different types of mapping population and development of mapping population in ornamental crops are mentioned

1. APARNA VELURU
ROLL NO- 10134

2. Components of a Molecular Mapping Programme
Marker
Software Population

3. Genetic Map Construction
 Selection of suitable parents
 Generation of appropriate mapping
population and its genotyping
 Calculation of pair-wise recombination
frequency between markers
 Identifying Linkage groups
 Estimation of map distances
 Determining map order

4. Selection of parents
 Source of parents
 Contrasting phenotype
 Sufficient variation at DNA level

5. Mapping Population
Types
• Mortal mapping population
• Immortal mapping population

6.  The population as such can be reproduced but it is
difficult or improbable to identify the individuals of
same genetic make up
F2 population
F2 derived F3 (F2:3) population
Backcross population
Mortal Mapping Population

7. Produced by selfing of the F1s between selected parents
Merits Appropriate populations for preliminary mapping
 Useful in identifying heterotic QTLs
 Requires less time and efforts for development
Demerits
 Linkage established using F2 population is
based on one cycle of meiosis
 Quantitative traits cannot be precisely mapped using F2
population
 Not an immortal population
 Of limited use for fine mapping and map saturation

8. F2 population: Genetic mapping in monkey flowerF2 population: Genetic mapping in monkey flower
Mimulus cardinalisMimulus lewisii X
Rodney Mauricio, 2001

9. Segregation pattern of a Co-dominant marker
in an F2 population

10. F2 derived F3(F2:3) population
 Obtained by selfing F2 individuals
 Suitable for
mapping quantitative traits
mapping recessive genes
 Useful for reconstitution of individual F2 genotypes
Demerit
 Like F2 population, it is not immortal

11. AA aa
F1
F2 AA Aa aa
All AA AA, Aa, aa All aaF3
Aa
Parents

12. Backcross population
 Generated by crossing F1 with either of the parents,
usually the recessive parent (test- cross)
 Requires less time for development
 Can be utilized for marker assisted backcross breeding
 Recombination from only one parent (F1) is accounted
 Population is not immortal
Demerits

13. Back cross design :Genetic mapping in Louisiana irises
Iris fulva
Iris brevicaulis
F1 X Iris brevicaulis
BC 1
F1 X Iris fulva
BC2
Rodney Mauricio, 2001

14. A population which can reproduce itself or can be
reproduced without any change in genetic make
up of constituent individuals
 Doubled Haploids (DHs)
 Recombinant Inbred Lines (RILs)
 Immortalized F2 population
 Near - Isogenic Lines (NILs)
 NILs- F2
 MAGIC

Immortal Mapping Population

15. Anther culture
Haploids
Chromosome doubling
Parent 1 x Parent 2
F1 plants

16. Doubled Haploids
Merits Demerits
 Permanent population
 Instant production of
homozygous lines
 Suitable for mapping both
qualitative and quantitative
traits
 Recombination from male side
alone is accounted
 Non-availability of suitable
haploid production techniques
 Anther culture induced variation
 Differential regeneration
response of parents
Since recombination information is derived from only one parent, BC and DH
require twice the population size than F2

17. Recombinant Inbred Lines (RILs)
 Produced by selfing or sib-mating F2
individuals till they reach homozygosity
 Self incompatibility
 Inbreeding depression
 Population size

18. Production of RILs

20. Segregation pattern of a Co-dominant marker
in a RILs population

21. Recombinant Inbred Lines
Merits Demerits
 RILs are immortal
 Of immense use for QTL
mapping
 Suitable for fine mapping &
map saturation
 RILs are twice as efficient as
an F2 population
 Require many seasons/
generations to develop
 Inbreeding depression if
present, could hinder RILs
production

22. Near- Isogenic Lines
 Can be developed either through selfing or backcrossing
Parent A x Parent B
F1 (Selfing)
F2
Selection and selfing
NILs
Hom. Dom: Het. : Hom. Rec.
Parent A x Parent B
F1 x Parent B
BC1: Selection and backcrossing
NILs

23. Development of NILs through selfing
Parent 1 Parent 2X
AA BB CC RR aa bb cc rr
Aa Bb Cc RrF1
F2 AA bb CC Rr
AA bb CC RR AA bb CC rr
Isogenic Lines
 Identification of heterozygote for target trait
 NILs would differ from parents
 Simple procedure

24. Merits Demerits
 Immortal populations
 Suitable for gene tagging
 Useful in functional genomics
 Require many generations
to develop
 Not useful for linkage
mapping
 Linkage drag
Near -Isogenic Lines

