AGRY 520 Final exam

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AGRY 520 Final exam
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2014-12-15 19:57:15
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Plant breeding
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Fall 2014 final exam
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  1. Concept and importance of intellectual property in plant breeding
    Intellectual property- how an inventor is protected from unfair use of his invention. Recognizes that "invention" has a price tag
  2. What is a patent?
    Exclusive rights of an invention granted to the patentee.
  3. Types of patents
    • Utility- greatest amount of protection but must submit detailed description of the invention
    • Design- protects a unique shape (ex. shape of a bottle)
    • Plant- protects new plant variety from  ASEXUAL reproduction methods
  4. Regulatory agencies for biotechnology
    • USDA- plant pests, plants veterinary biologics
    • EPA- Microbial/plant pesticides, new uses for existing pesticides, novel microorganisms
    • FDA- Food, feed, food additivies, veterinary drugs, human drugs, medical devices
  5. Regulatory role of USDA-APHIS
    Regulates interstate movement, importation, field testing, or organisms altered through BT that are/are suspected of being plant pests or have genes from plant pests
  6. Regulatory role of FDA
    • A sample must be submitted to the FDA for testing for anything fitting under: 
    •       unexpected effects
    •       Known toxicants
    •       nutrient level
    •       new substances
    •       allergenicity
    •       antibiotic resistance selectable markers
    •       plants developed to make specialty non-food products (ex pharmaceuticals)
    •       Issues specific to animal feeds
  7. Regulatory role of EPA
    • Regulates pesticides
    •       PIP- Plant integrated pesiticides
  8. Seed Certification
    a legal mechanism to maintain the original genetic identity and purity
  9. Seed certifying agencies
    • -Official Seed Certifying Agencies- in the US, most state agencies are a member of the organization
    • -Organization for Economic Cooperation and Development- facilitates movement of international certified seed
  10. Classes of certified seed
    • Breeder
    • Foundation
    • Registered
    • Certified
  11. Breeder seed
    In direct control of the plant breeder. Should have the highest genetic purity.
  12. Foundation seed
    First generation increase from breeders seed
  13. Registered seed
    Source of certified seed. Usually grown by farmers under contract with the seed company
  14. Certified seed
    Grown in isolation. This is the class of seed that farmers plant
  15. Certification process
    • Application- standards are set by each state but cannot be inferior to AOSCA
    • Soucre of seed- must be either foundation or registered
    • Site selection- must be free of contaminants. Ex volunteer plants or weeds
    • Management- field must be kept weed-free
    • Field inspection- certified inspectors look for noxious weeds, seed-borne diseases
    • Harvesting- equipment must be cleaned thoroughly to avoid contamination
  16. Concept and role of GxE
    • GxE occurs when the relative performance of a line changes across environments
    • If a GCA (general combining ability) table has no residuals, then you know that you have accounted for all the variation with the main effects (G or E). If there are residuals, there will be residuals
  17. Field plot design
    • Soil variability
    • To reduce error: use border rows, proper plot size, number or replications, minimize operator erros
  18. Plot design- No design
    • + inexpensive and easy, evaluate large number of genotypes
    • - can't account for spacial variability and poor choice for low heritability traits
  19. Plot design- Grid
    + reduces effects of soil heterogeneity, suitable for selecting low heritability traits, selection intensity can be varied by selecting more than one plant per block
  20. Plot design- Honeycomb
    • Plants are equidistant from one another.
    • - conventional equipment is not suitable, complex
  21. Plot design- Unreplicated tests
    • + saves space & $$, large number of genotypes can be evaluated
    • - Can't account for spacial variability, hard to estimate experimental error
  22. Plot design- Complete randomized design
    • + simplest to use and analyze, highest number of degrees of freedom, missing data is tolerable
    • - not conducive for field studies
  23. Plot design- Randomized complete block design
    • As many block as there are replicates
    • + flexible, statistically straight forward, can estimate unbiased error
    • - not suitable for a large number of entries
  24. Crop registration process
    • Over 50 crop groups can be registered. 
