Crop Improvement

1. Crop Improvement

2. Sexual and Asexual Reproduction Long term survival requires reproduction. Even the longest-lived organisms are less than 10,000 years old. Cellular machinery wears out, or gets clogged with waste products. Environmental conditions change Plants often reproduce asexually, through cuttings or runners or buds (e.g. potatoes). The resulting plants are clones: they are genetically identical to the parent. Used to preserve good combinations of traits. Sexual reproduction is also found in plants, and in all animals. Sexual reproduction means combining genes from two different parents, resulting in new combinations of genes. Each parent contributes a randomly-chosen half of their genes to the offspring. This can be a good thing, because some new combinations will survive better than the old ones. It can also be bad: lack of uniformity in the offspring.

3. Vegetative Propagation • Plant meristems are usually capable of generating all the tissue types found in a plant. • Some plants naturally propagate vegetatively, usually through modified stems: flower bulbs, corms, and rhizomes; suckers; stolons (runners). • Artificial vegetative propagation can be down by taking a cutting from the stem (containing at least one meristem) and encouraging it to grow roots. • Citrus trees use “nucellar embryony”. Some of the cells surrounding the ovule (nucellus cells) spontaneously turn into embryos when the ovule is fertilized by pollen. The seeds contain both the regular embryo derived from male x female, and also the nucellar embryos (maternal genes only) • More advanced methods include grafting and tissue culture.

4. Grafting • Grafting is common among fruit trees: the stem tissue of one plant is fused to a stem from another plant. • Commonly done: a hardy rootstock is grafted to the stem of a better fruit variety. • Another method: attaching a bud form one plant to the stem of another. You can produce an apple tree bearing several different types of apple this way. • The cambium layers of the two plants being grafted need to be brought into contact. This allows the xylem and phloem to connect to each other • It is possible to graft a potato rootstock to a tomato top, so both underground potato tubers and aboveground tomato fruits are formed on the same plant.

5. Tissue Culture • A more modern way of propagating plants vegetatively is through tissue culture. This is often called “micropropagation”. • Useful for genetically engineered plants, for plants that don’t set viable seeds, and for rare and valuable plants. • Unlike animals, many plant cells, especially in the meristems, are totipotent: they can generate an entire plant under the proper conditions. • Pieces of the plant are cut out and placed on an agar medium under sterile conditions. • Manipulating plant hormones is the key: an excess of auxin produces roots, and excess of cytokinin produces shoots, and a balanced mixture allows the cells to multiply as an undifferentiated mass of cells called a callus. • Pieces of the callus can be cut out and propagated indefinitely.

6. Sexual Reproduction • Diploid: having 2 copies of each chromosome, one set from each parent. • Humans have 46 chromosomes, 23 from each parent. • Almost any organisms you can see: plant, animal, fungus, is diploid. • Haploid: having only 1 copy of each chromosome. • Sperm and eggs (=gametes) are haploid • moss, a primitive plant, is haploid for most of its life • Plants, animals, and other eukaryotes alternate between haploid and diploid phases. This is called alternation of generations.

7. Life Cycle Diploid organism generates haploid gametes using the process of meiosis. The gametes combine during the process of fertilization to form a new diploid organism. In animals, the haploid phase is just one cell generation, the gametes, which immediately do fertilization to produce a diploid zygote, the first cell of the new individual. In plants, the haploid phase is several cell generations at least. Lower plants are mostly haploid Higher plants are haploid for only a few cell generations The diploid plant is called the sporophyte, and the haploid plant is called the gametophyte.

8. Genetics The science of genetics is devoted to understanding the patterns of how traits are inherited during sexual reproduction. It was founded by Gregor Mendel in the 1850's, using pea plants. Despite the obvious differences, humans and peas have very similar inheritance patterns. The fundamental observation of genetics: within a species, there are a fixed number of genes, and each gene has a fixed location on one of the chromosomes. This allows genes to be mapped: a gene's neighbors are always the same. Most species of higher organism have about 25,000 different genes distributed onto 10-30 different chromosomes.

