Genetic Diversity and Its Maintenance

8/9/2019 Genetic Diversity and Its Maintenance

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GeneticDiversit

yandits

maintenanc

e

B y

M r . S a r a d i n d u G h o s h


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Composed of ThreeComponents

Genetic Resource Management

Genome Databases

Genetic Characterization and Genetic Improvement


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Criteria used for ImpactAssessment

varieties or improved germplasm released

germplasm accessions conserved and distributed

genetic/genomic tools developed

genome information provided to users


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Genetic Mitigation of Abioticand Biotic Stress

Medium-high impactStrengthen programs in abiotic

stress, while continuing strongsupport for biotic stress resistanceWork to set priorities for crop

improvement by species

Develop and implement projects thatseek to improve crops for low inputsituations such as organicproduction


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aintenance of Genetic Diversity

Levels of genetic diversity result from the joint:impacts of

&Mutation migration adding variation&Chance directional selection removing variation

Balancing selection impeding its loss

The balance between these factors dependsstrongly on population size and differs across.characters


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onservation biologists need to understand hownetic diversity is maintained through natural

ocesses if conservation programs are to be.signed for its maintenance in managed populations

aintenance of extensive genetic diversity in,tural populations is one of the most important

,rgely unresolved questions of evolutionary.netics


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e balance of forces maintaining geneticversity differs between large and small.pulations

.lection has a major impact in large populations,wever its impacts are greatly reduced in small

pulations where genetic drift has an.creasingly important role


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ive major points about geneticiversity in :mall populationsGenetic drift fixes alleles more rapidly in

.smaller populations

Loci subjected to weak selection in largerpopulations approach effectively neutral in small.populations

-Mutation selection equilibria are lower in smaller

.than larger populations


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The effects of balanced polymorphisms depends;upon the equilibrium frequency the frequency offixation of intermediate frequency alleles is,retarded but balancing selection accelerates

.fixation of low frequency alleles

Balancing selection can retard loss of genetic

,diversity but it does not prevent it in small.populations

he consequence of these effects is that genetiche consequence of these effects is that geneticiversity in small populations is lower for bothiversity in small populations is lower for botheutral alleles and those subjected to balancingeutral alleles and those subjected to balancingselectionelection


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The influence of the deterministic forces ofnatural selection is directly related to population.size The fate of alleles in most small populations

of endangered species is predominated by random.factors

, ,Inbreeding with consequent loss of fitness

.becomes inevitable in small populations

(Effective population size Ne) as opposed to,census size determines loss of genetic diversity

.and inbreeding


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Effects of Sustained Population Size Reductionon Genetic Diversity

:Five mechanisms by which genetic diversity is lost

&Extinction of species populations( elatively uncommonelatively uncommon)

Fixation of favorable alleles by selection( elatively uncommonelatively uncommon)

Selective removal of deleterious alleles

-Random loss of alleles by inter generational sampling in.small populations

.Inbreeding within populations reducing heterozygosity


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, (In each generation a proportion /2N2N e) of.neutral genetic diversity is lost

Such effects occur every generation and losses.accumulate with time

:The predicted heterozygosity at generation t is

Ht = [ - /1 2N= [ - /1 2N e]tH0


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s is usually expressed as the predicted heterozygosity as a proportion of the i:erozygosity as follows

t/HH 0 = [ - /1 2N= [ - /1 2N e]t e e - /2Ne/2Nedicted declines in heterozygosity with time

.different sized populations


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:The important points of this relationship areLoss of genetic diversity depends upon the

effective population size rather than the.census size

Heterozygosity is lost at a greater rate in smaller

.than larger populations


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For example the proportion of heterozygosity

retained over 50 generations in a population withNe = :500 is

Ht/H0 = [ - /( )]1 1 2 X 500 50 = ( / )999 1000 50 = .0 951

Whereas for a population with Ne = , :25 it is

Ht/H0 = [ - /( )]1 1 2 X 2550 = ( / )49 50 50 = .0 364


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Loss of genetic diversity depends upon generationsNOTOT .years

,The shorter the generation length the more

.rapid in absolute time will be the loss

,Loss of heterozygosity continues with generations.in an exponential decay process

Half of the initial heterozygosity is lost in

.4N4N e .generations


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ffective population sizeffective population size -- All of the adversegenetic consequences of small populations dependson the Ne.

