PLANT BREEDINGAGR 3204

GENETICS AND VARIABILITY IN CROP

PLANTS

Genetics and variability of traits are grouped by:

Qualitative traits

Traits that show variability that can be classified into discrete (clear-cut) classes that are easily identifiable.

Eg. Flower colour, fruit shape, stem colour etc. Quantitative traits

Traits that show variability in continuous form, and could only be identified through measurements. They do not show any particular discrete form.

Eg. Sugar content, plant height, fruit size, number of fruits per plant etc.

QUALITATIVE TRAITS

Controlled by few number of genes, 1-3 loci (major gene)

Mostly expressed in dominant/ recessive forms

Absence / very minimum influence of environment on their expression

Example of Qualitative Trait

Red(RR) Red (Rr) White (rr)

EFFECT OF SELECTION ON QUALITATIVE TRAITSA) Recessive traits

Only expressed in the homozygous form in composition of segregating generation (e.g. F2)

RR 2Rr rr

No. of Loci(n) Rate of Recessive Homozygous Individuals (1/4)n

123

1/41/161/64

A) Recessive Traits(cont.) Can be recognized and selected in

one generation only – but required an appropriate minimum population size (big enough) to detect its presence.

Dominant gene can be eliminated in one generation of selection.

EFFECT OF SELECTION ON QUALITATIVE TRAITS

B) Dominant traits Expressed in the homozygous (RR) and

heterozygous (Rr) forms.

RR 2Rr rr

EFFECT OF SELECTION ON QUALITATIVE TRAITS

EFFECT OF SELECTION ON QUALITATIVE TRAITS

B) Dominant Trait (Cont.) More difficult to select for dominant traits

– need more than one generation of selection.

Example to select Red Petunia with red flowers Colour of petunia flower: Red (RR, Rr) and white

(rr). F2 – ¾ red (RR, Rr) and ¼ white.

B) Dominant Traits (Cont.) Methods:-1. Select for plant with red flower- 1/3 RR & 2/3 Rr2. Selfed pollinate plants with red flowers and grow

seeds from them. Selfing of Rr – gives progenies that are ¾ red & ¼ white

flowers Selfing of RR – gives all progenies with red flowers (RR).

3. Select only the plants that give progenies with all red flowers. Discard the plants with progenies segregating for the flower colour.

4. To select dominant gene or to eliminate the recessive gene requires two generations.

First generation: selection Second generation: progeny testing

EFFECT OF SELECTION ON QUALITATIVE TRAITS

QUANTITATIVE TRAIT

Most of the economically valuable characters.

Controlled by many genes - polygenes. Each gene has cumulative contribution

to the expression of the character. Expression of quantitative genes usually

influenced by environment effects.

PHENOTYPIC VARIATION (VP) OF QUANTITATIVE TRAITS

Consist of: 1. Genetic Variance (VG)

2. Environmental Variance (VE)

3. Variance Due to Interaction between Genetic and Environment (VGE)

Therefore: VP = VG + VE + VGE

HERITABILITY

DEFINITION: Contribution of genetic component to a certain character, compared to that of the environment

Heritability (%) = VG / VP X 100

VG

Heritability calculated based on all genetic factors over phenotypic variance is called BROAD-SENSE HERITABILITY

VG + VE + VGE

X 100

MAJOR COMPONENT OF GENETIC EFFECT

Genetic effect are divided to 3 components: 1. VA – Additive variance: Indicates the

number of favorable alleles needed for a particular locus

2. VD – Dominance variance: Interaction between alleles within the same locus

3. VI – Epistasis: Interaction among genes of different loci

Therefore: VG = VA + VD + VI

Ratio of additive variance over phenotypic variance is called NARROW-SENSE HERITABILITY

Narrow-sense Heritability = VA x 100

VP

Narrow-sense heritability is more meaningful because:

Additive effect are transmitted to the next generation

Dominance (interaction between alleles within the same locus) and epistasis (interaction between loci) varied between generations.

Epistasis effects are usually small and could be neglected.

MAJOR COMPONENTS OF GENETIC EFFECTS

EXAMPLE

Consider plant height controlled by one locus A/a

A=45 cm and a= 15cm

Additive effect: AA = 90cm, Aa = 60 cm aa=30cm

Dominance effect: AA = Aa = 90cm aa=30cm

aa=30cm

Aa = 60cm

AA = 90cm

aa=30cm

M AA = Aa = 90cm

EXAMPLE

GENE EFFECTS

FEMALE PARENT

MALE PARENT

AVERAGE HEIGHT OF PROGENIES

(F1)

No Dominance(Completely additive)

Complete Dominance

AA (90 cm)

AA (90 cm)

aa (30 cm)

aa (30 cm)

Aa (60 cm)

Aa (90 cm)

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY

Crosses between 2 homozygous parents

Parent P1 x Parent P2

F1

A1A2

F2

1(A1A1) 2(A1A2) 1(A2A2)

(A1A1) (A2A2

)

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY (Cont.)

