Plant Breeding, Genetics, and Cell Biology Notes

Domestication of Crops and Historical Plant Breeding

Domestication of Crops: Selection for Non-Shattering Trait

Crop domestication involved selection for desirable traits, such as the non-shattering trait, which prevents seeds from dispersing naturally, allowing for easier harvest. This process began thousands of years ago in various regions:

• Barley (Hordeum vulgare): Fertile Crescent, younger than $9,000$ BC

• Wheat (Triticum spp): Fertile Crescent, younger than $8,000$ BC

• Beans (Phaseolus spp): Middle and South America, younger than $7,000$ BC

• Rice (Oryza sativa): South of Himalaya Mountains, younger than $6,000$ BC

• Maize (Zea mays): Mexico/Guatemala, younger than $3,000$ BC

• Soybean (Glycine max): Central China, younger than $2,800$ BC

• Peanut (Arachis hypogaea): South America, younger than $1,800$ BC

• Grain Sorghum (Sorghum bicolor): Africa, younger than $1,000$ BC

Historical Aspects of Plant Breeding

Plant breeding has a long history, with key advancements over millennia:

• Hippocrates ($460-377$ BC): Developed a theory similar to Darwin's later "pangenesis theory," suggesting that the human body produced "gemmules" collected in semen as the basis of heredity, approximately $2,200$ years before Darwin.

• Egyptians/Mesopotamians ($700$ BC): Artificially pollinated date palms.

• 1676: Crew suggested the function of ovules and pollen.

• 1716: Cotton Mather noted the effects of cross-pollination in maize.

• 1859: C. Darwin published "Origin of Species."

• 1865: G. Mendel published his work quantifying segregation, independent assortment, dominance, and recessiveness.

• 1868: Beal suggested commercial $F_1$ hybrid maize.

• 1875: ‘Pringle’s Progress’ was the first oats cultivar developed from artificial hybridization.

• 1879: Blount developed a maize cultivar from hand pollination.

• 1900: Mendel’s work was independently verified by de Vries, Correns, and von Tschermak.

• 1902: Garrod showed the relationship between genes and enzymes.

• 1903: Johannsen developed the Pure Line theory of plant breeding.

• 1908: Hardy and Weinberg independently described the expected relationship between gene frequencies, forming the Hardy-Weinberg Equilibrium.

• 1908: E.M. East reported effects of inbreeding in maize.

• 1913: Emerson and East published on the inheritance of quantitative traits.

• 1918: Jones proposed double crosses in maize.

• 1941: Beadle and Tatum’s work led to the $1$–gene–$1$–enzyme theory.

• 1953: Watson and Crick elucidated the molecular structure of DNA.

• 1994: Genetically modified crops became commercially available:

  • 1994: Soybean resistant to sulfonylurea herbicides.

  • 1995: Bromoxynil-resistant cotton.

  • 1996: Bt cotton, maize, soybean.

  • 1997: Roundup-resistant cotton, maize, soybean.

What is Plant Breeding?

Definition and Goals

Plant breeding is the genetic adjustment of plants to serve humankind. It is an applied science focused on improving plants for human use, aiming to enhance the quantity or quality of economic products from plants. This includes:

• Increasing fruit production (e.g., apples, beans, melons, nuts).

• Increasing the entire plant biomass (e.g., common Finger grass).

• Improving protein quality in maize or grasses.

• Improving harvest efficiency (e.g., by delaying the deterioration of the peanut peg).

Interdisciplinary Nature

Plant breeding is an applied science that integrates various basic sciences, including:

• Genetics

• Pathology

• Entomology

• Biochemistry

• Statistics

• Computer Science

• Agronomy
  Modern plant breeders often work as part of a plant improvement team, collaborating with molecular geneticists, entomologists, pathologists, and plant physiologists.

Origins of Plant Breeding

Plant breeding represents one of the oldest accomplishments of mankind, beginning when humans transitioned from hunting to gathering. It started in many different places at various times with diverse crops:

• Fertile Crescent: Grains

• China: Rice

• Pakistan/India: Cotton

• Central America: Beans, squash, cotton

Nature versus Man Selections in Domestication

Nature's Selections

Natural selection prioritizes survival and dispersion:

• Shattering: Generally a dominant trait, ensuring survival by widely dispersing seeds. A corn plant, for instance, would struggle to survive in the wild without human intervention due to its non-shattering characteristic.

