SlideShare a Scribd company logo
1 of 23
Download to read offline
Deleterious Alleles in Maize
Jeffrey Ross-Ibarra
www.rilab.org
@jrossibarra
rossibarra

January 11, 2014
Many new mutations, most deleterious

≈90 mutations per meiosis1
Maize HapMap2 : new mutations of large effect: 2Ne s > 100

1
2

Clark et al. 2005 MBE, Jiao et al. 2012 Nature Genetics
Hufford et al. 2012 Nat. Genetics, Stoletzki & Eyre-Walker 2011 MBE
Many new mutations, most deleterious
Nongenic

Genic

15000

3000

10000

2000
maize
teo

5000

Taxa

count

count

Taxa

maize
teo
1000

0

0
−2

0

Tajima's D

2

4

−2

0

2

Tajima's D

≈90 mutations per meiosis1
Maize HapMap2 : new mutations of large effect: 2Ne s > 100
Purifying selection retards recovery of diversity in genic regions

1
2

Clark et al. 2005 MBE, Jiao et al. 2012 Nature Genetics
Hufford et al. 2012 Nat. Genetics, Stoletzki & Eyre-Walker 2011 MBE
Inbreeding depression and segregating deleterious variants

Likely cause of inbreeding depression in Zea3
Purging: fewer, lower frequency premature stops in maize4
≈8% filtered genes ≥ 1 premature stop codon segregating
Exponential growth since domestication increases number of
weakly deleterious mutations

3
4

Jones 1924 Genetics; Hufford & Gepts Unpublished
Chia et al. 2012 Nature Genetics
Residual heterozygosity suggests complementation

Residual heterozygosity in RILs correlates negatively with
recombination5,6

5
6

Gore et al. 2009 Science
McMullen et al. 2009 Science
Residual heterozygosity suggests complementation

5
6

Gore et al. 2009 Science
McMullen et al. 2009 Science
Deleterious alleles in the 282 association panel

Explore patterns of deleterious alleles and associations with
agronomic phenotypes (heterosis)7
GBS data8 for 282 inbreds
Inbred and hybrid yield data9 from crosses to B73 and Mo17
A priori identify putatively deleterious alleles10

7

Mezmouk & Ross-Ibarra 2014 G3
Romay et al. 2013 Genome Biology
9
Flint-Garcia et al. 2009 PLoS ONE
10
Ng & Henikoff 2003 Nucl. Acids Res., Stone & Sidow 2005 Gen. Res.
8
Deleterious alleles in the 282 association panel

Explore patterns of deleterious alleles and associations with
agronomic phenotypes (heterosis)7
GBS data8 for 282 inbreds
Inbred and hybrid yield data9 from crosses to B73 and Mo17
A priori identify putatively deleterious alleles10
Physicochemical properties of amino acids
Amino acid conservation across plant genomes

7

Mezmouk & Ross-Ibarra 2014 G3
Romay et al. 2013 Genome Biology
9
Flint-Garcia et al. 2009 PLoS ONE
10
Ng & Henikoff 2003 Nucl. Acids Res., Stone & Sidow 2005 Gen. Res.
8
Deleterious alleles at lower frequencies
Constraint, not positive selection patterns deleterious SNPs
0.5

0.4

del

KN KS

0.3

Deleterious
None

0.2

0.1

NotC

C

0.0

Not selected: 4% at high freq, 9% significant PHS11
No hitchhiking: <3% of these are in domestication features12
Genes with deleterious SNPs have higher mean
11
12

Toomajian et al. 2006 PLoS Biology
Hufford et al. 2012 Nature Genetics

KN
KS
Deleterious alleles not correlated with recombination

No relationship of abundance or frequency with recombination
Low recombination is effective over long time scales13

13

Haddrill et al. 2007 Genome Biology
Low FST and few fixed deleterious variants among groups
Deleterious allele frequencies consistent with BPH

BPH increases with distance from B73 tester
Significant BPH even among stiff-stalk lines
GWA hits enriched for genes with deleterious alleles

No enrichment for individual deleterious SNPs (too rare)
All traits show enrichment at the gene level
No gene enrichment for synonymous SNPs
Higher % VA and more causal SNPs under growth

Number of causal variants

A
250

●
●
●

200
150
●
●

●
●
●

100
●

50
BN

BN+growth

Old growth

Number of causal variants

B
250
200

Exponential growth leads to more rare causal variants14 , and
these explain a larger proportion of VA
●
●
●