Most theoretical predictions in conservationgenetics are couched in terms of Ne.

,Thus it is important to have a clear understandingof the concept of Ne.


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Neis the number of individuals that would give,rise to the calculated loss of heterozygosity

,inbreeding or variance in allele frequencies ifthey behaved in the manner of the IdealizeddealizedPopulationopulation.The primary factors responsible for Neto be

: - ,smaller than census size are sex ratio high,variance in family size and fluctuating

.population sizes over generations


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-nequal Sex Ratios-nequal Sex RatiosIn many wild populations the number of breeding

.males and breeding females is not the same

(Many mammals have harems polygamyolygamy) where one,male mates with many females while many males

make no genetic contribution to the next.generation

,In a few species this situation is reversed(polyandryolyandry).


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-The equation for accounting for unequal sex ratios:is Ne = (4NmNf)/(Nm + Nf)

: ,As the sex ratio deviates from 1 1 the Ne/N.declines

,For example an elephant seal harem with 1 maleand 100 females has an Ne .of 4

, - -However it is the life time sex ratio over.generations that is important


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,In practice harem masters often have limited-tenure so that the average sex ratio over a

complete generation is usually much less skewed

.than that occurring during a single breeding season

, -Overall unequal sex ratios have modest effects inreducing effective population sizes below actual

, %.sizes resulting in average reductions of 36

ariation in Family Sizeariation in Family Size -- The higher the variance,in family size the lower the effective population.size

,If family sizes are equalized Vk = 0 then Ne .2N

.This is critical to captive breeding programsEqualization of family sizes potentially allows the

limited captive breeding space for endangered.species to be effectively doubled


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,Because of this equalization of family sizesforms part of the recommended managementregime for captive breeding of endangered

species.


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luctuations in Population Sizeluctuations in Population Size -- the effectivesize of a fluctuating population is not the

average but the harmonic mean of the effective.population sizes of t generations

- ,This is the long term overall effective population.size

Fluctuations in population size are the mostimportant factor reducing Ne, on average reducing

%.it by 65


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nbred populationsnbred populations -- Inbreeding reduces:effective population size as follows

Ne = /( + )

N 1 F

verlapping Generationsverlapping Generations -- Most natural populations.have overlapping rather than discrete generations

The effect on Neof overlapping generations are,not clearly in one direction however they are more

likely to reduce Ne .relative to N


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v v ol ut i on a ry c om p ut a ti on i m u l a t e s t h e at ur al e vo lu ti on n ac o m p u t e r

E v o l u t i o n a r yE v o l u t i o n a r y

C o m p u t a t i o nC o m p u t a t i o n

ro c e s s le a d i ng t o m ai n t e n an c e o r i nc r e a s e o f a po pu l a t i o nbi l i t y to s u rv i v e n d re p r od u c e i n a sp e c if i c e n v ir o n me n t

u a n t i ta t i v e l y m e as ur e d b y v o l u t i o n a r yf i t n e s sv o a l o f n a t u r a l e v o l ut io n - o g e ne r a te p o p u l a t i o n fi n d i v i d u a l s w i t h

n c r e a s i n g f i t n e s sv o a l o f e v o l u t i o n a r y c om p u t a t io n - o g en e r at e s e t f o l u t i o n s( o a )r ob l e m o fn c r e a s i n g q u a l i t y


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a tur al e vo lu ti on -i m u l a t i o n o r e of t h e :v ol ut io n ar y a lg or i th m s p ti m is at io n a lg o ri th ms ( t e ra t i ve l y i m pr o v e t h e q u a li t y o fh e s ol u t i o n s u n t i l a n /pt im al f ea sib le s ol ut io n )s f o u n d

E v o l u t i o n a r yE v o l u t i o n a r y

A l g o r i t h m sA l g o r i t h m s

Initial population creation (randomly)

Fitness evaluation (of each chromosome)

Terminate?

