Success of Illinois Long Term Selection Experiment Due To:

1
Success of Illinois Long Term Selection
Experiment Due To

• People Plants
• Science Technology
• Institution Infrastructure
• Civilization Peace

2
Strains Cycle 76
Alex Cycle 57
Born Cycle 7 8
3
Bob Cycle 45
Strains Cycle 46
Large Germ Small Kernel
Small Germ Large Kernel
4
Strains Cycle 96
John Cycle 63
5
Using the High Powered Comptometers
Strains Cycle 26 or so
Alice and Daisy Average Cycle 29
6
Strains Cycle 99
University of Illinois Cycle 134
7
Strains Cycle 103
U.S.A. Cycle 226
U.S.A. Cycle

Civilization Cycle ?
Maize Cycle ?
8
Without All These Factors Continually in Place

• Would Not Have the Same Amount of Progress
• My Part Falls Into Science Technology
• (I am a People Too.. )

9
In 1990, We Started to Isolate DNA from the
Strains

• Very Exciting Totally Cool!
• Perform RFLP Analyses
• A.H.D. Brown had done some earlier isozyme work
  Inconclusive

10
Me
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What are Levels of RFLP Marker Polymorphism?

• DNA from 50 Plant Bulks
• Earliest Most Recent Cycles
• Cycle 90 and 65 (69/87)
• Baseline - Polymorphism
• Found Lot of Polymorphism

12
Just Scored Whether Fragment Present or Not
Strains Cycle 93
13
Oil Strains Cycle 90250 RFLP Probes

• Polymorphism
• IHO vs. ILO 65
• IHO vs. RHO 45
• ILO vs. RLO 49

14
Protein Strains Cycle 91225 RFLP Probes

• IHP vs. ILP 64
• IHP vs. RHP 51
• ILP vs. RLP 50

15
Number Loci at Complete FixationOil Strains
Cycle 9052 Plants 49 RFLP Probes

• IHO 57 RHO 48
• ILO 68 RLO 61

16
Number of Loci at FixationProtein Strains Cycle
9125 Plants 35 RFLP Probes

• IHP 51 RHP 17
• ILP 43 RLP 23

17
Looked At Two Cycles In Protein Strains - Fixation

• IHP65 23 RHP65 14
• IHP91 51 RHP91 17
• ILP65 26 RLP65 14
• ILP91 43 RLP91 23

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Level Fixation Not Consistent with Theoretical
Inbreeding Coefficients

• For Cycle 90 F .88
• Between Cycles F .42
• 65 to 91

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Basis of Discrepancy?Lets Look at Population
Size

• 12 Ears Selected Each Cycle
• Inbreeding Eq.- Males 12 Females
• However, Tassels Collected and Bulk Pollinations
  Performed

20
Many Kernels from Selected Ears Used for Next
Cycle Bulk
21
Number of Females is 12 But There are More Males

• 12 Females - Two Alleles 24
• However Bulks Come from
• Many Kernels Pollinated by
• Many Different Plants
• Need to Recalculate Population Size

22
Transitions in Frequencies Consistent with
Response to Selection

• Trend Defined As A Variant
• IHO gt 0.5 ILO lt 0.5
• RHO lt 0.5 RLO gt 0.5

23
A Predominant
B Predominant
B Predominant
24
Example - Trend in Oil Strainsumc157 Bin 1.02
Cycle 90

• IHO ILO RHO RLO
• AA 52 0 14 13
• AB 0 5 17 19
• BB 0 47 21 14

25
Example - Trend in Oil Strainsumc147 Bin 5.01
Cycle 90

• IHO ILO RHO RLO
• AA 0 40 0 8
• AB 0 3 0 28
• BB 48 1 52 16

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Trends Detected In Oil Strains

• 3 of 49 in RHO
• 11 of 49 in RLO
• Few? Other Considerations
• Fixation by Cycle 48
• Multiple Alleles A, B, C

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If Fixed Cycle 48, Can Not Respond
28
If a Locus Is Fixed By Cycle 48, Can Not Respond
to Reverse Selection

• IHO RHO 14/49 Fixed
• ILO RLO 15/49 Fixed
• Same Allele Fixed in Forward and Reverse Strain

29
No Trend in Oil Strainsumc44 Bin 10.06 Cycle
90

• IHO ILO RHO RLO
• AA 52 0 52 0
• BB 0 52 0 52

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What About Multiple Alleles?Assessment Breaks
Down if Third Allele Becomes Frequent in a
Reverse Strain

• Allele A Frequent IHO
• Allele B Frequent ILO
• Allele C Frequent in RHO

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Allele A Predominant
Allele C Predominant
Allele B Predominant
32
Third Allele Selected in RHOnpi277 Bin 7.02
Cycle 90

• IHO ILO RHO RLO
• AA 51 1 0 36
• AB 0 0 0 14
• BB 0 43 0 0
• BC 0 7 0 0
• CC 0 1 52 0

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Selection for Low Oil in a Kernel That Has Gone
48 Cycles of Selection for High Oil 12-13
Can Not Assume Analagous to Selection on Kernels
in Burrs White 4-5 Oil
34
There are Differences Between Cycle 0 and Cycle
48 High Oil