●
●

150
●

●
●
●

●

100
●

50
14

Lohmueller 2013 arXivOld growth
BN
BN+growth
Allele frequency change in Iowa RRS

Significant increase in yield over time15

15
16

Rouse, Hinze, Lamkey, Unpublished
Gerke, Edwards, Guill, Ross-Ibarra, McMullen In Review
Allele frequency change in Iowa RRS

Significant increase in yield over time15
Allele frequency change over time using 55K16
15
16

Rouse, Hinze, Lamkey, Unpublished
Gerke, Edwards, Guill, Ross-Ibarra, McMullen In Review
No overlap in selected haplotypes: complementation
No overlap in selected haplotypes: complementation
Consistent with QTL for heterosis

QTL for heterosis enriched in centromeric regions17

17

Lari`pe et al. 2012 Genetics
e
Consistent with change in inbred and hybrid yield?
GENETIC PROGRESS IN YIELD OF U.S. MAIZE
199

om 98 SSR loci distributed
cal series of widely grown
s of change in allele frer of alleles per group is
t al. (2004a). Copyright ©
material is used by permis-

FIGURE 7 - Yields of single crosses (SX) and their inbred parent

Selection means (MP), and heterosis as SX – MP.regions pedigrees are inbreds?
in high recombination Single-cross improve
based on heterotic inbred combinations in the Era hybrids during

Haplotype blocks in1930s through 1980s, 12 inbreds maintain heterosis?18
the six decades, low recombination and six single

18

crosses per decade. Means of trials grown in three locations in
1992 and two locations in 1993 at three densities (30, 54, and 79
thousand plants/ha) with one replication per density. From DUVICK et al. (2004b). Copyright © 2004 by John Wiley & Sons, Inc.
This material is used by permission of John Wiley & Sons, Inc.

Duvick 205 Advances in Agronomy
Conclusions

Deleterious mutations common in maize.
Large effect mutations likely removed by inbreeding.
Weak-intermediate effect mutations abundant, but low
frequency
Deleterious mutations enriched in GWAS for heterosis
Simple complementation consistent with patterns of evolution
in Iowa RRS, QTL for heterosis, and perhaps inbred and
hybrid yield trends
Acknowledgements
People

Sofiane Mezmouk

Justin Gerke

UC Davis

U. Missouri

Funding

Jode Edwards
(Iowa State)
Mike McMullen
(U. Missouri)

More Related Content

What's hot

Complex adaptation in Zea
Complex adaptation in ZeaComplex adaptation in Zea
Complex adaptation in Zeajrossibarra
 
Introgression and the origin of maize in Mexico and the Southwest US
Introgression and the origin of maize in Mexico and the Southwest USIntrogression and the origin of maize in Mexico and the Southwest US
Introgression and the origin of maize in Mexico and the Southwest USjrossibarra
 
Population genetics of maize domestication, adaptation, and improvement
Population genetics of maize domestication, adaptation, and improvementPopulation genetics of maize domestication, adaptation, and improvement
Population genetics of maize domestication, adaptation, and improvementjrossibarra
 
Deploying genome sequence information for pigeonpea improvement
Deploying genome sequence information for pigeonpea improvementDeploying genome sequence information for pigeonpea improvement
Deploying genome sequence information for pigeonpea improvementICARDA
 
Beyond GWAS QTL Identification and Strategies to Increase Yield
Beyond GWAS QTL Identification and Strategies to Increase YieldBeyond GWAS QTL Identification and Strategies to Increase Yield
Beyond GWAS QTL Identification and Strategies to Increase YieldKate Barlow
 
Fine-mapping of QTL using high-density SNP genotypes
Fine-mapping of QTL using high-density SNP genotypesFine-mapping of QTL using high-density SNP genotypes
Fine-mapping of QTL using high-density SNP genotypesJohn B. Cole, Ph.D.
 
New tools for genomic selection in dairy cattle
New tools for genomic selection in dairy cattleNew tools for genomic selection in dairy cattle
New tools for genomic selection in dairy cattleJohn B. Cole, Ph.D.
 