    • Procedure: 
    •    1. Name or identificaiton assigned time of release
    •    2. Scientific name
    •    3. experimental number/designation during development
    •    4. Names of all agencies/organizations involved in development
    •    5. Description of material
    •    6. Probable regions of adaptation, area of production, generations of seed increase
    •    7. Who is responsible for maintenance of basic stock
    •    8. Any limatations on availability
  25. Polyploidy
    • Species has more sets of chromosomes than is represented in the diploid state
    • Diploid=2n=2x=14
    • Tetraploid=2n=4x=28
    • Hexaploid=2n=6x=42
  26. Euploidy
    individuals contain multiple complete chromosome sets
  27. Aneuploidy
    individuals contain incomplete chromosome sets
  28. Autoploidy
    Euploids conatin multiples of the same genome
  29. Alloploidy
    Euploids contain a combination of genomes ex. wheat
  30. Effects of polyploidy
    • All polyploids- usually slower growing, reduced tillering in grasses, flower later and longer.
    • Autoploidy- should look like parents, increases cell size (usually thicker, broader, shorter leaves), other organs may increase in size (gigas features). Gigas contributes more to moisture content then actual biomass.
    • Alloploid- appear as an intermediate of its two parents
  31. Importance of autopolyploids in crop production
    Autopolyploids rarely outperform their diploids. Generally best for species with: low chromosome number, vegetative organ is important (forages, becasue of gigas features), cross pollinated (promotes recombination for a better chance of a balanced genotype), vegetatively propagated (because of common infertility), or perennial growth habit
  32. Genetics of autoploids
    More complicated because where a diploid has 2 alleles at 1 loci, a polyploid may have 4. This means there are 5 different possible combinations. Homozygosity is achieved less often because it takes 4 of the same allele instead of 2. It is also difficult to test for genotype with a progeny test.
  33. Examples of alloploids in nature
    Wheat, oat, tobacco, cotton, strawberry, blueberry
  34. Genetics of Alloploidy
    • Most alloploids exhibit diploid-like inheritance of qualitative and quantitative traits
    • Alloploids can be created by crossing two species and then doubling the chromosome number (triticale)
  35. Importance of polyploids in breeding
    • Heterozygosity
    • Interploid genetic exchange/recombination
    • Develop sterile cultivars (ex seedless fruit)
    • Increase gene copy number (disease resistance)
    • Restore fertility
    • Gigas properties
    • Increased vigor
    • Haploids/double haploids
  36. Mutigenesis
    Mutigenesis- process by which new alleles are created
  37. Types of mutations
    • Gene- change in nucleotide sequence
    • Chromosome structure variation- translocations, inversions, ...
    • Ploidy variation- gain or loss in chromosomes or sets of chromosomes
  38. Mutation effects at the protein level
    • Silent- no change in AA
    • Neutral- similar AA
    • Missence- changes AA
    • Nonsense- stop codon
    • Frameshift- alters reading frame
  39. Mutagenic agents
    • Physical- principally ionizing radiations (X-ray, gamma ray,...)
    • Chemical- generally more mild effect. One of the most effective groups are alkylating agents that react with the DNA by alkylating the phosphate groups as well as the purine/pyrimidine
  40. Types of mutigenesis
    • Forward genetics-screen for mutant phenotypes then look for the genes responsible
    • Reverse genetics-look for mutant genes then characterize the phenotypes
    • Gene silencing- RNA interference
    • Gene editing- Zinc fingers
  41. Steps in mutagenesis breeding program
    • Create mutagen population
    • Screen either forward (pick phenotypes and then look for the responsible gene) or reverse (find interesting genes and then look for resulting phenotype). Forward genetics was how they found dhurrin-free (mutation in dhurrin metabolism so it can't be released) sorghum.
  42. Limitations of mutagenesis
    associated side effects, need a large population, mutants are often recessive, limited pre-existing genome, mutations are random
  43. Advantages of MAS over conventional breeding
    • 1. Distinguishing between heterozygous and homozygous phenotypes
    • 2. Early generation discrimination
    • 3. Convenient screening
    • 4. Reduced space needed for screeing
    • 5. Reduced breeding time
  44. Steps in developing MAS QTL
    • 1. Develop mapping population- select parents and cross
    • 2. Conduct QTL mapping- QTL analysis, linkage map, phenotypic evaluation for trait(s) of interest
    • 3. Validate QTL- confirm the position and effect of QTL, verify QTL in independent populations, test in different genetic backgrounds, high resolution mapping
    • 4. Validate marker- testing of markers in important breeding material
    • 5. Implement MAS- identify tightly linked markers that reliably predict a trait phenotype for MAS
  45. MAS in marker assisted backcrossing
    • 1. molecular markers may be used to screen for the target trait
    • 2. use markers to select progeny with the target gene and the tightly linked flanking markers so as to reduce linkage drag
    • 3. use markers to select backcross progeny that have previously been selected for target trait and possess the back-ground markers. 

