Arabidopsis, tomato) and crop plants where its genetics is well known and there is plenty of phonotyping information (Corn). However in other species like fruit crops, forest trees, forages, etc.), there is limited information available, so the practical use of metabolomics and other omics is not a trivial task, and much information is needed before this technology become a practical tool for the generation of new cultivars. 22/03/

34 THE END THANKS A LOT!