SCSC 304 Exam 2

Heritability

Degree to which variability of a quantitative trait is transmitted to progeny

P (phenotype) =

G (genotype) + E (environment)

V_p=

V_G + V_{E +} V_GE

V_G

V_{A +} V_{D +} V_I

Broad Sense Heritability (H)

V_{G /} V_P

Narrow Sense Heritability (h²)

V_{A /} V_P X 100

Heritability from Variance Components

H = σ²_g / ( σ²_g + σ²_gy + σ²_gl + σ²_gyl + σ²_e)

σ²_{g = total genetic variance}

σ²_{gy = genotype * year variance}

σ²_{gl = genotype * location variance}

σ²_{gyl = genotype year location}

σ²_{e = experimental error}

5 Heritability from Parent Assumptions?

1. Trait has diploid mendelian inheritance

2. Population from which the parents are taken are in random mating equilibirum

3. No linkage

4. Parents are non-inbred

5. No environmental relationship between the performance of the offspring and parent

Parent-Offspring Regression

h²= b * 100

b = Σ ( x – x ) ( y – y ) / Σ ( x – x )²

x = parent value

y = progeny value

Parent-Progeny Regression

y = a + bx

y = response or dependent variable

x = predictor or independent variable

a = y-intercept of line

b = regression coefficient, slope of line

Broad Sense vs Narrow Sense Heritability Table

Uses of Heritability in Selection

• determine the relative importance of genetic effects which could be transferred from parent to offspring

• determine which selection method would be most useful to improve the character

• predict gain from seletion

• if additive gene action is only important gene action, than an h² estimate is needed

Selection Intensity and Genetic Advance

G_s = (i) (√VP) (h²)

G_s= predicted genetic advance

i= constant based on selection intensity in standard deviation units

√VP= square root of phenotypic variance

Gain per Year

G_s = [( c ) (i) (√V_p) (h²)] / y

y = # of years required to complete breeding cycle

if selection is based on one parent, c = 0.5

if two parents, c = 1.0

Complex Inheritance

Cannot be predicted by Mendelian ratios

Additive Gene Action

each gene enhances trait expression

aabb=0, Aabb=1, AAbb=2, AABb=3, AABB=4

Dominance Gene Action

Heterozygote is more like one parent or the other

aa=0,Aa=2, AA=2

Epistatic Effects

Nonallelic interactions- individually genes have no effect, but together they do

AAbb=0, aaBB= 0, A_B_=4

Overdominance

Each allele contributes, but together they exceed the sum of individual allele contribution

aa=1, AA=1, Aa=3

Gene Interactions (Epistasis)

• Complementary

• Modifying

• Inhibiting

• Masking

• Duplicate

• Additive

• Pleiotropic genes

Complementary Action

Two non-allelic genes required to produce a single effect

AB= resistant; Ab, aB, ab = susceptible

Modifying Action

One gene produces an effect only in the presence of a second gene at another locus

In corn, Pr =purple aleurone color in the presence of dominant R.

• But expresses no effect in the absence of R.

  • PrR=purple aleurone

  • prR=red aleurone

  • Prr and prr = colorless aleurone

Inhibiting Action

One gene inhibits action of another gene

• In corn, the dominant gene R for red kernel color does not produce an effect in the presence of a dominant “inhibitor” gene I.

  • Ri= red

  • RI, rI, and ri = white

Masking Action

One gene may hide the effect of a second gene when both are present

• In oats, a dominant gene Y produces yellow seed coat color

• A dominant gene B produces a black seed coat.

• The gene Y will have no visible effect in the presence of B because the black seed coat color will mask the yellow color.

• BY, By = black

• bY=yellow
• by=white

Duplicate Action

Either of the two genes may produce a similar effect, or the same effect is produced by both of them together

• Common shephards purse has a triangular-shaped seed capsule produced from either of the dominant genes C or D , or by both together, CD.

• With both recessive, the seed capsule has an ovoid shape.

  • Cd, cD, CD = triangular shape seed capsule.

  • cd= ovoid shape seed capsule

Additive Effect

Two genes may produce the same effect, but the effects are additive if both genes are present

• In barley, either A or B will produce medium-length awns, while the two dominant genes together produce long awns.

• The recessive genes produce awnless plants.

  • Ab, aB= medium length awns

  • AB= long awns

  • ab= awnless

Pleiotropic Effects

Single gene having more than one effect- simultaneous influence over size, shape, color, or function of several organs

• In barley, the “uzu” gene in the recessive state may shorten stem and rachis internodes, reduce seed size, and produce an erect coleoptile leaf.

  • Uz= normal appearance

  • uz= semi-dwarf, dense spike, short awns, small seeds, short erect flag leaf.

Uses of Molecular Markers

• selection of parents

• mapping

• marker assisted selection

• cultivar identification

• genetic diversity studies

4 Important Applications of Molecular Markers in Plant Breeding?

1. Screening single traits

2. Speeding up breeding programs

3. Germplasm evaluation

4. Cultivar identification and protection

Types of Molecular Markers

• Isozymes- codominant

• RFLPs- codominant

• RAPDs- dominant

• SSRs- codominant

• AFLPs- dominant

• SNPs- codominant

Advantages & Disadvantages of Commonly Used DNA Markers

Simple Sequence Repeats (SSRs)

• microsattellites- short, repetitive sequences common in eukaryotes

• random repeat of 2-5 nucleotides

• PCR bases

Single Nucleotide Polymorphisms (SNPs)