• Many small seeds: Increases the chance of some seeds surviving.

• Non-uniform maturity: Spreads out the risk of adverse environmental conditions.

• Dormancy: Allows seeds to survive unfavorable periods and germinate when conditions are optimal.

• Maintenance of variation: Ensures survival across varying environmental conditions year to year.

• Discards most mutations or aberrant types: Favors stable, well-adapted forms.

Mankind's Selections

Harnessing plants for human benefit involves selecting for traits that increase utility and efficiency:

• Non-shattering: Seeds remain on the plant for easier harvest.

• Uniform maturity: Allows for efficient, synchronized harvesting.

• Large seed: Increases yield and caloric return.

• Increased yield: Maximizes agricultural productivity.

• No dormancy: Ensures quick and predictable germination.

• Higher quality: Improves taste, nutritional value, or other desirable traits.

• Lodging resistance: Prevents plants from falling over, making harvesting easier.

• Insect resistance: Reduces crop loss to pests.

• Disease resistance: Protects crops from pathogens.

• Resistance to temperature extremes: Broadens cultivation areas.

• Drought resistance: Allows cultivation in arid regions or during dry spells.

• Allelopathy: Ability of a plant to inhibit the growth of surrounding plants, reducing weed competition.

• Seedling vigor: Ensures strong initial growth.

• Hard seededness (in some cases).

• Anther culturability and regenerationability: Important for modern breeding techniques.

Plant breeding began as an art, involving simple selections by early humans for desirable plants based on taste and energy return. Today, it is both an art and a science, encompassing many disciplines.

The Power of Selection: Examples

The power of artificial selection to bring about change is evident in animal breeding, such as various dog breeds, all descended from a common ancestor through human selection.

• Terriers: Selected in England to drive game out of burrows, requiring specific physical and behavioral traits.

• Retrievers: Selected to retrieve fallen game, often from cold water, requiring strong swimming ability, scent, and obedience.

Similarly, plant breeding can dramatically alter crops. For example, to improve the food quality of maize by increasing lysine and methionine content, a breeder needs to:

• Understand existing variability.

• Determine heritability.

• Locate sources of desirable variability (e.g., wild relatives).

• Choose appropriate breeding techniques (e.g., inbred lines, hybrid crosses).

• Develop efficient sampling methods (e.g., whole ears, individual kernels, specific plant parts) and determine sample size ($N$).

Success in selection hinges on extensive screening and large numbers of individuals to identify rare desirable traits.

The Value and Importance of Plant Breeding

Plant breeding has been a major contributor to global yield increases, alongside factors like climate change, commercial fertilizers, herbicides, power equipment, and plant growth regulators (PGRs).

The contribution of genetics is measured as Genetic Gain:

• Maize (Iowa, 1930-1980): $92$ kg/ha/yr, or $89\%$ of the yield gain, was attributed to improved genetics.

• Wheat: $50\%$ attributed to genetic gain.

• Sorghum (1956-1980): $39\%$ of yield increase attributable to genetics.

• Cotton: $7$ kg/ha/yr, or $0.74\%$/yr gain in yield potential from genetics.

Note: Genetic gain varies based on location, time, and genotypes, so there are no universal hard numbers.

Plant breeders, notably Norman Borlaug and the Green Revolution (starting in developed countries in the $1920s$, and developing countries in the $1950s$), created crop varieties that dramatically increased harvest yields (tons/hectare). Approximately $50\%$ of these increases are due to improved varieties (genetics) and $50\%$ to more inputs (water, fertilizer, weed control, pest control).

Plant Cell Biology and Genetics

Plant Cell Parts

Plant cells have specific organelles and structures:

• Cell Wall: Stiff outer layer providing protection and support; acts as a doorway regulating substance passage.

• Cell Membrane: Located below the cell wall, providing further protection and support.

• Nucleus: The control center containing DNA (chromosomes - information for life).

• Cytoplasm: A clear, thick, jelly-like fluid surrounding the organelles.

• Mitochondria: The cell's powerhouse, responsible for making energy.

• Vacuole: A large storage tank in plant cells for food, waste, and water.

• Chloroplasts: Green-colored organelles that capture sunlight for photosynthesis (making glucose).

• Endoplasmic Reticulum: Network of transportation tubes.

• Ribosomes: Protein factories located on the ER walls and in the cytoplasm.