    This allows the breeder to select for the desired gene within the donor genome, speeding up back-crossing
  46. MAS with gene pyramiding
    Gene pyramiding most often used to obtain horizontal resistance to disease. The MAS assay is able to test for multiple genes at one time and is non-destructive.
  47. BILs
    • Backcross inbred lines- populations of plants derived from repeated backcrossing of a recombinant line with a wild type.
    • BILs are immortal lines that are near isogenic to recurrent parent.
    • Genes that are not found in and F2 analysis are more likely to be found in BILs.
    • BILs tend to reveal QTLs not involved in interactions thus making introgression of the wild trait into commercial cultivars straightforward
  48. Limitations of MAS
    • Can't accurately localize QTLs
    • Strong influence of environment on quantitative traits
    • Cost
  49. Importance of genetic maps in plant breeding
    Mapping position of genes along the chromosomes helps breeders understand their architecture and thereby facilitate their manipulation
  50. Types of genetic maps
    • Genetic/linkage- examine recombination events in progeny, map distances based on likelihood of recombination between genes (genes further apart on chromosome are more likely to have more recombinations), classic breeding designs used
    • Physical- use of sequencing to determine order of genes on the chromosome
    • For best results use both
  51. Selecting mapping populations
    Selection of parents is crucial. Parents must: exhibit variation for traits of interest, not too exotic, more individuals=better
  52. Mapping population types
    • F2
    • F2 derived F3
    • Recombinant inbred lines (RIL)
    • Double haploids
    • Near Isogenic Lines
  53. Mapping Population:F2
    • Selfed F1
    • + easy and quick to create, simple segregation ratios
    • - limited recombination=> limited information to be gained, cannot be exactly replication
  54. Mapping population: F2:3
    • +Additional generation of meiosis=> greater recombination, smaller linkage blocks
    • - still not exactly replicable
  55. Mapping population: backcross
    • F1 crossed to parent
    • Same issues as F2
  56. Mapping population: RIL
    • Selfing F2 until lines are completely inbred
    • +reproducible, greater recombination, great for QTL mapping
    • -same 1:1 segregation for dominant and codominant, long time to self down F2 to create RIL
  57. Mapping population: Near isogenic lines
    • +Completely identical lines except for a few loci, very useful is the NILs differ at the desired QTL
    • - requires a lot of time to create, linkage drag, not good for linkage mapping
  58. Mapping population: Double haploid
    • +permanent, quick to create
    • - minimum recombination, skill to create a haploid population
  59. Methods of mapping QTL
    • Single Marker analysis
    • Simpler interval mapping
    • Composite interval mapping/multiple interval mapping
  60. QTL mapping: Single Marker Analysis
    • uses linkage map and basic statistics
    • simple, but underestimates QTL effect
    • distance of markers from controlling gene greatly impacts ability to detect
    • need many evenly spaced markers
  61. QTL mapping: Simple interval mapping
    • Uses pairs of markers to flank regions of interest
    • assumes only a single QTL of interest
    • uses likelihood-ratio test statistic (LOD)
  62. QTL mapping: Composite interval mapping/multiple interval mapping
    • CIM- uses SIM + multiple regression, accommodates missing genotypic information, computationally more intensive
    • MIM- Similar to CIM but allows for identification of multiple QTLs, controls residual variation of a QTL to identify others on the same chromosome
  63. Genetic marker
    Genetic marker- indentifier of a landmark on a chromosome. May be a DNA sequence of known order that falls near or within a gene
  64. Use of genetic markers in plant breeding
    • 1. Understanding breeding materials within a program
    • 2. Expediate the introgression of a simple trait into a population
    • 3. Selection before pollination/harvest
    • 4. Completing tasks not previously possible (separate gene of interest from undesirable linkage drag)
