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Genetic Diversity and the Effects of Artificial Selection in Maize . Maize Diversity Project Team. Molecular Diversity. How has selection shaped molecular diversity in maize? What is the relationship of selected genes to agronomic traits? Goal: Identify genes exhibiting selection

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Genetic Diversity and the Effects of Artificial Selection in Maize

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Genetic diversity and the effects of artificial selection in maize

Genetic Diversity and the Effects of Artificial

Selection in Maize


Maize diversity project team

Maize Diversity Project Team


Molecular diversity

Molecular Diversity

How has selection shaped molecular diversity in maize?

What is the relationship of selected genes to agronomic traits?

Goal: Identify genes exhibiting selection

  • Domestication, agronomic improvement, and local adaptation

    Community resource: SNP marker collection


Genetic diversity and the effects of artificial selection in maize

Teosinte

Landraces

Inbreds/Hybrids

Photos courtesy J. Doebley


Major predictions for the model

Major predictions for the model

Those genes have contributed most to maize improvement, i.e. have experienced the strongest history of selection have the least genetic variability left to contribute to crop improvement by classical breeding.

These genes will not be detected in standard QTL experiments because all lines will contain similar alleles.


Can we develop genomics screens to identify genes that have undergone selection

Can we develop genomics screens to identify genes that have undergone selection?

Invariant SSR approach (Vigouroux et al. 2002 PNAS 99:9650)

Directly contrast sequence diversity among teosintes and inbreds (Wright et al. 2005 Science 308:1310)

Are genes with low inbred diversity enriched for selected genes? (Yamasaki et al. 2005 Plant Cell 17:2859)

[email protected] for .pdfs


Summary of sequencing on random genes irie vroh bi masanori yamasaki kate houchins

Summary of Sequencing on Random Genes(Irie Vroh Bi, Masanori Yamasaki, Kate Houchins)

MPZ inbreds – (temperate) B73(2), Mo17(2), Hp301, Il14H, Ky21, M37W, Oh43, (tropical) CML69, CML247, CML322, CML333, KUI3, KUI11, NC350.

1095 alignments - 6169 SNPs.

MPZ inbreds + 16 teosinte partial inbreds

774 alignments – 3463 SNPs MPZ inbreds – 6136 SNPs in teosintes.


Genetic diversity and the effects of artificial selection in maize

Sequence statistics for 1095 genes

for diverse maize inbred lines.

NLTotal LSTotal S π

All Maize13.1280.43070345.66169 0.0067

Temperate6.7292.23103064.34560 0.0065

Tropical 6.6290.83088164.24427 0.0061

N = number of sequences, L = length of alignment,

S = number of segregating sites, π average number

of pairwise differences per bp.


Inbred teosinte sequence summary

Inbred-Teosinte Sequence Summary

  • Number of alignments >5 in both sets774

  • Average sample size inbreds12.0

  • Average sample size teosinte12.7

  • Average alignment length294

  • Total SNPS in inbreds3463

  • Total SNP in teosintes6136


Genetic diversity and the effects of artificial selection in maize

Diversity in maize inbreds vs. teosinte

0.07

0.06

0.05

0.04

q inbreds

0.03

0.02

0.01

0

0

0.02

0.04

0.06

0.08

q teosintes

Average q.inbred/q.teosinte0.57

Excluding q.inbred=0 values0.63


To identify the selected genes we need new statistical approaches

To identify the selected genes we need new statistical approaches

  • There are two models: a selection model and a bottleneck model

  • We must estimate the size of the bottleneck

  • For each model, we estimate the probability of the model given the data (the likelihood) for each gene

  • This is very simulation and computer intensive!

  • This approach allows us to estimate the proportion of genes under selection and to identify the candidates


Genetic diversity and the effects of artificial selection in maize

Na

t1

Nb

Na

t2

Np

t1

Nb

t2

Np

Two models: To be considered selected need to fail the

neutral model and be accepted by the selected model.

selected

neutral


Genetic diversity and the effects of artificial selection in maize

Genes significant for selection


On a genomic scale

On a genomic scale….

  • Assume 40,000 genes in maize

  • 40,000 x 0.04 = 1600 selected genes

  • Before genome scans, 11 genes had been identified as selected by population genetic approaches

  • By sequencing 1000 genes, have ~30 novel candidates

  • These genes need to be divided between domestication and improvement


What genes show evidence of selection

What genes show evidence of selection?

  • Genes involved in amino acid synthesis or metabolism

  • Genes involved in growth response.

  • Transcription factors and signal transduction components.

  • Unique genes with no significant BLAST homologies.


Genetic diversity and the effects of artificial selection in maize

Are genes with low inbred diversity enriched for domestication and improvement candidates?(Masanori Yamasaki)

Chose 35 genes with no diversity among the MPZ inbred set.

Sequenced same region in 16 haploid landrace samples, 16 teosinte partial inbreds and a Tripsacum dactyloides sample.

Performed Hudson-Kreitman-Aguadé(HKA) (tests for selection) on inbreds, landraces and teosintes against the neutral genes adh1, glb1, fus6 and bz2.

Performed coalescent simulations of domestication (CS) of inbreds vs. teosintes and landraces vs. teosintes.