Plant vs. Animal Cells

Mitosis and Meiosis

Types of Cell Division

• Mitosis: Division of somatic (body) cells. One diploid cell ($2n$) divides into two genetically identical diploid daughter cells, each having a full set of chromosomes.

• Meiosis: Division of gametes (sex cells). Involves two rounds of division, resulting in four haploid ($n$) daughter cells, each with half the number of chromosomes of the parent cell.

Meiosis Key Concept

Gametes have half the number of chromosomes that body cells have.

Somatic Cells and Gametes

• Body cells (somatic cells) are diploid ($2n$) and have $23$ pairs of chromosomes (a total of $46$ chromosomes in humans). Homologous pairs of chromosomes have the same structure, with one chromosome from each parent.

  • Chromosome pairs $1-22$ are autosomes.

  • Sex chromosomes (X and Y) determine gender.

• Germ cells develop into gametes (sex cells: egg and sperm).

  • Gametes are haploid ($n$) cells with one copy of every chromosome (e.g., $22$ autosomes and $1$ sex chromosome).

  • Gametes have DNA that can be passed to offspring.

• Fertilization: The union of haploid egg and sperm during sexual reproduction, restoring the diploid state.

Mitosis Phases

Mitosis involves several phases that ensure accurate chromosome distribution to daughter cells:

• Interphase: The cell prepares to divide; genetic material doubles (DNA replication).

• Prophase: Chromosomes thicken and shorten, becoming visible as two chromatids joined by a centromere. Centrioles move to opposite poles, the nucleolus disappears, and the nuclear membrane disintegrates. Chromosomes pair up visually but homologous chromosomes do not associate.

• Metaphase: Chromosomes align at the cell's equator and attach to spindle fibers via centromeres. Chromosomes meet in the middle.

• Anaphase: Spindle fibers contract, pulling sister chromatids to opposite poles of the cell. Chromosomes get pulled apart.

• Telophase: Chromatids (now individual chromosomes) uncoil, spindle fibers disintegrate, centrioles replicate, and the nuclear membrane reforms around the two sets of chromosomes. The cell then divides (cytokinesis), resulting in two daughter cells. Now there are two.

Meiosis Process

Meiosis reduces the chromosome number in half and creates genetic diversity.

• Involves two sets of cell division (Meiosis I and Meiosis II).

• DNA is replicated before Meiosis I, but not between Meiosis I and Meiosis II.

• Meiosis I: Divides homologous chromosomes in four phases (Prophase I, Metaphase I, Anaphase I, Telophase I). In Prophase I, homologous chromosomes pair up and crossing over occurs, exchanging segments and increasing genetic diversity.

• Meiosis II: Divides sister chromatids in four phases (Prophase II, Metaphase II, Anaphase II, Telophase II). This second division is similar to mitosis.

• Result: Four haploid daughter cells, each genetically unique.

Meiosis vs. Mitosis

Mendelian Genetics

Mendel's Groundwork

Gregor Mendel (the "Father of Genetics") demonstrated that traits are inherited as discrete units. His work laid the foundation for modern genetics, which is the study of biological inheritance patterns and variation. He used garden peas (Pisum sativum) for his experiments due to their suitability for the monastery environment, availability of distinct varieties, obligate self-pollination (allowing controlled crosses), and meticulous record-keeping and statistical analysis.

Mendel's Key Decisions and Observations

Mendel made three crucial decisions in his experiments:

1. Use of purebred plants: Ensured consistent starting material.

2. Control over breeding: He removed male flower parts (stamens) to prevent self-pollination and manually cross-pollinated.

3. Observation of seven "either-or" traits: Traits with clear, distinct forms (e.g., tall/short, purple/white flowers).

Mendel's experimental process:

• P (Parental) generation: Crossed purebred plants that differed in a single trait (e.g., tall x dwarf).

• F$1$ (First Filial) generation: All offspring displayed one of the parental traits (e.g., all tall). These $F</em>1$ plants were all heterozygous.

• F$2$ (Second Filial) generation: The $F</em>1$ plants were allowed to self-pollinate. In the $F_2$, the hidden (recessive) trait reappeared in a predictable ratio (e.g., $3/4$ tall, $1/4$ dwarf).

Mendel's Conclusions (Law of Segregation)

Mendel drew three important conclusions:

1. Traits are inherited as discrete units (now called genes).

2. Organisms inherit two copies of each gene, one from each parent.

3. The two copies segregate during gamete formation (each gamete receives only one copy). This is known as the Law of Segregation.