Backcross 1 to parent P1 (BC1P1)

Parent P1 x Parent P2

F1

(A1A2)

BC1P1

1(A1A1) 1(A1A2)

(A1A1) (A2A2

)

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY (Cont.)

Backcross 1 to parent P2 (BC1P2)

Parent P1 x Parent P2

F1

A1A2

BC1P2

1(A2A2) 1(A1A2)

(A1A1) (A2A2

)

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY (Cont.) All populations are planted at the

same time in the same environmentPopulation Variance

Expected Variance Components

Genotype

VP1

VP2

VF1

VF2

VBC1P1

VBC1P2

VE

VE

VE

VA+VD+VE

½VA+VD+VE

½VA+VD+VE

A1A1

A1A1

A1A1

A1A2

2A1A2

A1A2

A1A2

A2A2

A2A2

A2A2

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY (Cont.)

1. Environmental Variance (VE)

VE = (VP1 + VP2 + VF1)/3

2. Phenotypic Variance (VP)

VP = VG + VE = VA + VD + VE = VF2

3. Genetic Variance (VG) VG = VP - VE

= VF2 –[(VP1 + VP2 + VF1)/3]

METHODS TO DETERMINE GENETIC VARIANCE COMPONENTS AND HERITABILITY (Cont.)

4. Additive Variance (VA) 2VF2 = 2VA + 2VD + 2VE VBC1P1 + VBC1P2 = VA + 2VD + 2VE VA = 2VF2 - (VBC1P1 + VBC1P2 )

5. Dominance Variance (VD) VD = VG - VA

= {VF2 –[(VP1 + VP2 + VF1)/3]} - {2VF2 - (VBC1P1 + VBC1P2 )}

METHODS TO CALCULATE HERITABILITY

1. Based on P1, P2, F1, dan F2 Population Variation Broad-sense Heritability (HB) = VG/VP

= VF2 –[(VP1 + VP2 + VF1)/3]

VF2

2. Based on F2 , BCP1 & BCP2 Population Variation Narrow-sense Heritability (HN) = VA/VP

= 2VF2 - (VBC1P1 + VBC1P2 )

VF2

METHODS TO CALCULATE HERITABILITY (Cont.)3. Parent (X) to Offsprings (Y) Regression

Method

Y= a + bX

High Heritability value = character from the parent is highly inherited by the offsprings

Y

X

METHODS TO CALCULATE HERITABILITY (Cont.)3. Parent (X) to Offspring (Y)

Regression Method Arrangement of parent and offspring

dataFemale Parent

Male Parent

Parent Average

Offspring

X1 X1 X1 Y1

X2 X2 X2 Y2

X3 X3 X3 Y3

. . . .

. . . .

Xn Xn Xn Y4

SX SX SX SY

Parent- Offspring Regression (bxy)

= Sxy - {(SxSy)/n}Sx2 - {(Sx)2/n}

where: y = offspring value

x = parent value If X is the value of one of the parent (male or female):

Narrow-sense Heritability (HN) = 2b If X is the average value of the parents:

Narrow-sense Heritability(HN) = b

METHODS TO CALCULATE HERITABILITY (Cont.)

4. Components in Analysis of Variance (ANOVA) Method

Source of variation

d.f. Mean squares

Expected Mean Squares

ReplicationGenotypeError

r-1g-1(r-1)(g-1)

M1M2

se2 + rsg

2

se2

METHODS TO CALCULATE HERITABILITY (Cont.)

Computation of Variance Components:

VG = sg2 = (M1 – M2)/r

= (se2 + rsg

2 - se2)/r

= rsg2/r

= sg2

VE = se2 = M2

Broad-sense Heritability (HB) = VG /(VG + VE )

Genetic Advance From Selection From heritability value, genetic advance

from selection can be estimated:

Original populati

on

Selected

parent

Progenies (offspring) of

selected parents

XO =10 t/ha

XS=14 t/ha

XE = ?

Original population

Selected population

Progenies of Selected population

Genetic Advance From Selection (Cont.)

Genetic Advance From Selection (Cont.)

Computation of Genetic Advance (GA) and population mean of progenies of selected population (XE):-Consider the Heritability (H) = 60% GA = (XS- XO)H

= (14 – 10)0.6=2.4 t/ha

XE = XO + (XS - XO)H= 10 + 2.4 t/ha= 12.4 t/ha