Marker assisted selection MAS

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Marker assisted selection(MAS)
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Difficulties of using MAS

• Still a relatively high cost technology
• Difficult to apply in population sizes used by
  breeders (1 million genotypes grown per year)
• For many traits the desirable genes (alleles)
  have not been identified
• QTLs for important traits often have small
  effects or markers are not close enough to the
  gene of interest

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How do we attain the next breakthroughs in rice
breeding?

• In many areas of South and Southeast Asia,
  widely-grown varieties with favorable features
  are rare achievements
• Many newly released varieties, while often
  showing superiority in breeders tests, do not
  replace the existing varieties

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These varieties are each grown on millions of
hectares
Samba Mahsuri
Mahsuri
Khao Dawk Mali 105
Swarna
RD6
IR64
CR1009
BR11
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Marker assisted backcrossing (MAB)

• Approach to rapidly introduce a favorable gene
  into a superior genetic background (widely grown
  variety or variety with rapidly expanding area)
• Smaller population sizes that are easier to
  handle with markers
• Clear advantage over conventional approach in
  speed of product development

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Targets for MAB
Mahsuri
Swarna
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Number of individuals to obtain desiredgenotype
in following BC generation (q0.99)
FL1
FL2
R
FL1
FL2
R
d1
d2
d1
d2
d (cM)
From Frisch, Bohn Melchinger 1999
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Backcross F1 (BC1F1)
Recurrent parent
Donor
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NIL (near isogenic line) (BC4F1)
Recurrent parent
Donor
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(BC2F2)
Recurrent parent
Donor
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MAB for Sub1
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Graphical genotypes of a MAB population
Swarna allele
Donor allele heterozygote
Sub1
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Individual withhighest Swarna alleles (242)
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Chromosome 9of individual 242
Sub1
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Timeline for MAB products
0
1
Recombination/background
BC2F1
Recombination/background
BC2F2
Background
2
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What we need for MAB

• Donor with a QTL or major gene that adds
  significant value
• Target cultivar or breeding line of high value
• Closely linked markers (flanking markers and
  cosegregating marker)

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Target QTLs for Abiotic Stress Tolerance
Approximate map position based on
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P uptake
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Pup1 LOD 16.5 R2 78.8
From Wissuwa Ismail
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Fine mapping salinity tolerance gene
Chromosome 1
58.1
RM23
60.6
AP3206-124201
62.5
AP4253-20757,RM3412
63.9
AP3722-9700
Saltol gene
64.9
RM140, S13927/AluI
65.4
AP3211-28
66.5
CP10135
67.6
AP2869-104052, AP2869-17620, RM8115
67.9
AP3143-072/DraI
73.7
RM113,RM24
LOD 6.7 R2 43.9
From G. Gregorio
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Cold tolerance
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LOD 8.36, R2 20.8
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LOD 20.34, R2 40.6
From Andaya Mackill 2003
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Al toxicity
Nguyen, Brar
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MAS in GAMMA
High-throughput mini prep DNA extraction
Lyophilize leaf samples
Add stainless steel balls
Place samples in 96 deep well plates
Use GenoGrinder to pulverize samples
Use automated liquid dispenser for DNA extraction
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High throughput manual SSR genotyping
High throughput automated genotyping using
fluorescently labeled primers
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GAMMA lab genotypers