9. Genetics Alleles. Many genes have several variant forms, which are called alleles. For example, a gene the produces color in the flower might have a purple allele and a white allele. These alleles are designated P and p. Differences in alleles are what makes each human different from all others True-breeding lines. If you cross close relatives with each other for many generations, eventually all the offspring look alike. Mendel started with several true-breeding lines, which differed from each other in 7 distinctive characteristics

10. Genetics • In many plants, you can self-pollinate: cross the male parts of a plant with the female parts of the same plant. • In this case, both copies of any given gene are identical. This is called homozygous. The plants are homozygotes, either PP (purple) or pp (white). • The closest cross you can do in animals is brother x sister. • Hybrids. If you cross two true-breeding lines with each other and examine some trait where the parents had different alleles, you produce a heterozygote: the two copies of the gene are different. • Surprisingly, you often find that the heterozygote looks just like one of the parents. The Pp heterozygote is purple, just like its PP parent. • This is the F1 generation in the diagram.

11. Genetics Dominant and recessive. If a heterozygote is identical to one parent, the allele from that parent is dominant. The allele from the other parent is recessive. That is, the heterozygote looks like the dominant parent. This is why we say purple is dominant to white, and give purple the capital letter P. Phenotype and genotype. Phenotype is the physical appearance, and genotype is the genetic constitution. The heterozygote in the previous paragraph has the same phenotype as the homozygous dominant parent (i.e. purple flowers), but a different genotype (the heterozygote is Pp and the parent is PP).

12. Genetics • Now we want to move to the next generation, by self-pollinating the heterozygotes. • When a heterozygote undergoes meiosis to produce the haploid gametes, half are P and half are p. • These gametes combine randomly, producing 1/4 PP, 1/2 Pp, and 1/4 pp offspring. • Since PP and Pp have the same phenotype, 3/4 of the offspring are purple and 1/4 are white.

13. Independent Assortment • Much of Mendel’s work involved pairs of genes: how do they affect each other when forming the gametes and combining the gametes to form the next generation? • Simple answer: in most cases pairs of genes act completely independently of each other. Each gamete gets 1 copy of each gene, chosen randomly. • Two genes: • 1. seed shape. Dominant allele S is smooth; recessive allele s is wrinkled. • 2. seed color. Dominant allele Y is yellow; recessive allele y is green. • Heterozygous for both has genotype Ss Yy, which is smooth and yellow. Gametes are formed by taking 1 copy of each gene randomly, giving ¼ SY, ¼ Sy, ¼ sY, and ¼ sy. • These gametes can be put into a Punnett square to show the types of offspring that arise. • Comes out to 9/16 smooth yellow, 3/16 smooth green, 3/16 wrinkled yellow, and 1/16 wrinkled green. • 3/4 are yellow, 1/4 are green, and 3/4 are round, 1/4 are wrinkled

14. Continuous Variation • Many traits don’t seem to fall into discrete categories: height, for example. Tall parents usually have tall children. Short parents have short children, and tall x short often gives intermediate height. In all cases, wide variations occur. • Simple interactions between several genes can give rise to continuous variation. Also: variations caused by environment, and our inability to distinguish fine distinctions lead us to see continuous variation where there actually are discrete classes.

15. Linkage • Most pairs of genes assort independently. • However, if two genes are close together on the same chromosome, they are said to be linked, which means the genes don’t do into the gametes independently of each other. • The closer two genes are, the more the parental combination of alleles stays together. This relationship can be used to make maps of genes on chromosomes.

16. Lessons from Genetics • Inheritance is controlled by a relatively small number of distinct objects: the genes • Genes are in fixed locations on chromosomes, and they are inherited by a few simple rules: • Each gamete gets one of the two copies of each genes, chosen randomly • Most genes are inherited independently of each other • Genes close together on chromosomes are usually inherited together (linkage) • Genes are usually passed from parent to offspring without change • They are not affected by the events of our lives: there is no “inheritance of acquired characteristics” (Lamarck) • But, sometimes random changes (=mutations) occur in individual genes • The physical characteristics (phenotype) of an individual is determined by the interaction of genes with each other and with the environment • Dominant vs. recessive, for example • But often in more complex ways

17. Methods of Crop Improvement • The idea that we can improve the inherited characteristics of crop species is fundamental. Very few of the plants we use are unmodified wild plants: most of them have been modified to make them easier to grow and harvest, and to increase the quality and quantity of the desired product. • We will see many examples of crop improvement this semester. Here are some of the basic methods used.

18. When Asexual Reproduction is Impossible • Maize ( and other cereal grains) only reproduces sexually. How can good combinations of traits be preserved? • The simplest approach: inbreeding. • Self-pollinate for many generations: the plants become almost completely homozygous • They are now a pure-breeding line, in which all plants are genetically identical. • Problem: inbred plants are low yielding, sickly, small, and weak. This is called inbreeding depression. • Many genes have alleles that are recessive and which cause bad effects when they become homozygous : recessive deleterious alleles. • The positive side of inbreeding depression: the plants that survive inbreeding have had most of their bad alleles bred out.