Genetic diversity and the effects of artificial selection in maize

ARF

Amino Acid Transporter

0.01

0.02

0.01

0

1

1000

2000

3000

0

1

500

1000

Unknown

GTP-binding Protein

0.02

0.02

0.01

0.01

0

0

1

500

1000

1500

1

500

1000

1500

Ankyrin repeat

F-box (circadian clock)

0.03

0.08

0.06

0.02

0.04

0.01

0.02

0

0

1

1000

2000

3000

1

1000

2000

0.02

Fruit protein

Chromatin remodeling

0.03

0.02

0.01

0.01

0

0

1

1000

2000

3000

1

500

1000

1500

p

Nucleotide position (bp)


Do genes exhibiting signatures of selection control agronomic traits sherry flint garcia

Do genes exhibiting signatures of selection control agronomic traits?(Sherry Flint-Garcia)

  • Hypothesis: manipulation of the expression of domestication and improvement genes will alter key agronomic traits

  • Methods: use genetic and transgenic approaches to examine teosinte, exotic, and inbred alleles

  • Test case: amino acid composition in kernels

  • Evidence for selection for cysteine synthase, chorismate mutase, dihydrodipicolinate synthase and hexokinase


Genetic diversity and the effects of artificial selection in maize

To what extend has diversity in amino acid synthesis genes been reduced by selection? (Sherry Flint-Garcia)

  • Whitt et al., 2002 demonstrated that 3 of 6 genes in starch synthesis pathway in maize show solid evidence of artificial selection

  • Evidence for selection for cysteine synthase, chorismate mutase, dihydrodipicolinate synthase and hexokinase from random sequencing

  • Chose 16 additional genes for important steps in amino acid synthesis, sequenced in teosintes, landraces and inbreds and conducted tests of selection


Genetic diversity and the effects of artificial selection in maize

30

25

Teosinte (n = 7)

25

Landraces (n = 11)

20

Maize (n = 27)

20

15

15

Percent of Kernel Weight

Percent of total amino acid

10

10

5

5

0

0

Teosinte vs. Landraces

**

**

**

**

**

ns

ns

**

ns

**

**

**

**

**

**

ns

**

**

**

Teosinte vs. Inbred Lines

**

**

**

**

**

**

**

**

**

**

**

**

**

**

**

ns

**

ns

**

Valine

Lysine

Serine

Proline

Alanine

Glycine

Leucine

Arginine

Histidine

Tyrosine

Cysteine

Total Amino Acid

Isoleucine

Threonine

Methionine

Tryptophan

Aspartic Acid

Glutamic Acid

Phenylalanine


Genetic diversity and the effects of artificial selection in maize

Trans-cinnamic

acid

Lignin

PAL

Glucose

Phenylalanine

Tyrosine

Glycine

Serine

O-Acetylserine

3-Phospho-

glycerate

Prephenate

Cysteine synthase

Erythrose 4-P

Chorismate

mutase

Cysteine

2-isopropyl-

malate

synthase

Phosphoenol

pyruvate

DAHP

Shikimate

Chorismate

Leucine

Anthranilate

Synthase β

Pyruvate

Alanine

Pyruvate

Anthranilate

Valine

Acetyl-CoA

Acetohydroxy

acid synthase

Indole-3-glycerol

phosphate

Asparagine

Isoleucine

Tryptophan

Synthase β1

Aspartate

Amino-

transferase

Asparagine

synthetase

Tryptophan

2-Ketobutyrate

Aspartate

Oxalo-

acetate

Threonine deaminase

TCA Cycle

Aspartate

kinase

Glutamate

Threonine

Aspartate

4-seminaldehyde

NH4

Arginine

α-Keto-

glutarate

DHDP

synthase

Proline

Homoserine

4-phosphate

Proline

dehydrogenase

Glutamate

dehydrogenase

Cysteine

2,3-Dihydro-

dipicolinate

Cystathionine γ-synthase

Glutamate

Cystathionine

Homocysteine

Lysine

Glutamine

NH4

NO3–

NO2–

Methionine

Nitrate

Reductase

Histidine

SAM synthetase I

SAM synthetase II

Hexokinase

(N:C sensing)

S-Adenosyl-

methionine

ntl1 --nitrogen regulating protein


Sequencing candidate genes

Sequencing candidate genes

  • Goal is to sequence 1000 candidate genes in all inbreds for the 25DL, 16 teosintes, 2 Tripsacum, and W22 R-std

  • Shared responsibility by E. Buckler and

    M. McMullen laboratories

  • Develop SNP (or sequence) based assays for association analysis

  • Develop a mechanism to accept candidate gene suggestions for outside the project

  • www.panzea.org


Genetic diversity and the effects of artificial selection in maize

100%

80%

60%

38,000 genes

1,000 genes

1,000 genes


Implications for gem

Implications for GEM

  • For the vast majority of genes inbreds lines retain on average 60% of common diversity of teosinte and 80% of the diversity of landraces. Therefore the problem of loss of diversity is a specific problem to particular genes and traits rather than a general problem

  • Most of the diversity lost in unselected genes is in rare alleles and therefore hard to capture


Implications for gem1

Implications for GEM

  • Our studies to date have not addressed specific adaptation, possibly a more important justification for GEM than limited diversity per se

  • It is hard for me to think about how to tap diversity for specific adaptation without considering diversity in a trait context.


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