Plant Breeding as an Art and Science

1. Plant Breeding as an Art and Science Origins of Agriculture Harlan (1992) outlined six regions in which agricultural origins occurred We will examine, briefly, the Near East and Meso-America. The Near East serves as a general introduction to self-pollinated species, focusing on common wheat (Triticum aestivum, 2n=6x=42, genomes ABD) Meso-America serves as a general introduction to cross -pollinated species focusing on corn (Zea mays L., 2n = 2x = 20).

2. The Near East At the eastern end of the Mediterranean Sea, across a broad arching zone of grasslands and open oak-pistachio woodlands called the Fertile Crescent the world’s first agricultural economies emerged between 10,000 and 8,000 years ago (the Neolithic revolution). Landraces of Self-Pollinated Species The heterogeneous populations grown by Neolithic farmers are called landraces—heterogeneous cultivated forms that evolved from natural populations of plant species.

3. Landraces of Self-Pollinated Species Wheat is a self-pollinated species with low levels of outcrossing. Any given plant in a Neolithic farmer’s field was homozygous at most, or all, loci. In general, seeds harvested from any individual plant faithfully reproduced the parental genotype the following generation. This constancy was maintained through generations in the absence of outcrossing to a different genotype or the occurrence of spontaneous mutations. If a second plant was considered in this Neolithic farmer’s field, the same constancy of genotype from generation to generation occurred. But there was a noticeable difference--this second plant likely had different alleles at many loci when compared locus-by-locus with the first plant.

4. Landraces of Self-Pollinated Species At harvest, the seeds from individual plants were not kept separate, but a conglomeration of seeds from all genotypes in the field was bulked into a seed store. The following season a random sample of this seed was planted. This random sample of seed contained a random sample of the genotypic array found in the field the previous season.

5. The Composition of an Autogamous (Self-Fertilizing) Landrace Population • Contain many genetically distinct homozygous plants—e.g., AABBCC; AABBcc; aaBBcc. They have similar alleles at corresponding loci on homologous chromosomes. • Although these plants exist side-by-side, they remain more or less independent of each other in reproduction. • Plants in these populations are generally fully vigorous homozygotes. Deleterious recessives are rare and are eliminated rapidly. • 4. Prolonged inbreeding is tolerated in the absence of inbreeding depression. •  5. Local adaptation of individuals is high. Reproductive isolation shields adapted gene complexes from breakup through recombination. • As a result, individuals have a low flexibility of response to a changing environment.

6. Homozygous genotypes do not imply a homogeneous population. Landraces of self-pollinating species contain a preponderance of homozygous plants, but they are not homogeneous. Homogeneity in a population exists only if all individuals have the same genotype. Individual loci can be homozygous or heterozygous in a homogeneous population.

7. Essentialism in BiologyBefore evolution was developed as a viable scientific theory, there existed an essentialist view of biology that posited all species to be unchanging throughout time. Some religious opponents of evolution continue to maintain this view of biology. The bottom line was--essentialists could not handle intraspecific variation; as a result, they could never be plant breeders.

8. Confusion Over the Significance of Intraspecific Variation Carl Von Linnaeus (1707-78) Species Hybridizers Newton’s physical laws were exact and dealt in constancy of the universe and its systems, thus scientists assumed that biological laws must have similar rigid descriptions.

9. The Plant Breeders • Individual plant selections were made within landraces and seed was used to form a) a pure line or b) an improved landrace • 2) Intraspecific crosses were made between cultivars differing in one or two characteristics.

12. The Swedish Seed Association The organization that has received the most notoriety for utilizing the Pure Line Method on a grand scale is the Swedish Seed Association at Svalof in southwestern Sweden. Under the direction of Nilson in the 1880s, a large-scale program of selecting single heads from landraces followed by progeny tests was initiated. Early Development of Cultivars Through Hybridization Pringle released an oat cultivar in 1875 in Vermont and Jones released a wheat cultivar in New York in 1893 that resulted from artificial hybridizations. Farrer had notable success during the same period in Australia. Following the rediscovery of Mendel’s laws governing particulate inheritance, the popularity of hybridization to develop breeding populations for cultivar development increased

13. The Influence of Darwin and Mendel on Plant Breeding Darwin began the age of population thinking. It replaced the abstract or metaphysical view of variation of the Essentialist with the materialist view of the Darwinist by focusing on the variation among organisms as a pivotal fact of nature. Darwin considered intraspecific variation to be the cornerstone of evolution. The variation among members of a single species was no longer considered an annoying distortion of the ‘ideal’ divine creation. Darwin believed that evolution was simply the application of the plant and animal breeder’s activities to the mechanisms of nature as a whole. Mendel put emphasis on the variation among the offspring of his crosses rather than on an average description of them. He divided the progeny into categories, counted the number of offspring in each category, and then calculated ratios of numbers of individuals in each category. Unlike his predecessors who seemed to be satisfied to just obtain progeny from crosses, Mendel’s approach considered the whole population and sought out the underlying mechanisms controlling the variation in the populations.