19. Hybrid Vigor • Inbreeding doesn’t work as a method to preserve good sets of genetic traits, because of inbreeding depression. • However, if you make a hybrid between 2 inbreds, the resulting offspring are genetically uniform. • Each hybrid offspring gets the exact same alleles from the inbred parents as every other hybrid offspring. • The hybrids are genetically identical, but heterozygous • Hybrids show hybrid vigor. They are stronger and healthier than the inbred parents. • So, by first inbreeding to purify the genes, then crossing inbred to make a hybrid, you get the benefits of genetic uniformity as well as the benefits of being heterozygous. Left: elite inbred B73; Right: elite inbred Mo17 Center: B73 x Mo17 hybrid

20. Hybrid Corn • One of the major developments in agriculture during the early 20th century was scientific plant breeding based on Mendel's genetic principles. • Corn yield has increased 5-10 fold since 1900 because of this. • Traditional method: save the best seed to plant the previous year. Leads to slow improvement.

21. Single Gene Traits and Mutation • Single gene traits. Many useful traits are controlled by a single gene. Spontaneous mutations can lead to important, abrupt changes • A good example: sweet corn. The recessive mutation su (sugary) produces kernels that are 5-10% sugar. But, only when homozygous: the non-sugary allele (Su) is dominant. • Single gene mutations occur rarely, but often enough so that observant people notice and propagate them. • Sweet corn was recognized and propagated by several Native American tribes. The Iroquois introduced it to European settlers. • Mutation rate: 1 in 10,000 to 1 in 1,000,000 plants. • Artificially-induced mutation occasionally works, but most are spontaneous. • Single gene traits are inherited in a Mendelian fashion: • each individual carries one copy of the gene from each parent, • the relationship between phenotype (sweet vs. starchy corn) and genotype (homozygous or heterozygous) is determined by dominance vs. recessiveness.

22. Polygenic Traits and Selection Polygenic traits. Many traits are controlled by many genes, each of which contributes a small amount to the phenotype. Grain yield is a good example: lots of genes contribute to this. Such traits respond well to selection. In the simplest sense, selection means using the best seeds to start the next generation. If this is done consistently, the crop slowly improves over many generations. Genetic research has led to an understanding of what happens during selection. This allows much faster and more effective selection than just saving the best seeds. This is often called “conventional breeding” or “traditional plant breeding”. It has been the main way crops have been improved for a long time.

23. Polyploidy • Normal diploids have 2 copies of every chromosome. Sometimes it is possible to double this number, making a tetraploid, 4 copies of every chromosome. • Can occur spontaneously • The drugcolchicine does this by causing meiosis to produce diploid gametes instead of the normal haploids. Then, diploid sperm + diploid egg = tetraploid embryo. • Tetraploids are often bigger, healthier, more nourishing than their diploid parents. • Examples: cotton, durum wheat, potato, daylily • Tetraploid is a form of polyploid, which means having more than 2 sets of chromosomes (2 sets = diploid). • There are triploid (e.g. banana and watermelon), hexaploid (bread wheat, chrysanthemum), and octoploid (strawberry, sugar cane) crops • Triploids are sterile Diploid vs. tetraploid daylilies Diploid vs. octoploid strawberries

24. Hybridization Interspecies hybrid of Drosera (sundew), a Carnivorous plant • Plants are not as rigid in maintaining species boundaries as animals are. It is often possible to produce hybrids between two different, but closely related species. • Members of the same genus will often hybridize • The resulting plants often have characteristics different from both parents • Often sterile, but many plants can be propagated vegetatively • The grapefruit is a naturally-occurring hybrid between a pomelo (native to Indonesia) and a sweet orange (native to Asia). It was discovered in Barbados in 1750, then brought to Florida and propagated. • Hybrids have an “x” in their species name: Citrus x paradisi • Sometimes, a hybrid will spontaneously double its chromosomes, so you end up with a tetraploid . These interspecies tetraploids are usually fertile, and they benefit from the general effect of tetraploidy: bigger, healthier plants.

