Genetic architecture of kernel composition in the nested association mapping nam population
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Genetic Architecture of Kernel Composition in the Nested Association Mapping (NAM) Population. Sherry Flint-Garcia USDA-ARS Columbia, MO. Outline. Development of NAM Population Kernel Composition Joint Linkage Mapping Genome-Wide Association Mapping. Genotype Phenotype Composite

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Genetic architecture of kernel composition in the nested association mapping nam population

Genetic Architecture of Kernel Composition in the Nested Association Mapping (NAM) Population

Sherry Flint-GarciaUSDA-ARS Columbia, MO


Outline
Outline

  • Development of NAM Population

  • Kernel Composition

    • Joint Linkage Mapping

    • Genome-Wide Association Mapping


Linkage based qtl mapping

Genotype

Phenotype

Composite

Interval Mapping

b1520

b2077

u1622

u1552

b2277

m231

b1225

b2248

Linkage-Based QTL Mapping

  • “Genome Scan”

  • Identify genomic regions that contribute to variation and estimate QTL effects

Position (cM)

Parent 1

Parent 2

100

110

120

130

140

50

60

80

90

30

40

70

10

20

0

9

8

7

6

5

LOD Score

F1

4

3

F2 population

2

1

0


Linkage (QTL) Mapping

Nested Association Mapping

Structured families nested within an unstructured population

High Power

High Resolution

Analysis of many alleles

Association Mapping

Genome scan

Structured population

High power

Low resolution

Analysis of 2 alleles

Candidate gene testing

Unstructured population

Low power

High resolution

Analysis of many alleles


Nam founders
NAM Founders

CM37

R4

K148

Mo46

Ky228

Hi27

Oh7B

Mo47

NC344

K4

DE-3

Yu796-NS

NC360

Mo45

Mo17

B97

CMV3

CO106

A682

Mt42

W401

CI91B

NC362

NC262

NC222

A556

DE811

NC258

B103

Tzi25

B105

NC342

NC364

CI187-2

CI3A

B77

W117HT

Tzi16

MS153

DE1

SD40

A641

NC290A

A214N

NC250

STIFF STALK

B164

NC236

CM7

N7A

N28HT

H100

DE-2

B57

H84

I205

B64

C123

H105W

A635

CO109

ND246

A632

C103

B68

CO125

B79

H91

A634

B84

B14A

Hy

B76

Ky21

CM174

B104

A661

WD

CM105

A554

B75

CI21E

38-11

B37

MS71

Os420

NC260

NC328

R229

Mo44

A679

Mo1W

A680

R168

B73

B73Htrhm

NC294

NC326

B109

NC368

N192

NC324

NC292

NC314

NC322

NC330

W64A

Pa875

NC308

NC372

NC306

NC312

CH9

H49

NC268

NC310

A619

B10

WF9

B46

SD44

OH43

A239

Pa880

T8

A188

Pa762

C49A

C49

VA26

Va102

Ky226

Oh43E

A654

W153R

Va35

Va14

Va59

A659

CI-7

Oh40B

Va17

R177

Va22

W22

H95

W182B

Va99

PA91

H99

NON STIFF STALK

M14

CI90C

33-16

Va85

CH701-30

NC33

VaW6

4226

NC232

L317

B115

R109B

MoG

I137TN

K55

CI66

CI44

NC230

81-1

CI31A

MEF 156-55-2

M162W

CI64

IL677A

K64

Ia5125

E2558W

N6

SWEET

IA2132

P39

IL14H

CML52

T234

SC357

L578

IL101

CML69

CML14

CML38

B52

CML287

EP1

Tzi11

F2

NC366

CML103

CML108

F7

SC213R

CO255

CML9

GT112

CML61

NC238

CML254

CML5

T232

GA209

CML314

CML264

Mp339

CI28A

CML258

Q6199

CML10

B2

U267Y

CML341

CML332

CML11

CML45

MS1334

CML261

CML331

Mo24W

D940Y

Sg1533

SG18

IDS28

F2834T

M37W

HP301

IDS69

SA24

IDS91

CML277

CML238

CML322

CML321

A6

F44

Ki14

CML247

Ki11

4722

Ki2021

F6

I-29

TROPICAL-SUBTROPICAL

POPCORN

CML157Q

Ki44

Oh603

Ki43

CML328

NC340

Ki21

CML323

Ki2007

CML228

NC300

CML92

Tx303

A272

CML218

NC320

NC356

NC302

CML77

NC318

NC332

SC55

A441-5

Ki3

NC338

NC358

NC334

CML154Q

NC354

TZI18

NC370

TZI10

NC264

Ab28A

CML220

Mo18W

Tzi9

TX601

CML349

0.1

NC350

CML333

CML158Q

NC304

MIXED

CML91

Tzi8

CML311

Based on 89 SSR loci

CML281

NC346

NC296A

parvi-03

NC336

NC352

NC296

ssp. parviglumis

Flint-Garcia, et al. (2005) Plant J.