25. Immortalized F2
population
Parent 1 Parent 2
AAbb X aaBB
F1 AaBb
Conventional F2 population Immortalized F2 population
RILs produced from
AAbb X aaBB
AABB, AAbb
aaBB, aabb
Six possible RIL
combinations
Six heterozygous
genotypes
AABB X AAbb
X aaBB
X aabb
AABb
AaBB
AaBb
AAbb X aaBB
X aabb
AaBb
Aabb
aaBB X aabb aaBb
AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB AaBB AaBb aaBB aaBb
ab AaBb Aabb aaBb aabb
F2

26. Development of Chromosomal Segment
Substitution Lines (CSSLs)

27. Association mapping (AM)- process of identification of genetic markers for qualitative or
quantitative traits using statistical tools on population of unrelated individuals

28. MAGIC – a 2nd
generation mapping resource
-a new generation tool for gene-trait association for multi-genic
trait or QTLs in crop plants with large genome size leading
towards candidate gene isolations.
Inter-cross ‘n’ lines
for n/2 Gen
RILs
Selfing
Cavanagh et al., 2008,

29. Step-2: Genotype the RILs with markers
Step 1: Creation of inbred lines
NESTED ASSOCIATION MAPPING
Reference line

30. X
A
a
b b
C c
d d
E e
a a
B b
c c
D d
E e
a aA a A a a a
B bB bb bb b
c cC cc cC c
d d D dD dd d
E E E e E e E e
P1 P2 1 2 3 4
M1
M2
M3
M4
M5
1:1
3:1

31. Marker Nature Genetic Segregation Ratio
F2 RILs DHs Backcross
B1 B2
RFLP Codominant 1:2:1 1:1 1:1 1:1 1:1
RAPD Dominant 3:1 1:1 1:1 1:0 1:1
AFLP Dominant 3:1 1:1 1:1 1:0 1:1
SSR Codominant 1:2:1 1:1 1:1 1:1 1:1
Genetic Segregation Ratio in Different
Marker-Population Combination

32. Precautions in molecular mapping
 Selection of suitable populations and marker
system
 Proper phenotypic characterization of mapping
populations
Replicating over location and time
Estimation of G x E effect
Use of proper scales (disease resistance)
 Segregation distortion of the traits or the markers

33. Bulk segregant analysis (BSA)
Resistant Parent Susceptible ParentX
F1
F2 individuals
R P S P R B S B R R S R S S
Michelmore et al, 1991

34. BSA- Some insights
 Probability of false positive is extremely low (2-19
- 2x10-6
)
even in 10 plants bulk
 Markers detection Vs recombination window
Recombination window Marker detection
20 cM Detectable by presence/ absence
>20 cM Detected by intensity
Michelmore et al, 1991

35. Number of recombinants:
AC = 6/20 (1, 3, 10, 13, 18, 19)
AD = 4/20 (1, 3, 10, 13)
CD = 2/20
C = 1/20 (plant number 18)
D = 1/20 (plant number 19)
calculation of recombination distance

36. 36
1.detection of polymorphic loci
A B
sizestd
sizestd
S
R
19479
19477
19478
19479
19480
300
400
500
600
700
STS markers (RGA
marker)
probeA8
R S
F1 individuals
RFLP markers
AFLP markers
SSR markers

37. 37
2. Analysis of segregation of markers

38. 38
3. Analysis of segregation of markers

39. 39
4. Selection of linkage groups

40. 40
5. Map construction –
genetic distances

41. 4 quantitative traits (FS, DF, LS and PM) were scored
Join Map 3.0 ( 1:1 monoparental, 3:1 biparantal)
LOD-5, Kosambi mapping function
Map QTL 4.0, IM and MQM
133 (130 RAPD, 1morphological, 2 microsatellites)
Construction of QTL map for 4 traits
Dugo et al, 2005

42. Population
designation
Female parent Male parent
V 23 (BC1 F1) V23 X R51-F1 V 23
R 51 (BC1 F1) V23 X R 51-F1 R 51
M V23 X R 51-F1 Mitchell (DH)
VRM V23 X R 51-F1 V23,R51,Mitchell
W137 V26 X W137-F1 W 137
DH Mitchell- Petunia hybrida X P. axillaris
Strommer et al, 2002

43. Strommer et al, 2002
VRM (BC) progeny + RFLP and AFLP
Petunia hybrida –genetic map

44. Genetic map of petunia hybrida (w 137 BC progeny)
Strommer et al, 2002

45. conclusion
High level of heterozygosity
Polyploidy nature
Complex hybrids
Propagation barriers
Self –incompatibility
Inbreeding depression
Availability of markers
Limited soft ware programmes