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...Premier Publishers
 
Farm animals in aquatic systems - Anna Troedsson-Wargelius
Farm animals in aquatic systems - Anna Troedsson-WargeliusFarm animals in aquatic systems - Anna Troedsson-Wargelius
Farm animals in aquatic systems - Anna Troedsson-WargeliusOECD Environment
 
Chasing a Unicorn for Model Host-Microbiome-Systems
Chasing a Unicorn for Model Host-Microbiome-Systems Chasing a Unicorn for Model Host-Microbiome-Systems
Chasing a Unicorn for Model Host-Microbiome-Systems Jonathan Eisen
 
Genomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingGenomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingCIMMYT
 
Genomic selection and systems biology – lessons from dairy cattle breeding
Genomic selection and systems biology – lessons from dairy cattle breedingGenomic selection and systems biology – lessons from dairy cattle breeding
Genomic selection and systems biology – lessons from dairy cattle breedingJohn B. Cole, Ph.D.
 
Tyler impact next gen fri 0900
Tyler impact next gen fri 0900Tyler impact next gen fri 0900
Tyler impact next gen fri 0900Sucheta Tripathy
 
Genomic Selection in Dairy Cattle
Genomic Selection in Dairy CattleGenomic Selection in Dairy Cattle
Genomic Selection in Dairy CattleJohn B. Cole, Ph.D.
 
A bad genetic history of maize
A bad genetic history of maizeA bad genetic history of maize
A bad genetic history of maizejrossibarra
 
Status of Cassava Genetic Transformation at CIAT.
Status of Cassava Genetic Transformation at CIAT. Status of Cassava Genetic Transformation at CIAT.
Status of Cassava Genetic Transformation at CIAT. CIAT
 
Genomic selection on rice
Genomic selection on riceGenomic selection on rice
Genomic selection on riceCIAT
 

What's hot (20)

Danforth 2015
Danforth 2015Danforth 2015
Danforth 2015
 
Complex adaptation in Zea
Complex adaptation in ZeaComplex adaptation in Zea
Complex adaptation in Zea
 
Introgression and the origin of maize in Mexico and the Southwest US
Introgression and the origin of maize in Mexico and the Southwest USIntrogression and the origin of maize in Mexico and the Southwest US
Introgression and the origin of maize in Mexico and the Southwest US
 
Population genetics of maize domestication, adaptation, and improvement
Population genetics of maize domestication, adaptation, and improvementPopulation genetics of maize domestication, adaptation, and improvement
Population genetics of maize domestication, adaptation, and improvement
 
Deploying genome sequence information for pigeonpea improvement
Deploying genome sequence information for pigeonpea improvementDeploying genome sequence information for pigeonpea improvement
Deploying genome sequence information for pigeonpea improvement
 
Beyond GWAS QTL Identification and Strategies to Increase Yield
Beyond GWAS QTL Identification and Strategies to Increase YieldBeyond GWAS QTL Identification and Strategies to Increase Yield
Beyond GWAS QTL Identification and Strategies to Increase Yield
 
Fine-mapping of QTL using high-density SNP genotypes
Fine-mapping of QTL using high-density SNP genotypesFine-mapping of QTL using high-density SNP genotypes
Fine-mapping of QTL using high-density SNP genotypes
 
New tools for genomic selection in dairy cattle
New tools for genomic selection in dairy cattleNew tools for genomic selection in dairy cattle
New tools for genomic selection in dairy cattle
 
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...
Genetic Variability, Heritability and Genetic Advance Analysis in Upland Rice...
 
Farm animals in aquatic systems - Anna Troedsson-Wargelius
Farm animals in aquatic systems - Anna Troedsson-WargeliusFarm animals in aquatic systems - Anna Troedsson-Wargelius
Farm animals in aquatic systems - Anna Troedsson-Wargelius
 
Chasing a Unicorn for Model Host-Microbiome-Systems
Chasing a Unicorn for Model Host-Microbiome-Systems Chasing a Unicorn for Model Host-Microbiome-Systems
Chasing a Unicorn for Model Host-Microbiome-Systems
 
Genomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingGenomic Selection & Precision Phenotyping
Genomic Selection & Precision Phenotyping
 
My publication-1
My publication-1My publication-1
My publication-1
 
Genomic selection and systems biology – lessons from dairy cattle breeding
Genomic selection and systems biology – lessons from dairy cattle breedingGenomic selection and systems biology – lessons from dairy cattle breeding
Genomic selection and systems biology – lessons from dairy cattle breeding
 