Genes, Alleles, Genotype, and Phenotype

• Gene: A segment of DNA that directs a cell to make a specific protein, determining a trait.

• Locus: A specific position of a gene on a pair of homologous chromosomes.

• Allele: Any alternative form of a gene at a specific locus. Each parent donates one allele for every gene.

• Homozygous: Describes two identical alleles at a specific locus (e.g., $AA$ or $aa$).

• Heterozygous: Describes two different alleles at a specific locus (e.g., $Aa$).

• Genome: All of an organism’s genetic material.

• Genotype: The genetic makeup of a specific set of genes (e.g., $AA$, $Aa$, or $aa$).

• Phenotype: The physical expression of a trait (e.g., tall, short, red flowers).

Dominant and Recessive Alleles

• Dominant allele: Expressed as a phenotype when at least one copy is present. Represented by uppercase letters (e.g., $A$).

• Recessive allele: Expressed as a phenotype only when two copies are present (i.e., homozygous recessive). Represented by lowercase letters (e.g., $a$).

• Both homozygous dominant ($AA$) and heterozygous ($Aa$) genotypes yield a dominant phenotype.

• Most traits occur in a range and do not follow simple dominant-recessive patterns.

Punnett Squares

The Punnett square is a grid system used to predict all possible genotypes and phenotypes resulting from a genetic cross. The axes represent the possible gametes of each parent, and the boxes show the possible genotypes of the offspring. It yields the ratio of possible genotypes and phenotypes.

• Monohybrid Cross: Examines the inheritance of a single trait.

  • Homozygous dominant x homozygous recessive ($AA imes aa$): All offspring are heterozygous ($Aa$) and display the dominant phenotype.

  • Heterozygous x heterozygous ($Aa imes Aa$): Genotypic ratio $1:2:1$ ($AA:Aa:aa$); Phenotypic ratio $3:1$ (dominant:recessive).

  • Heterozygous x homozygous recessive ($Aa imes aa$): Genotypic ratio $1:1$ ($Aa:aa$); Phenotypic ratio $1:1$ (dominant:recessive).

• Testcross: A cross between an organism with an unknown genotype and an organism with the recessive phenotype. This helps determine if the unknown organism is homozygous dominant or heterozygous.

• Dihybrid Cross: Examines the inheritance of two traits simultaneously.

  • Mendel’s dihybrid crosses with heterozygous plants yielded a $9:3:3:1$ phenotypic ratio for two unlinked traits.

  • This led to Mendel's Law of Independent Assortment, stating that allele pairs separate independently of each other during meiosis.

Genetic Diversity

Sexual reproduction creates unique combinations of genes through:

• Independent assortment of chromosomes during meiosis.

• Random fertilization of gametes.

Crossing over further increases genetic diversity:

• It is the exchange of chromosome segments between homologous chromosomes.

• Occurs during Prophase I of Meiosis I.

• Results in new combinations of genes on a chromosome.

• Genetic linkage: Genes located close together on a chromosome tend to be inherited together. The farther apart two genes are, the more likely they are to be separated by crossing over, allowing genetic linkage to be used to calculate the distance between genes.

Genetics Definitions in Detail

• Reproduction: Sequence of events involved in the multiplication and perpetuation of cells and organisms.

  • Sexual: Increase of plants through seed formed from the union of male and female gametes.

  • Asexual: Increase of plants through ordinary cell division and differentiation (e.g., vegetative propagation).

• Chromosome: Structural units in the nucleus that carry genes in linear order, made of DNA (deoxyribonucleic acid).

• Gene: The unit of inheritance; determines the sequence of a given protein.

  • Proteins are made by reading RNA (ribonucleic acid), including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

• Allele: An alternate form of a gene.

• Homozygous: Alleles for a trait are identical.

• Heterozygous: Alleles for a trait are not identical.

• Genotype: An organism’s genetic constitution.

• Phenotype: Outward expression of the genotype.

• Dominant gene: When genes are heterozygous for a certain trait, one is expressed.

• Recessive gene: When genes are heterozygous for a certain trait, one is not expressed (only expressed in homozygous recessive state).

• Complete dominance: The dominant gene is the only one expressed, completely masking the recessive allele (e.g., $AA$ and $Aa$ both result in Red flowers if $A$ is dominant for Red).