• PCR bases

• Single base pair site in genome that is unique per individual

• often linked to genes

Requirements for Mapping QTLs

1. Trait phenotypes

2. Polymorphic markers

3. Genetic structure of populations

Single Marker Analysis

• Compare trait means of different classes for each marker locus individually in the form of a single factor ANOVA

• tests the association between a single marker and a trait

Single Marker Analysis Drawbacks

• cannot accurately estimate QTLs effect

• Doesn’t indicate on which side of the marker the QTL is located

Interval Mapping

• QTL lies between two linked marker loci

• Analyzed by statistical software (MapMarker/QTL)

Interval Mapping Drawbacks

• can only map a single QTL location

• many genes throughout genome affect quantitative traits

Functional Marker (FM)

• derived from genomic region of trait-controlling gene

• directly linked to a plant phenotypic trait

• enable efficient characterization of germplasm without recombination

• can be used to select for complex traits

• 100% predictive of a phenotype

Association Mapping (AM)

identifies polymorphisms near or within a gene of interest that controls the phenotypic differences within genotype

Linkage Disequilibrium (LD)

• certain alleles are more likely to be found together on the same chromosome than expected if they were inherited independently

• can be maintained for several generations between loci that are genetically linked, which enables marker assisted selection (MAS)

Random DNA Markers (RDMs)

• most common markers for indirect selection

• usually located near gene of interest, but don’t always lead to a selection of the desired phenotype

Genome Wide Association Studies (GWAS)

• covers entire genome to identify regions associated with phenotypic traits

• pinpoints which parts of genetic code are associated with traits

Methods of Transforming Plants

1. Agrobacterium

2. Particle bombardment

3. Electroporation

Promoters

drive DNA expression by determining the level of transcription of a selectable coding sequence

Constitutive Promoters

• Promote frequent transcription and constantly “turned on.”

• A common promoter is from the cauliflower mosaic virus called CaMV 35S

Tissue-Specific and Developmentally Regulated Promoters

Genes are only expressed in certain tissues or at certain times.

Inducible Promoters

Expression in response to injury, chemical, temperature stress, etc.

Agrobacterium

invades a plant’s DNA, performs a coup de’tat, and makes the plant form a gall for the benefit of the pathogen

Particle Bombardment

• considered direct gene transfer

• gene gun

• not very efficient

• plants with larger cells usually more successful

Electroporation

• Callus culture, or explants such as immature embryos or protoplasts, is placed in a cuvette.

• It is inserted into an electroporator.

• This procedure widens the pores of the protoplast membrane by

  means of electrical impulses.

• The widened pores allow foreign DNA to enter and become integrated with nuclear DNA

GMO

the insertion of DNA (gene) into a species where the gene is not normally found or expressed

Non-GMO

the insertion of DNA (gene) that is found to exist naturally in the same species (taxa) or closely related and often cross-compatible species. (e.g. CRISPR)

CRISPR

• Bacteria capture pieces of viral DNA when they are infected

• These pieces are inserted into the bacteria’s DNA

• These segments are called CRISPR arrays

• Scientists have repurposed this system to edit DNA in living organisms

Mutations

• source of all variation in plants

• most are recessive

• chromosomal- rearrangement, loss, or duplication of chromosome segments

• loss or duplication of entire chromosomes

Tissue often treated to induce mutations

• seed (most often)

• vegetative tissue (rhizomes, stolons, bulbs, corms)

• pollen

• callus(tissue culture)

frame-shift mutations

• changes reading frame

• usually results in complete silencing or malfunction of gene

Germplasm

genetic source material used by plant breeders to develop new cultivars

Sterility

failure to complete fertilization and obtain seed as a result of defective pollen or ovules, or other aberrations

1. Flower parts may not exist or function

2. pollen may not be compatible with stigma, etc

3. Embryo may not be able to survive

4. Resulting hybrid progeny may be infertile

Incompatibility

results from the failure to obtain fertilization and seed formation after self-pollination, usually due to failure of the pollen tube to penetrate the stigma or due to reduced growth of the pollen tube in the style

• encourages cross-pollination

• discourages inbreeding

Male Sterility

• failure to form functional anthers or pollen

• flowers can be cross-pollinated

Genetic male sterility

nuclear genes inhibit normal development of anthers and stamens

Male sterility genes

recessive(ms)- inhibits male floral function

Uses of male sterility in breeding programs

• eliminates emasculations for producing hybrid progeny

• increases natural cross-pollination in normally self-pollinated crops

Cytoplasmic Male Sterility (CMS)

• controlled by factors in cytoplasm, but influenced by genes in nucleus

• flowers have non-functional male parts

• result of nuclear chromosomes in foreign cytoplasm

How CMS Works

• Fertility restoring genes, located in the chromosome, can make cytoplasm operative.

• Parent with the sterile cytoplasm used as the female plant

• Parent with fertility restoring gene used as the male parent

Utility of CMS

production of hybrid seed in many crops

Chemically Induced Male Sterility

• flexible system that kills pollen or prevents its formations

• drawback is getting complete pollen sterility is often difficult

Apomixis

seeds formed without union of sperm and egg

Obligate apomixis

plants reproduce only by apomixis

facultative apomixis

sexual and asexual embryos may coexist in the same ovule or same plant

Chasmogamous flowers

• when flowers open male and female floral parts at same time

• promotes cross-pollination

Cleistogamous flowers

• flowers are closed when male and female floral parts mature

• promotes self-pollination

Dichogamous flowers

• male and female floral parts mature at different times- either within a flower or in different flowers on the same plant

• promotes cross-pollination