    • 5. Distinguishing between different lines
  65. Types of molecular markers: Restriction fragment length polymorphism (RFLP)
    • Differences in length of fragments based on single nucleotide substitutions
    • First opportunity for non-coding sequences to be analyzed
    • Had to utilize large amounts of DNA, radioactive probes, and x-ray film
    • Difficulties in analysis of RFLPs did not make them popular for long
  66. Types of molecular markers: Minisatellite markers
    • Rely on genomic repeats of a simple sequence
    • Issues: still require hybridization step, are not able to assign alleclic variants to specific loci, non-random distribution of markers makes this system less ideal for QTL studies
  67. Types of molecular markers: Random Amplified Polymorphic DNA (RAPD)
    • PCR-based markers
    • Does not require knowledge of DNA sequence of interest
    • Random primer sequence for amplification
    • Highly dependent upon PCR amplification protocl
  68. Type of molecular markers: Amplified Fragment Length Polymorphism
    • PCR-based marker
    • Basically selective RFLP
    • Reliable, robust, and withstands small PCR variations
    • Larger number of markers
    • Useful for distinguishing closely related genotypes
  69. Types of molecular markers: Microsatallites
    Similar to minisatallites but shorter sequences
  70. Type of molecular markers: Single Nucleotide polymorphisms (SNPs)
    • Most abundant markers in the genome
    • Single base pair alteration
    • Often linked to genes => good for mapping
    • Increased ability for: population structure analysis, evolutionary genetics, high density genetic map construction, linkage disequilibrium analysis (GWAS)
    • Problems: Costly, time intensive, require validation, highly variable dependent upon isolation strategy
  71. Categories of clonally propagated species
    • 1. Normal flower & seed set- can reproduce sexually but in crop production it is preferred to produce them asexually
    • 2. Normal flowers & poor seed set- clonal propagation allows for reliable reproduction
    • 3. Produce seeds by apomixis- apomixis- produces seeds without fertilization. 
    • 4. Non-flowering- obligate asexually propagated
  72. Genetic issues with clonally propagated species
    • 1. Genetic make-up- all progeny are identical because they are the product of mitosis. Any variation in from the environment
    • 2. Heterozygosity and heterosis- many clonally propagated are highly heterotic. Asexual reproduction allows the hybrid vigor to be "fixed"
    • 3. Ploidy- many clonally propagated species are interspecific hybrids or have high ploidy
    • 4. Chimerism- the only natural variation comes from mutations in somatic tissue (chimerism) so the lines are stable over many generations
  73. Mutation breeding of clonally propagated species
    Difficult to create mutans.
  74. Breeding apomitic species- advantages
    • Sterility in not a factor
    • Uniform commercial product
    • Micropropagation can be used to quickly multiply material
    • Heterosis is fixed
  75. Breeding apomitic species- disadvantages
    • Clonal propagules are bulky to handle
    • Clones are susceptible to devastation by an epidemic
    • Clonal propogules are difficult to store for a long time
  76. Historical background of hybrid seed
    George Shull- father of heterosis
  77. Hybrid vigor theories
    • Dominance hypothesis- deleterious recessive alleles from one parent are hidden by the dominant alleles of the other parent
    • Over-dominance hypothesis- heterozygosity produces a physiological stimulus that increases with the diversity of the uniting gametes
    • Non-homologous DNA complementation- each line contains unique genes  that combine to create a superior hybrid. In other words the hybrid has more genes than either parent
  78. Hybrid vigor
    the increase in size, vigor, and overall productivity of a hybrid plant over the mid-parent value
  79. Recurrent Selection
    • Cyclical selection of a population to improve one or more traits
    • 3 phases:
    •    1. Extract families for selection
    •    2. Evaluate families for performance
    •    3. Inter-mate selected lineages to create the new population
  80. Half-sib selection
    • Method