25. Genetic Engineering Blue rose, with blue pigment gene from delphinium Dead volunteer corn in a glyphosate-resistant soybean field • In the last 30 years it has become possible to take a gene out of one organism and put it into the DNA of another organism. This process is called genetic engineering. The resulting organisms are genetically modified organisms (GMOs) and the gene that has been transplanted is a transgene. • There are no real interspecies barriers here: all organisms use the same genetic code, so genes from bacteria (for example) will produce the correct protein in a corn plant. • However, some modifications must be made to the signals that control gene expression, since these are more species-specific. • A few examples: • Bt corn. Bacillus thuringiensis, a soil bacterium, produces a protein that kills many insect pests, especially the corn earworm. The gene for this protein has been transplanted into much of the US corn crop. • Roundup Ready soybeans (plus other crops). Roundup is the Monsanto brand name for the herbicide glyphosate. A bacterial gene that confers resistance to this herbicide has been transplanted to many crops. The farmer can then spray the fields with glyphosate and kill virtually all the weeds without harming the crop. About 87% of the US soybean crop is now Roundup Ready transgenic plants. • Some cultural issues here: are GMOs safe to eat? (Most scientific opinion is that they are probably harmless)

26. Molecular Cloning The first step in genetic engineering is molecular cloning. Molecular cloning means taking a gene, a piece of DNA, out of the genome and growing it in bacteria. The bacteria (usually E. coli) produce large amounts of this particular gene. The cloned gene can then be used for further research, or to produce large amounts of protein, or to be inserted into cells of another species (to confer a useful trait). The basic tools: 1. plasmid vector: small circle of DNA that grows inside the bacteria. It carries the gene being cloned 2. Restriction enzymes: cut the DNA at specific spots, allowing the isolation of specific genes. 3. DNA ligase, an enzyme that attached pieces of DNA together. 4. transformation. Putting the DNA back into living cells and having it function.

27. The Cloning Process 1. Cut genomic DNA with a restriction enzyme. 2. Cut plasmid vector with the same restriction enzyme. 3. Mix the two DNAs together and join them with DNA ligase. 4. Put the recombinant DNA back into E. coli by transformation. 5. Grow lots of the E. coli containing your gene. The real trick, however, is to find the gene that confers your desired trait.

28. Transgenic Plants • Once a gene of interest has been identified and cloned, it must be put into the plant. • Usually done with plant tissue culture. Small pieces of a plant can be grown as an undifferentiated mass of cells on an artificial growth medium. • Then, when treated with the proper plant hormones, these cells develop roots and shoots. They can then be transferred to soil and grown as regular plants. • To make transgenic plants, DNA gets put into the tissue culture cells, by one of several methods: • One method is the gene gun: tiny gold particles are coated with the DNA, and then shot at high speed into the cells. The gold particles penetrate the cell wall and membrane. Some end up in the nucleus, where the DNA gets incorporated into the chromosomes. • An important issue: the proteins produced by transgenes are identical to those produced in the original species, because the genetic code is universal. • However, the signals needed to express these genes are plant-specific, not universal.

29. Centers of Domestication • Primary theory came from NikolayVavilov, • Vavilov was a Russian who came to a bad end in one of Stalin’s prison camps in Siberia. He believed in Mendelian genetics, which was considered “bourgeois” and thus evil by the Communist Party. (Lysenko) • “Centers of domestication”. The idea is that a plant was probably first domesticated where there are many wild relatives living and where there is a lot of variation in the domesticated plant. Lots of diversity near a domestication center. • Eight major centers: • Southern Mexico and Central America: maize, beans, cotton, pepper, sweet potato • South America (mostly Peru): potato, common bean, tomato, cocoa, tobacco • Mediterranean: pea, mustard, flax, cabbage, asparagus, clover, olive • Middle East (Turkey and eastward): wheat, alfalfa, rye, lentil, melon, fig • Ethiopia: barley, millet, coffee, indigo, sorghum • Central Asia: onion, apple, carrot, almond, grape • India: sugar cane, yam, cucumber, chickpea, orange, coconut, banana, pepper • China: rice, soybean, buckwheat, peach, opium poppy, tea Diversity of maize from Mexico Diversity of potatoes from Peru

30. Centers of Origin

31. More Domestication • More recently, Jack Harlan (from U of Illinois) examined genetic data and found that many crops were domesticated multiple times in multiple locations. Also, some were domesticated over very wide areas that don’t seem much like “centers”. • Nevertheless, our current crops come from many different areas of the world. We will look at the origins of specific crops as we study them.