  • Example (Red/White flowers, A=Red, a=White):

    • $AA imes aa <br>ightarrow$ all $Aa$ (Genotypic Ratio $1$, Phenotypic Ratio $1$ Red).

    • $Aa imes Aa <br>ightarrow$ $1 AA:2 Aa:1 aa$ (Genotypic Ratio $1:2:1$); $3$ Red:$1$ White (Phenotypic Ratio $3:1$).

    • $Aa imes aa <br>ightarrow$ $1 Aa:1 aa$ (Genotypic Ratio $1:1$); $1$ Red:$1$ White (Phenotypic Ratio $1:1$).

• Incomplete dominance: Both genes play into the phenotype, resulting in an intermediate phenotype (e.g., Red x White = Pink).

  • Example (Red/Pink/White flowers, AA=Red, Aa=Pink, aa=White):

    • $AA imes aa <br>ightarrow$ all $Aa$ (Genotypic Ratio $1$, Phenotypic Ratio $1$ Pink).

    • $Aa imes Aa <br>ightarrow$ $1 AA:2 Aa:1 aa$ (Genotypic Ratio $1:2:1$); $1$ Red:$2$ Pink:$1$ White (Phenotypic Ratio $1:2:1$).

    • $Aa imes aa <br>ightarrow$ $1 Aa:1 aa$ (Genotypic Ratio $1:1$); $1$ Pink:$1$ White (Phenotypic Ratio $1:1$).

• Gamete: Sex cell or nuclei (egg cell or sperm nuclei) produced during meiosis.

• Self-pollination: Transfer of pollen from the male structure to the female structure of a flower on the same plant.

• Cross-pollination: Transfer of pollen between flowers on different plants (plants must differ genetically).

• Fertilization: The actual union of male and female gametes.

• Hybrid: The first generation offspring of a cross between two individuals differing in one or more genes.

Genetics After Mendel: Beyond Simple Dominance

• Codominance: When both alleles are expressed equally in the phenotype, not creating an intermediate, but showing both traits (e.g., a cross between red and yellow flowers resulting in orange flowers where both pigment types are expressed).

  • In codominance, the $F_2$ generation from a heterozygous self-cross would show a $1:2:1$ phenotypic ratio, not $3:1$.

• Multiple Alleles: Many genes have more than two possible alleles in a population, although an individual only has two. For example, flower color could involve alleles like $P^R$ (red), $P^Y$ (yellow), and $p$ (no pigment), leading to combinations like $P^R P^R$ (red), $P^R P^Y$ (orange), $P^Y P^Y$ (yellow), $P^R p$ (pink), $P^Y p$ (cream), and $pp$ (white).

  • Human hair color is also determined by multiple alleles (e.g., $H^B n$=brown, $H^B d$=blonde, $h^R$=red, $h^b k$=black) and their combinations.

Important Note: Dominance does not mean frequency. A recessive allele can be very common (e.g., green seed, wrinkled seed, dwarf stature, and white flowers are all recessive traits but common in garden peas).

Quantitative Inheritance

Many traits, such as crop yield and human skin color, are controlled by multiple genes, exhibiting quantitative inheritance. These traits show a continuous range of phenotypes rather than discrete categories.

• High Crop Yield: Could be represented by a combination of many dominant alleles (e.g., $AABBCCDD EE$).

• Intermediate Crop Yield: Heterozygous combinations (e.g., $AabbCCDdEe$).

• Lowest Crop Yield: All recessive alleles (e.g., $aabbccddee$).

• Similarly, skin color varies greatly due to the combination of many genes.

Phenotype = Genotype + Environment

The observed phenotype of an organism is a result of the interaction between its genotype and the environment.

• Crop Yield: Genotype + Minerals + Water + Light - Pests, etc.

• Human Skin Color: Genotype + Sun (UV) Exposure - Aging Factors.
  Optimizing environmental factors for a given genotype is crucial for agricultural productivity.

Inbreeding Depression vs. Hybrid Vigor

• Inbreeding Depression: Occurs when related parents mate, increasing the likelihood of offspring inheriting two copies of deleterious recessive alleles. Examples include hemophilia in European royalty, Tay-Sachs in Jewish populations, hip dysplasia in German Shepherds. This is the biological basis for the incest taboo.

• Hybrid Vigor (Heterosis): Occurs when combining genetically distinct parents. The dominant alleles from one family can