    •   Select desired half-sibs from the base population
    •    Grow and evaluate half-sibs in replicated trials
    •    Select best families and then recombine in isolation
    • Considerations
    •    Commonly used in forage grasses and legumes
    •    Tester is the base population
  81. Full-sib selection
    • Method
    •    Generate full-sibs from the base population
    •    Evaluate full-sibs in replicated trials
    •    Recombine the best families
    • Considerations
    •    Commonly used in maize
    •    High response to selection
  82. S1 family selection
    • Method
    •    Extract S1 or S2 families from base population
    •    Select good families from desired progeny rows
    •    recombine best families
  83. Half-sib family selection
    • Method
    •    Extract S1 or S2 families from base population
    •    Grow ear to row to select good families
    •    Testcross and evaluate hybrids to determine combining ability
    •    Recombine best families
  84. Synthetic cultivar
    • Advanced generation of cross fertilized seed mixture of parent lines. Must be re-synthesized every few years
    •    Assemble parents
    •    Assess GCA
    •    Random mate selected entries
  85. Testing for GCA
    • Polycross-many diverse pollinators
    • Topcross- a few selected cultivars are used as pollinators in isolation seed increase
    • Diallel crossing design- A mating design can be used to create a structured population of full sib and half-sib hybrids
  86. Reciprical Recurrent selection
    • Improve 2 populations at the same time
    • Select and self S0 plants from each population
    • Grow selected S1 plants and pollinate with the pollen from the other population
    • Evaluate test cross in replicated trials
    • Recombine selected S1 plants
  87. Mass selection
    • Plant heterogenous population
    • Select desired plant type
    • Bulk seed and repeat as needed

    • Effective for selection of highly heritable traits
    • Responses to selection reflect population dynamics
  88. Pureline selection
    • Plant heterogenous population
    • Select desired plant types
    • Grow, evaluate, and select progeny of desired lineages over 1-2 generations

    • Effective in self-pollinating populatons
    • Narrow genetic variation
  89. Pedigree Selection
    • Make planned cross and produce F2 progeny
    • Select plants from desired progeny rows each generation until you reach homogeneity
    • Evaluate select progeny over 1-2 generations

    • Genetic crosses 
    • Record keeping
    • Selection on phenotype and genotype
  90. Single Seed decent
    • Make planned cross
    • Advance as many lines as possible from F2 to homogeneity (F5)
    • Select highly heritable traits
    • Trial selections for yield

    • Genetic crosses with rapid fixation
    • Selection on pheno/genotype
  91. Backcross/ Trait introgression
    • Identify cultivar weakness
    • Make planned cross with trait donor
    • Backcross to elite recurrent parent
    • Self-pollinate advance BC generations to identify plants with introduced traits

    • Effect for major genes but not quantitative
    • Linkage drag
  92. Multiline breeding
    • Identify/develop cultivars with contrasting resistance/adaptation traits
    • Create a blend that increases diversity to improve stability of performance

    Generally used in reference to isolines
  93. Types of abiotic stress
    Drought, heat, cold, salinity, mineral toxicity, oxidative, water-logging, mineral deficiency
  94. Breeding for drought stress
    • Indirect breeding- exposing genotypes to a stress they are not being selected for
    • Direct breeding- submitting genotypes to the stress you are selecting for
    •    Field selection- difficult because temperature and heat are unpredictable and the stress can occur at different growth stages in different years
    •    Managed stress environment- this is where most drought breeding is done
    •    Selection based on yield per se- the hybrid with the most stable yield (lowest GxE) is selected 
    •    Selection on developmental traits- root size and growth rate, stem reserve utilization, etc. 
    •    Selection based on plant water status and plant function- assessing stress symptoms such as leaf rolling, senescence.
