Marker Assisted Selection in Tomato Pathway approach for candidate gene identification and introduction to metabolic pathway databases. Identification of polymorphisms in data-based sequences MAS – forward selection, background selection, combining traits, relative efficiency of selection Why (population) size matters
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Marker Assisted Selection in Tomato
Pathway approach for candidate gene identification and introduction to metabolic pathway databases.
Identification of polymorphisms in data-based sequences
MAS – forward selection, background selection, combining traits, relative efficiency of selection
Why (population) size matters
Dist MarkercM Name
CT233
17.1
TG672.1LEOH36
20.0
TG1252.0CT62
24.7
CT1497.2
LEOH17*
12.8
TG2739.3
TG599.9
CT191
10.7TG465
5.8TG2601.1LEOH7
15.1
TG25510.1
TG580
Chr 1
Dist MarkercM Name
TG608
13.9
CT205
10.7TG1653.8 LEOH23
10.9TG14
18.4
CT2446.1
TG4695.2
TG645
10.6TG537
7.0TG1673.1TG151
10.2TG154
Chr 2
Dist MarkercM Name
TG15
12.4
TG483
23.6
CT157
18.5
LEOH377.7
CT1786.5
CT194
16.5
CT501.6TG500
13.6
TG1630.0LEOH10
Chr 4
Dist MarkercM Name
CT1017.9
TG4413.6CT167
18.5
CT933.0LEOH163.0TG96
12.5
TG100A
19.5
CT118
28.3
TG185
Chr 5
IL1-
1
IL4-
3IL
4-4
IL1-
2IL
1-3
Chr 3
IL2-
4
LEOH15*
IL4-
1
LEOH17*
IL5-
2
LEOH17*
Dist MarkercM Name
TG1145.2
TG130
18.5
CT141
13.4
TG520
23.5
CT829.1
CD5110.1
TG1295.7
TG2468.2
CT85
18.2
TG214
IL3-
2
LEOH17*
IL3-
1
LEOH15*
IL3-
3
LEOH17*
LEOH17*
LEOH36
LEOH10
LEOH37
Example: QTL for color uniformity in elite crosses
QTL Trait Origin2 L, YSD S. lyc.4 YSD S. lyc.6 L, Hue ogc
7 L, Hue S. hab.11 L, Hue S. lyc.Audrey Darrigues, Eileen Kabelka
Carotenoid Biosynthesis: Candidate pathway for genes that affect color and color uniformity.
Disclaimer: this is not the only candidate pathway…
Improving efficiency of selection in terms of 1) relative efficiency of selection, 2) time, 3) gain under selection and 4) cost will benefit from markers for both forward and background selection.
Remainder of Presentation will focus onWhere to apply markers in a programForward and background selectionMarker resourcesAlternative population structures and size
Relative efficiency of selection:r(gen) x {Hi/Hd}
Line performance over locations > MAS > Single plant
Comparison of direct selection with indirect selection (MAS).
F1 50:50
BC1 75:25
BC2 87.5:12.5
BC3 93.75:6.25
BC4 96.875:3.125
Expected proportion of Recurrent Parent (RP) genome in BC progeny
Accelerating Backcross Selection
Select for target allele
Select for RP genome at unlinked markers
Select for target allele
Select for RP recombinants at flanking markers
Select for RP genome at unlinked markers
Select for target allele
Select for RP recombinants at flanking markers
Select for RP genome on carrier chromosome
Select for RP genome at unlinked markers
Four-stage selection
Two-stage selection
Three-stage selection
References:
Frisch, M., M. Bohn, and A.E. Melchinger. 1999. Comparison of Selection Strategies for Marker-Assisted Backcrossing of a Gene. Crop Science 39: 1295-1301.
Progeny needed for Background Selection During MAS
n = 1 n = 2 n = 3 n = 4 n = 5-10 n > 10Total 806 596 106 34 22 38 10
n = 1 n = 2 n = 3 n = 4 n = 5-10 n > 10Total 127 not tested 64 22 11 23 7
Proportion 0.16 0.60 0.65 0.50 0.61 0.70
TA496 ESTs with SNPs VS H1706 BAC sequences
Where EST Coverage = Allele Coverage
Data based on estimated ~42% of sequence, therefore expect as many as 300 markers for a cross like E6203 x H1706
analysis by Buell et al., unpublished
QTL’s mapped in a bi-parental cross may not be appropriate for MAS in all populations…
Marker allele and trait may not be linked in all populations.
Genetic background effects may be population specific.
Original association may be spurious.
QTL detection is dependent on magnitude of the difference between alleles and the variance within marker classes.
What about mapping and MAS in unstructured populations?
A brief introduction to “Association Mapping” follows.
Y = μ REPy + Qw + Markerα + Zv + Error
“Association Mapping” statistical model – designed to account for population structure (Q), correct for genetic background effects (Z), and identify marker-trait linkage (Marker)