1. Plant breeding aims to produce gene combinations that improve crop yield In plants as in animals sexual reproduction involves a fusion of gametes (sex cells) produced by male and female sex organs. The male anthers produce pollen grains consisting of 3 haploid cells, one of which is the sperm cell. The female ovaries contain embryo sacs that each have one haploid egg cell. Pollination results in fertilization (union of gametes) and the formation of a diploid embryo. Meiosis which involves chromosome pairing and recombination of DNA strands is key to the formation of haploid gametes. If chromosomes can’t pair, plants are sterile.

2. A plant species is not strictly defined by the inability of two individuals to routinely produce offspring that is fertile; interspecific hybridizations do occur naturally and sometimes produce fertile offspring. Norman Ellstrand

3. The importance of Plant Breeding: Plant breeders created the crop varieties that made it possible to increase harvest yield (tons/hectare). This activity started in earnest in the developed countries in the 1920s and in the developing countries in the 1950s (Green Revolution). What would the world look like (area planted to crops) without plant breeding? Norman Borlaug 50% of these in- creases are due to better varieties (genetics) and 50 % to more “inputs” (water, fertilizer, weed control, pest control).

4. Plant breeders define their selection criteria. New Green Revolution varieties were selected for specific characteristics: Short stems Plants not dependent on day length for flowering (flowers any time of year) Plants responsive to nitrogen fertilizer Disease resistance All genetic material was freely available and exchanged between partners.

5. Even after much breeding certain crops perform best in certain climatic/soil areas. That is where they are grown. The areas for corn (originally from Mexico) and soybeans (domesticated in China) overlap, but sorghum (from Africa) is grown in a different area. Wheat (from the Middle East) is different again (not shown). Yield trials must be done in many different places at once if companies want to sell seeds to farmers in the entire area.

6. Breeding adapts plants to different climatic conditions In the northern hemisphere, winter wheats are planted in the fall, from September through December. Winter wheat sprouts before freezing occurs, then becomes dormant until the soil warms up in the spring. Persistent snow cover might be dis- advantageous; however, winter wheat needs a few weeks of cold before being able to flower. The wheat grows and matures until ready to be harvested by early July. Winter wheats are hard wheats and have more protein than softer spring wheats. Winter wheats are used for yeast breads. Spring wheat is any kind of wheat sown in the spring. Spring wheat has less protein than winter wheat and is used for cakes and other baked goods.

7. Some traits are encoded by single genes, others, called quantitative traits, by multiple genes. Disease resistance is often encoded by a single gene and transfer by introgression of that locus from a wild relative or land race to the cultivar will make the cultivar resistant. You select for phenotype (disease resistance) in the field. Many traits (yield, flowering time, drought resistance) are encoded by multiple genes situated at different places on the chromosomes and are called quantitative trait loci (QTLs). Transferring QTLs by introgression (back-crossing is more difficult because differences are smaller and not + and - (like disease resistance), but introgression can be facilitated by molecular markers and chromosome maps.

8. Introgression or back crossing With each subsequent backcross generation, there are fewer genes from the red parent. Each time you select in the field for the phenotype you are looking for. In the 7th generation you end up with 1.5 % of the red genome (400 genes) and with the crucial genes that encode the desired phenotype. However, because of crossing over it does not go down exactly as 50, 25, 12.5, 6.25, etc in all individuals. % of each genome varies considerably among individuals. Molecular mapping allows you to determine the % and if the locus you are interested in is present. But… how do you choose the right progeny at each step? Molecular maps and marker assisted selection are crucial, but you need to know the markers associated with your trait. Cultivar Wild relative

9. This is an “old-fashioned” linkage map. New linkage maps are made exclusively with unique short molecular probes called CAPs (cleaved amplified polymorphic DNAs). Linkage means that when you make crosses and you look at the progeny, certain traits (or molecular markers) are linked and do not segregate.

10. Screening of existing genotypes (landraces) for use in breeding programs. Some traits or phenoptypes can simply be identified and the seeds distributed to farmers. For others, introgression may be necessary. Wheat genotypes on low P calcareous soils Soybean genotypes on low P acidic soils Calcareous (kal′ker·ē·əs)soils have high levels of calcium and magnesium carbonate, with a pH of 7.6 to 7.8, which is too high for optimal growth of most crops. Iron is not available at high pH. Acidic soils with a pH of 5.0 to 5.5 are found in many tropical regions and are often highly weathered. The low pH solubilizes aluminum from the aluminosilicate soil minerals, which is toxic to the plants.

11. Genetic biodiversity in land races and wild relatives of crops has barely been exploited. Plant libraries of recombinant inbred lines (RILs) and introgression lines (ILs) are needed to screen for phenotypes and exploit structural and functional genomic information. Lycopersicon peruvianum Lycopersicon pimpinellifolium

12. Lycopersicum esculentum Lycopersicum peruvianum X One of the many children is bigger! Finding interesting genes in wild relatives

13. A plant library of introgression lines (ILs) Introgression of Indica rice chromosome segments into Japonica rice. Only 3 of the 12 chromosomes are shown. A library of 88 “lines” covers the entire rice genome. These lines can be tested in the field, and a specific trait (e.g. drought resistance of Indica rice can be assigned to a specific region of the Indica genome. You won’t know exactly which gene, because each segment has 50-200 genes. Making such a plant library, in combination with chromosome mapping is a big job!