  95. Mechanisms of stress response
    • Escape- modified development (early flowering) to escape stress
    • Avoidance- avoid stress by decreasing water loss
    • Tolerance- cellular adaptation to conditions of low water content
    • Rapid recovery- stability under stress that allows the plant to quickly return to normal growth once the stress is past
  96. Aluminum tolerance
    • 3 groups:
    • 1. those that exclude Al so  it does not accumulate in their roots
    • 2. those with less Al in shoot but more in root
    • 3. those with high accumulation of Al in the shoot

    Some genes have been identified
  97. Controlling plant pests/pathogens
    • Quarantine- plant isolation (hessian fly free date)
    • Cultural management- post-infection control of inoculum (crop rotation, residue management)
    • Host plant resistance- introduce resistance genes into the crop
    • Pesticide applications-
  98. Environmental basis for infection
    • Pathogenicity- capacity to cause disease
    • Aggressiveness- extent of potential disease protection
  99. Genetic basis for infection
    • Virulence- ability to infest crops regardless of host-plant resistance genes
    • Avirulence- inability to infect crops
  100. Disease Triangle
    Susceptible plant, pathogen, favorable environment
  101. Mechanisms of defence
    • Avoidance- reduces the probability of contact between pathogen or pests and crop (open panicle sorghum doesn't get grain mold)
    • Resistance- induced after the plant is challenged by the pathogen (aphid resistance in cereal crops)
    • Tolerance- induced after the plant is challenged by the pest. Attempt to reduce the extent of damage in the host plant (striga tolerance in corn)
  102. Vertical resistance
    • Controlled by major resistance gene
    • Based on strong host plant reaction such as hypersensitive response
    • Ex. Downy mildew in lettuce
  103. Horizontal resistance
    • Controlled by QTL with each having a small effect
    • More durable in agriculture setting because the pathogen has to overcome more than 1 gene to overcome the resistance
    • Ex rust resistance in maize
  104. Considerations for disease resistance
    • Introduce new R genes in succession to avoid single-gene resistance across all cultivars
    • Deploy multi-lines with different R genes
    • Stack multiple genes in new cultivars "gene pyramiding"
    • Combine major and minor gene resistance (BC major R genes into elite cultivars with quantitative resistance, combine qualitative and quantitative resistance with MAS, genomic selection for minor genes after controlling for major genes by MAS)
  105. Breeding for high protein in maize
    Maize is deficient in the AA lysine. High lysine lines of corn were made at Purdue in the 1960's. These lines had soft kernels and therefore did not gain popularity. CIMMYT developed Quality Protein Maize by improving the kernel phenotype of these lines.

    Long term IL studies show that corn is responds to selection for increased protein and oil content
  106. Improved oil content
    • Conventional breeding has been used to reduce palmitic acid in soybean oil (lowers saturated fat)
    • Transgenic soybeans with high oleate have been developed (decreases polyunsaturated fat)
  107. Yield
    Amount of the crop part of interest harvested from a given area within a given period
  108. Biological pathway to economic yield
    Yield/unit area= (plants/unit area) x (mean number of tillers with ears/plant) x (mean number of grains/ear) x (mean grain weight)
  109. Yield potential
    The optimum capacity to perform under a given environment
  110. Yield plateau
    The rate of increase in crop yield is declining. Yields are increasing, but at a decreasing rate.
  111. Yield stability
    Cultivars can sustain high performance over years and seasons
  112. Germplasm's role in plant breeding
    Germplasm provided the materials (parents) used to initiate a breeding program.
  113. Sources of germplasm for plant breeders
    • Commercial cultivars- both current and retired elite cultivars
    • Breeding materials- products of breeding programs that were not commercialized but are kept for later use
    • Landraces- farmer developed and maintained cultivars. Very well adapted to their specific environment
    • Plant introductions- bringing in genotypes from other countries
    • Genetic Stock- products of specialized genetic manipulations by researchers (ex. mutagenasis)
    • Undomesticated plants
    • Other species/genera
  114. Genetic vunerability
    refers to the genetic homogeneity and uniformity of a group of plants that predispose it to susceptibility to a pest, pathogen, or environmental hazard
  115. Methods of germplasm conservation
    In situ- preservation of variability in its natural habitat in its natural state. Ex. wildlife refuge

    Ex situ- planned conservation of targeted germplasm in gene banks
  116. Types of germplasm collections
    • Base collections- not intended for distribution
    • Backup collections- supplement base collection
    • Active collection- usually same material as base but is distributed to researchers
    • Working or breeders collection- mostly adapted elite germplasm and also breeding stocks
  117. 3 gene "pools"
    • Primary- biological species that can be freely intermated
    • Secondary- closely related species that can be intermated to produce at least some fertile hybrids
    • Tertiary- closely related species that can be intercrossed but crossing barriers must be overcome
  118. Domestication
    process by which genetic changes are brought about by human selection. Similar to evolution because it is "survival of the fittest" except that humans decide which are the "fittest"
  119. Domestication syndrome
    • Assortment of morphological and physiological traits that are modified in the process of domestication.