14. At the turn of the century the stage was set for the emergence of scientific plant breeding with the joining of Darwinian theory on the reproductive advantage of better adapted individuals and Mendelian interpretation of the inheritance of those adaptations. One of the triumphs of genetics is that it can explain both the constancy of inheritance and its variation. It explains the apparent contradiction--that individuals resemble their parents and differ from their parents. It contains elements for everyone--overall constancy for the Essentialist, yet the constancy is tempered by variation for the Darwinist Organisms resemble their parents (thesis) Variation in progeny Genetics (antithesis) (synthesis)

15. The Pure Line Theory His first conclusion was that selection for seed weight was effective. His second conclusion was that the original landrace consisted of a mixture of homozygous plants

16. Thus, his third conclusion was that the within-line phenotypic variation was environmental in nature and further selection within a pure line will not result in further genetic change Johannsen’s results clarified the difference between phenotype and genotype and gave selection a firm scientific basis.

17. Meso-America--A General Introduction to Cross-Pollinated Species We now shift focus to corn and discuss a cross-pollinated breeding system. Current evidence suggests that corn was domesticated from the annual wild grass teosinte (Zea mexicana) in the Balsas River drainage in south central Mexico (Harlan, Fig. 11-2; Galinat, Fig. 2). Mimicking the situation for self-pollinated species, many distinct types or races of corn evolved under human and environmental selection as the species spread through North and South America.

18. Monoecious: Staminate (Tassel) and Pistillate (Ear) inflorescences

19. Landraces of Cross-Pollinated Species Corn is a cross-pollinated species with high levels of outcrossing. Any given plant in an Aztec farmer’s field contained both heterozygous and homozygous loci. Heterozygosity occurred only at the loci for which more than one allele was present in the landrace population. The frequency of heterozygosity at a locus depended on the frequency of the different alleles in the population. Seed harvested from any individual plant in an open pollinated landrace did not faithfully reproduce itself the following season It was half-sib seed and the plants it produced the following generation represented the female parent plus the array of male parents that contributed pollen to the female’s silks. The following season a random sample of these seeds was planted. This random sample contained a random array of the genotypes found in the field the previous season.

20. The Composition of an Allogamous (Cross-Pollinating) Population 1. Comprised of a highly heterozygous and heterogeneous plant population--e.g., AaBbcc:AABbCc:AaBBcc:etc. 2. A consequence of open-pollination is the retention of recessive alleles in the population.

21. 3. An open-pollinated landrace has the best potential for evolutionary flexibility. This diversity is measured by the number and frequencies of alleles at each locus. One estimate of Gene Diversity or Polymorphic Index at a locus is:   n  Pi(1-Pi) i=1  where n = number of alleles at the locus and Pi the frequency of the ith allele. A locus with two alleles present at frequencies of 0.9 and 0.1 has a polymorphic index of 0.18. If the frequencies are more equitable at values of 0.5 each, say, the diversity measure increases to 0.5. How does a population with three alleles each present at a frequency of 0.33 rate relative to the former two?

22. Open-pollination in a heterozygous population promotes • effective recombination between linked alleles . • Approximating linkage equilibrium

23. Early Corn Improvement in the United States ( see Troyer (1999). Crop Sci. 39: 601-625) The early corn breeders all practiced a form of mass selection through the selection of desirable open-pollinated ears from superior plants Some open-pollinated cultivars were developed by crossing populations and conducting mass selection on the resulting progenies, eg. Reid Yellow Dent Blount was probably the first to conduct mass selection while controlling the pollen source. He utilized this approach during the 1870s in Tennessee.

29. It took approximately 15 years for the world’s population to grow from 4 to 5.3 billion. In 25 years the population will increase another 55% to 8.2 billion. By the last decade of your professional careers the world will be consuming twice the calories per day that were consumed when you were 10 years old.

30. Scientific advance good for society was unquestioned Nuclear age – watershed in public opinion Criticism of Green Revolution Southern Corn Leaf Blight epidemic. Genetic male sterility system GMO’s, Terminator technology, control of plant genetic resources, patenting life forms, etc., etc. ‘First the seed’ – Kloppenburg (1988) ‘Shattering’ – Fowler and Mooney (1990) The Frankenfood Myth: How Protest and Politics Threaten The Biotech Revolution - Miller and Conko (2004)

31. Plant Breeders – who employs them? Plant Variety Protection Act (PVPA), 1970: Cultivar owner determines who may market seed. Farmers could save their own seed, but problems arose with ‘Brown Bagging’, or the sale of excess seed Plant Variety Protection Act (PVPA), 1994: Limits quantity of seed an individual may save to the amount of seed needed to plant own farm. If plans change, can sell seed only with permission. Utility Patents: Protection of genetically engineered cultivars. May not save, clean or sell seed

32. Frey (1996); 2205 science person years employed in plant breeding Private sector 68% $340m $148-290,000 per SY University 24% $156m $293,000 per SY USDA 8% $153 $300,000 per SY Agronomic crops (71%), Horticultural crops (29%) Corn (~30%), soybeans (7%), wheat (6%), cotton (6%), temperate fruits and nuts (5%), tomato(4%), forage legumes(4%), and ornamentals(4%) Cultivar development (65%) Germplasm development (18%) Basic research (17%)

33. Consultative Group on International Agricultural Research 1000 scientists of 60 nationalities working in 40 developing countries