• Kernel Morphology Difference
• Some Loci Fixed, Not Available for Reverse
  Selection
• Two Reasons For
• Selection Different Subset of Genes, And Maybe
  Alleles Also

35
Bob Cycle 45
Strains Cycle 46
Large Germ Small Kernel
Small Germ Large Kernel
36
Only Five Common Loci Fixed in Both High Oil and
Low Oil

• Different Subset of Loci Fixed, Yet Gain from
  Reverse Selection
• Different Loci Available for Reverse Selection? -
  RHO RLO
• Multiple Alleles

37

• AA AA AA
• AB AB AB
• BB BB BB
• AC AC
• BC BC
• CC CC
• AD
• BD
• CD
• DD

Maintenance of Multiple Alleles Allows Many
Genotypes Selection of Different
Genotypes Recombination of Different Homologues
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umc65 Bin 6.04 Cycle 90

• IHO ILO RHO RLO
• AA 20 0 0 0
• AC 20 0 0 0
• AD 9 0 0 0
• BB 0 52 46 0
• CD 3 0 0 11
• DD 0 0 0 40
• (We know there is a major QTL/R linked)

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Microsatellite Markers in Region, a Different
StoryOil Strains Cycles 65 100

• 50 Plants Umc1014 phi452693 nc009
• IHO RHO Fixed Allele A
• ILO RLO Fixed allele B
• Except for 9 ABs and 12 BCs in cycle 65 of RLO
  for two markers

40
What About RFLP Variant Trends in the Protein
Strains?
Im Responsive
41
Frequency Trends Detected In Protein Strains

• 14 of 35 in Reverse High Protein
• 7 of 35 in Reverse Low Protein
• All 7 that showed trend in RLP, also in trend RHP
• (Remember RHP had Rapid Response)

42
What About Fixation in Protein Strains?Maybe
Different Story from Oil

• Only 2 of 35 Loci Fixed for same allele in IHP /
  RHP
• Only 1 of 35 Loci Fixed in ILP / RLP
• Could Look at Cycle 65 91

43
How Do the Trends Correspond to QTL
Detection?Protein Strains

• All 7 Markers with Trends in Both RHPRLP Assoc.
  QTL
• 13/14 Trends Assoc. QTL
• Remember Some Markers Selected Based on QTL

44
Oil Strains

• 6 of 14 Bins Associated with Trends Also Linked
  with QTL
• Random Markers
• Detection of Smaller QTL?
• Have Not Mapped Enough QTL
• Drift?

45
Relationship of Fixed Loci with Detection of Oil
QTL

• 8/14 Loci Fixed Associated with Oil QTL in IHO
  x ILO
• Two Populations,
• Five QTL Detected in Both,
• Three QTL Detected in Only One

46
Before 3 Focused QTL, Take Home

• Higher Levels Heterozygosity in Strains than
  Predicted
• Likely Larger Population Size than Predicted
• Multiple RFLP Alleles Maintained
• Good Agreement Between Trends and Fixation with
  QTL Detection
• Can Not Directly Compare Selection within Strains
  with QTL Detection HxL

47
QTL in IHO x ILO One Focused Example
48

• Major Oil QTL Bin 6.04
• Major Oleic Acid QTL Bin 6.04
• Consistent Detection for Both
• F23s BC1S1s NILs Testcrosses
• Random Mated IHO x ILO RM6
• Oil QTL, Some Sig SFAV, Not CIM
• Oleic QTL, Sig SFAV Mult Reg CIM
• Different Basis Oleic Single Gene Oil May
  be Number of Genes

49
QTL in IHP x ILP Candidate Gene
50

• Starch QTL umc63 Shrunken2
• ADP-GPP Starch Biosynthesis
• Different Allele Sequence IHP ILP
• Amino Acid, Insertion Sequences
• Physiologically Different Alleles
• AGP Activity Maps to Sh2 RIL, NIL
• Multiple Alleles in Strains
• Predominant Alleles Not Unique
• One Intragenic Recombination Event?

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• Random Mating IHP x ILP RM4
• umc63 Shrunken2 Stay Significant
• But Shrunken2 Drops off More
• Gene(s) linked umc63 larger effect, may serve
  as switch for carbon
• ILP Shrunken2 Allele Takes Better Advantage of
  Carbon
• Example of Coupling Phase Linkage?

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• Branch vs Spikelet Meristem Number
• QTL Maps to Regions with Ramosa1
• Fails to Complement Tassel
• Does Complement Ear
• Transcription Factor
• Different Alleles IHO IL0
• Not Unique Alleles to Maize
• IHO/B73 Something Nearby - Bigger

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Acknowledge the Many People That Worked on These
Materials, and Results Presented (In Reward Got
a Job) Acknowledge Various Funding Sources that
Provide Support for this Work
These will all be
published in the Proceedings Article