    • Increased seedling vigor- loss of dormancy, larger seeds
    • Modified reproductive system- increased selfing, vegetatively propagated, altered photoperiod sensitivity
    • Increased number of harvested seeds- non-shattering, reduced branching
    • Increased consumer appeal- attractive fruit/seed colors, enhanced flavor/texture, reduced toxic compounds, reduced spines/thorns
    • Altered plant architecture and growth habit- compact growth habit (dwarfism), reduced branching
  120. Genetic basis of domestication
    Most of the traits included in domestication syndrome are controlled by one or a few loci, and these loci are are found in clusters.
  121. Types of variation among plants
    • 1. Environmental- not hereditary
    • 2. Genetic
  122. Origins of genetic variation
    • 1. Gene recombination- only in sexually reproducing plants
    • 2. Gene transgression- some individuals in a segregating population from a cross express the trait of interest outside the boundaries of the parents (ex taller than either parent)
    • 3. Ploidy modification- change in ploidy number
  123. Genetic consequences of hybridization
    • Population development- gene transfer, recombination, introduction of diversity
    • Hybrid development- evaluation of parent lines (combining ability), create heterosis
    • Seed stock- maintenance of parent lines
    • Genetics- genetic analysis
  124. Wide cross
    • A cross made outside the cultivated pool
    • Made be used for economic crop improvement, new character expression, creation of new alloploids, scientific studies, curiosity/aesthetic value
  125. Over coming challenges of wide crosses
    • Reciprocal crosses- some crosses only work in 1 direction
    • Shorten the length of style- reduces length of pollen tube growth
    • Apply growth regulators
    • Modify ploidy level- crosses may require parents with similar ploidy, double to restore fertility
    • Used mixed pollen
    • Embryo rescue- abnormal embryo or endosperm growth may require nuture in tissue culture
  126. Natural mechanisms that favor allogamy
    • Allogamy= cross pollinated
    • species depend on agents of pollination such as wind and insects
    • Protandry- anthers release pollen before the stigma on the same flower are receptive (opposite is protogyny)
    • Dioecy- male and female plants
    • Monoecy- male and female flowers
    • Self- incompatability
  127. Importance of mode of reproduction to plant breeding
    • Genetic structure of plants depends on their mode of reproduction
    • Determines how to make a cross to study inheritance
    • Artificial hybridization methods depend on mode of reproduction
    • Determines the procedures for multiplication and maintenance of cultivars developed by plant breeders
  128. Self-incompatibility systems
    • Heteromorphic incompatibility- difference of the lengths of the stamens and styles of the flowers
    • Homomorphic incompatibility- 
    •    Gametophytic- ability of pollen to function is determined by its own genotype and not the plant that produces it
    •    Sporophytic incompatibility- the incompatability of the pollen is determined by the plant that produces it
  129. General combining ability
    Average hybrid performance of a line when crossed with other parents. Evaluates one parent
  130. Specific combining ability
    Performance of a line in a cross with a specific parent. Evaluates performance of one cross
  131. Quantitative genetics
    • Focuses on use of modern genetic tools (genomics, bioinformatics, computational biology) to reveal links between genes and complex phenotypes.
    • Different from population genetics- focuses on frequencies of phenotypes and alleles
  132. Polygenetic inheritance
    Polygenes- genes with effects that are too small to be individually distinguished
  133. Gene action
    • 1. additive- the effect of replacing A with a remains the same regardless of the allele with which it is combined
    • 2. dominance- extent of dominance is calculated as the deviation of the heterozygote (Aa) from the mean of the two homozygotes (AA, aa)
    • 3. Overdominance- the combined effect of each allele exceeds the independent effect of each allele. Each allele at a locus produces a separate effect on the phenotype
    • 4. Epistasis- interaction of alleles at different loci
  134. Factors affecting gene action
    • Type of genetic material
    • Mode of pollination
    • Mode of inheritance
    • Presence of linkage
    • biometrical parameters (sample size, method of calculation)
  135. Broad sense heritability
    estimated using total genetic variance (Vg)
  136. Narrow sense heritability
    estimated using additive variation only. More useful to plant breeders because additive variation determines response to selection
  137. Population
    Group of sexually interbreeding individuals
  138. Gene pool
    total number and variety of genes and alleles in a sexually reproducing population that are available for transmission to the next generation

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