NC348

NC298

parvi-14

parvi-30

parvi-49

parvi-36


Nam development
NAM Development

  • Current genetic map consists of:

    • 4699 RILs

    • 1106 SNP loci

  • Average marker density - one marker every 1.3 cM

Linkage

Association

Yu, et al. (2008) Genetics; McMullen, et al. (2009) Science


Kernel composition in nam
Kernel Composition in NAM

Starch

Fiber

Amylose

Zeins

Amylopectin

Protein

Oil

Amino Acid

Profiles

Fatty Acid

Profiles


The phenotypic data
The Phenotypic Data

  • 7 locations of NAM –

    • 2006: MO, NY, NC, PR, FL 2007: MO, NY

  • Self pollinated seed samples

  • NIR analysis for starch, protein, and oil content (% kernel - dry matter basis)

  • Two sweet corn families excluded

>6000 rows per location


Phenotypic data statistics
Phenotypic Data Statistics

  • Heritability Trait Correlations (23 Families)

H2

Starch 0.85

Protein 0.83

Oil 0.86

rProtein Oil

Starch -0.65 -0.40

Protein 0.32


Nam analysis in sas
NAM Analysis in SAS

  • Permutations for selection thresholds ~10-5

  • Joint stepwise regression; Proc GLMSelect

    • Family main effect & markers within families

  • Final model; Proc GLM

    • Estimate effects (P = 0.05)

  • Genome Scan; Proc Mixed

    • Maximum likelihood with background cofactors

  • Epistasis; all (611,065) pair-wise combinations


Nam kernel quality architecture
NAM Kernel Quality Architecture

  • Trait N R2(family) R2(QTL)R2(QTL+family)

  • Starch 21 28.7 58.1 59.1

  • Protein 26 25.8 59.9 61.0

  • Oil 22 44.5 69.0 69.7

Starch

Protein

Oil

No Epistasis

Observed at

the NAM Level


Additive allelic effects
Additive Allelic Effects

Starch

%

Sig. AllelesN Min Max

(P = 0.05) (%) (%)

Starch 180 -0.62 0.65

Protein 206 -0.38 0.34

Oil 174 -0.12 0.21

^

^

B73

Protein

Oil

B73

B73

%

%


Validation efforts
Validation Efforts

  • Near Isogenic Lines (NILs)

  • Genome Scan Association Analysis

  • Candidate Genes Association Analysis

  • Fine Mapping

Jason Cook


Genetic vs physical distance
Genetic vs. Physical Distance

Joint Linkage Mapping - Oil

Genetic Distance (cM)

Joint Linkage Mapping - Oil

Physical Distance (bp)


Genome wide association gwas
Genome Wide Association (GWAS)

  • 1.6 Million HapMap v1 SNPs projected onto NAM

  • Bootstrap (80%) sampling to test robustness

GWAS - Oil

BPP

Joint Linkage Mapping - Oil

Physical Distance (bp)


Chr 6 oil candidate dgat1 2
Chr. 6 Oil Candidate: DGAT1-2

  • Encodes acyl-CoA:diacylglycerolacyltransferase

  • Fine mapped by Pioneer-Dupont

    • Zheng, et al. (2008) Nature Genetics

    • High parent = 19% oil

    • High allele = 0.29% additive effect

  • DGAT is the largest effect kernel quality QTL in NAM

4.4%

5.3%

3.6%

3.9%

Phenylalanine insertion in

the C-terminus of the protein


DGAT 1-2 (Chr6: 105,013,351-105,020,258)

M1

  • M2:Phe Insertion

M3

M5

M4

NAM Population: 24 Total HapMap.v1 SNPs in DGAT

Association Panel: 2 Total 55K SNPs in DGAT


DGAT 1-2 (Chr6: 105,013,351-105,020,258)

M1

  • M2:Phe Insertion

M3

M4

M5

= B73 Allele

= Non-B73 Allele

?


What s next for nam
What’s Next for NAM?

  • NextGen sequencing of the 5000 NAM RILs

    • Potentially 30-50 Million SNPs

    • Identify very precisely where recombination events are in the mapping population.

  • This will VASTLY improve the mapping resolution of NAM and GWAS.


Conclusions
Conclusions

  • Genetic Architecture of Kernel Quality Traits

    • Governed by many QTL (N = 21-26)

    • Many QTL in common with prior studies

    • Effect sizes are small to moderate

    • Allele series are common

  • Genome Wide Association Studies (GWAS)

    • Results confirm many QTL and candidate genes

    • Resolution will improve with more markers on NAM RILs (define recombination events)


What does this mean to you
What Does This Mean To You?

  • Identifying Functional Markers for MAS

    • (Distantly) Linked markers not accurate

  • Parent Selection = Allele Mining

    • Valuable alleles are often masked.

    • Selection for specific alleles is more accurate than selecting based on parental phenotype.


Acknowledgements
Acknowledgements

Syngenta

Joe Byrum & Kirk Noel

NSF Maize Diversity Project

www.panzea.org


Gem allelic diversity project
GEM Allelic Diversity Project

  • Genome Wide Association Analysis

  • “mini-NAM”

  • Allele Mining


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