Selection of individuals (proportional with fitness)

Reproduction (genetic operators)

Replacement of the current population with the new

one

yes

no

Stop

Start

R u n

o ble m d ef in it io nc o di n g o f t he a nd ida te s ol uti ont nes s d ef in it io nu n c o di n g t h e be s t f it t e d=h r o m o s o m e o l u t i o nNew

gen

eration

as ic e v o l u t i o na r y al g o r i t hm


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C l a s s e s o f C l a s s e s o f

E v o l u t i o n a r yE v o l u t i o n a r yA l g o r i t h m sA l g o r i t h m s( )e ne ti c A lg o r i t h m s G A ( . . , )H H ol l a nd 19 7 5( )e ne ti c P ro g r a m m i n g G P ( . . , )R Ko z a 1 9 9 2

( )e ne E xp r e s s i o n P ro gr a mm in g G E P ( . , )F e r re i ra 2 00 1

a i n d i ff er en c esv n c o d i n g me th odv e pr od uct io n me th od


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P s e a r c h o r t h e o mp ut er p ro gr am ,o so l ve th e p ro b l em.o t f or t h e s o l u t i o n t o t h e pr o b l e m p r o g r a m - ny c o mp u t in g l a n gu ag e ( )n pr i n ci p le- L I S P ( )i s t P ro c e ss o r ( )n p ra c t ic eI S P - -ig h l y sy m b ol o r i en t ed

a*b-c (-(*ab)c)-

a t h e m a t i c a le x p r e s s i o n -e x p r e s s i o n

-r a ph ic a l r e p r e s en ta t i o n o f Se x p r e s s i o n

* c

a b

( + , * )u n c t i o n s n d ( , , )er mi n a l s a b c

: - - = >hr o m o s o m e S e x p r e s s i on v a ri ab l e l en g t h m o r e f l e x i b i l i ty- = >in t a x co n s tr a i nt s i n va l ide x p r e s s i o n s =>r o d u c e d i n th e e v o l u t i o n p r o c e s s m u s t b e e l i m i na t e d w a s t ef C P U

G e n e t i cG e n e t i c

P r o g r a m m i n gP r o g r a m m i n g

vE n c o d i n g

v e p r o d u c t i o n( ) ( )m b i na t i o n c r o s s ov er a n d M u t a t i o n u s u al y


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29

A n a l y s i sA n a l y s i sr a i n i n g s a mp l e

=o t a l 3 9 8 5 e v e n t s= 3 39 0 e v en t s= 5 95 e v e nt s

V a r i a b l e s - ( )doca distance of closest approach-RXY, |RZ ( )| region around interaction point- (|cos )|- ( )SFL Signed Flight Length

. = , =o o f g en es 1 H ea d l en g th 2


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S t a n d a r d c u tS t a n d a r d c u t

a n a l y s i sa n a l y s i s


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C o m p l e xC o m p l e x

c h r o m o s o m e sc h r o m o s o m e s


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P e r f o r m a n c eP e r f o r m a n c e

P a r a m e t e r sP a r a m e t e r s~ %92

~ %8


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Application of Molecular markers

Uses of molecular markerAssessment of genetic diversity and polymorphismCharacterization of different stocksMarker assisted selection

Different techniques involved

RAPD (Randomly Amplified Polymorphic DNA)RFLP (Restriction Fragment Length Polymorphism)DNA micro satellitesSCAR marker


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Protein allozymes: electrophoretic variants ofproteins produced by different alleles atprotein-colding genes.

Protein Electrophoresis Gel

Molecular Polymorphism


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DNA Variation

R F L P

R A P D

A F L P

V N T R


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Restriction Fragment LengthPolymorphism (RFLP)

Enzymes cut DNA at specific sequencesRestriction sites are often palindromes:6-cutter GAATTC 4-cutter TCGA

CTTAAG AGCT

d l lifi d l hi


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RAPD: randomly amplified polymorphicDNA

Size sorted


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AFLP: amplified fragment lengthpolymorphism

Digestion of DNA with twoenzymes

Ligation of adapters to

fragment ends

Primers complementary toadapters and to 3 region ofsome of the fragments


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AFLPs


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VNTR: variable number tandem repeats

Non-coding regions

Several to many copies of the same sequence

Large amount of variation among individuals in the number ofcopies


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Microsatellites

Not a tiny orbiting space craft

Most useful VNTRs

2, 3, or 4 base-pair repeats

A few to 100 tandem copies

Highly variable

Many different microsatellite loci (1000s) in any species


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Microsatellites

Design primers to flanking regions


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Microsatellite Gels


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Microsatellites

Advantages: highly variable, fast evolving, co-domininant

Relatively expensive and time consuming to develop


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HANK U

Genetic Diversity and Its Maintenance

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