Tyler impact next gen fri 0900
Tyler impact next gen fri 0900Tyler impact next gen fri 0900
Tyler impact next gen fri 0900
 
Genomic Selection in Dairy Cattle
Genomic Selection in Dairy CattleGenomic Selection in Dairy Cattle
Genomic Selection in Dairy Cattle
 
Genetics and Man
Genetics and ManGenetics and Man
Genetics and Man
 
A bad genetic history of maize
A bad genetic history of maizeA bad genetic history of maize
A bad genetic history of maize
 
Status of Cassava Genetic Transformation at CIAT.
Status of Cassava Genetic Transformation at CIAT. Status of Cassava Genetic Transformation at CIAT.
Status of Cassava Genetic Transformation at CIAT.
 
Genomic selection on rice
Genomic selection on riceGenomic selection on rice
Genomic selection on rice
 

Similar to Deleterious Alleles in maize, talk from PAGXXII

The genetic architecture of recombination rate variation in a natural populat...
The genetic architecture of recombination rate variation in a natural populat...The genetic architecture of recombination rate variation in a natural populat...
The genetic architecture of recombination rate variation in a natural populat...Susan Johnston
 
Variation in crop genomes and heterosis
Variation in crop genomes and heterosis Variation in crop genomes and heterosis
Variation in crop genomes and heterosis Shaojun Xie
 
Genetic variation and its role in health pharmacology
Genetic variation and its role in health pharmacologyGenetic variation and its role in health pharmacology
Genetic variation and its role in health pharmacologyDeepak Kumar
 
Target Inducing Local Lesions In Genome (Tilling)
Target Inducing Local Lesions In Genome (Tilling)Target Inducing Local Lesions In Genome (Tilling)
Target Inducing Local Lesions In Genome (Tilling)Ankit R. Chaudhary
 
ANU AGRI 2017.ppt
ANU AGRI 2017.pptANU AGRI 2017.ppt
ANU AGRI 2017.pptAnusheela3
 
Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...
 Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen... Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...
Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...surehuasb
 
Phylogenomic Revisit for Green Contribution to Diatoms
Phylogenomic Revisit for Green Contribution to DiatomsPhylogenomic Revisit for Green Contribution to Diatoms
Phylogenomic Revisit for Green Contribution to DiatomsAhmed Moustafa
 
Genetic manipulation of stay-green traits for croop imporvement
Genetic manipulation of stay-green traits for croop imporvement Genetic manipulation of stay-green traits for croop imporvement
Genetic manipulation of stay-green traits for croop imporvement Shantanu Das
 
Double Haploids in crop improvement.
Double Haploids in crop improvement. Double Haploids in crop improvement.
Double Haploids in crop improvement. Shilpa Malaghan
 
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...World Agroforestry (ICRAF)
 
Evaluation of genetic diversity of soybean introductions and north american a...
Evaluation of genetic diversity of soybean introductions and north american a...Evaluation of genetic diversity of soybean introductions and north american a...
Evaluation of genetic diversity of soybean introductions and north american a...hiensh02
 
Breeding Approaches Towards Disease Resistance In Livestocks
Breeding Approaches Towards Disease Resistance In LivestocksBreeding Approaches Towards Disease Resistance In Livestocks
Breeding Approaches Towards Disease Resistance In LivestocksSharadindu Shil
 
Powerpoint tips for scientists
Powerpoint tips for scientistsPowerpoint tips for scientists
Powerpoint tips for scientistsSara Barrento
 

Similar to Deleterious Alleles in maize, talk from PAGXXII (20)

Allele mining
Allele miningAllele mining
Allele mining
 
The genetic architecture of recombination rate variation in a natural populat...
The genetic architecture of recombination rate variation in a natural populat...The genetic architecture of recombination rate variation in a natural populat...
The genetic architecture of recombination rate variation in a natural populat...
 
Variation in crop genomes and heterosis
Variation in crop genomes and heterosis Variation in crop genomes and heterosis
Variation in crop genomes and heterosis
 
Epigenomics gyanika
Epigenomics   gyanikaEpigenomics   gyanika
Epigenomics gyanika
 
Genetic variation and its role in health pharmacology
Genetic variation and its role in health pharmacologyGenetic variation and its role in health pharmacology
Genetic variation and its role in health pharmacology
 
Target Inducing Local Lesions In Genome (Tilling)
Target Inducing Local Lesions In Genome (Tilling)Target Inducing Local Lesions In Genome (Tilling)
Target Inducing Local Lesions In Genome (Tilling)
 
ANU AGRI 2017.ppt
ANU AGRI 2017.pptANU AGRI 2017.ppt
ANU AGRI 2017.ppt
 
Induction of Genetic Variability in Soybean in M3 Generation for Quantitative...
Induction of Genetic Variability in Soybean in M3 Generation for Quantitative...Induction of Genetic Variability in Soybean in M3 Generation for Quantitative...
Induction of Genetic Variability in Soybean in M3 Generation for Quantitative...
 
Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...
 Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen... Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...
Seminar on Combining Traditional Mutagenesis with New High-Throughput Sequen...
 
Phylogenomic Revisit for Green Contribution to Diatoms
Phylogenomic Revisit for Green Contribution to DiatomsPhylogenomic Revisit for Green Contribution to Diatoms
Phylogenomic Revisit for Green Contribution to Diatoms
 
Genetic manipulation of stay-green traits for croop imporvement
Genetic manipulation of stay-green traits for croop imporvement Genetic manipulation of stay-green traits for croop imporvement
Genetic manipulation of stay-green traits for croop imporvement
 
Double Haploids in crop improvement.
Double Haploids in crop improvement. Double Haploids in crop improvement.
Double Haploids in crop improvement.
 
Linthoi credit seminar
Linthoi credit seminarLinthoi credit seminar
Linthoi credit seminar
 
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...
Genotype to phenotype forest tree genomics: genome sequencing (de novo and re...
 
Evaluation of genetic diversity of soybean introductions and north american a...
Evaluation of genetic diversity of soybean introductions and north american a...Evaluation of genetic diversity of soybean introductions and north american a...
Evaluation of genetic diversity of soybean introductions and north american a...
 
Breeding Approaches Towards Disease Resistance In Livestocks
Breeding Approaches Towards Disease Resistance In LivestocksBreeding Approaches Towards Disease Resistance In Livestocks
Breeding Approaches Towards Disease Resistance In Livestocks
 
Chiranjeev patel thesis viva voce
Chiranjeev patel thesis viva voceChiranjeev patel thesis viva voce
Chiranjeev patel thesis viva voce
 
Role of Epigenetics in Heterosis
Role of Epigenetics in HeterosisRole of Epigenetics in Heterosis
Role of Epigenetics in Heterosis
 
Powerpoint tips for scientists
Powerpoint tips for scientistsPowerpoint tips for scientists
Powerpoint tips for scientists
 
Molecular heterosis
Molecular heterosisMolecular heterosis
Molecular heterosis
 

More from jrossibarra

Adaptation in plant genomes: bigger is different
Adaptation in plant genomes: bigger is differentAdaptation in plant genomes: bigger is different
Adaptation in plant genomes: bigger is differentjrossibarra
 
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea maysParallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea maysjrossibarra
 
Genome size and adaptation in plants
Genome size and adaptation in plantsGenome size and adaptation in plants
Genome size and adaptation in plantsjrossibarra
 
Adaptive evolution of genome size across altitudinal clines in maize
Adaptive evolution of genome size across altitudinal clines in maizeAdaptive evolution of genome size across altitudinal clines in maize
Adaptive evolution of genome size across altitudinal clines in maizejrossibarra
 
Gene flow and cross-incompatibility in maize and teosinte
Gene flow and cross-incompatibility in maize and teosinteGene flow and cross-incompatibility in maize and teosinte
Gene flow and cross-incompatibility in maize and teosintejrossibarra
 
Demography and deleterious alleles in maize
Demography and deleterious alleles in maizeDemography and deleterious alleles in maize
Demography and deleterious alleles in maizejrossibarra
 
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"jrossibarra
 
Presentation at SMBEBA
Presentation at SMBEBAPresentation at SMBEBA
Presentation at SMBEBAjrossibarra
 
Advice for getting into grad school (in the biological sciences)
Advice for getting into grad school (in the biological sciences)Advice for getting into grad school (in the biological sciences)
Advice for getting into grad school (in the biological sciences)jrossibarra
 

More from jrossibarra (11)

Adaptation in plant genomes: bigger is different
Adaptation in plant genomes: bigger is differentAdaptation in plant genomes: bigger is different
Adaptation in plant genomes: bigger is different
 
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea maysParallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays
 
Genome size and adaptation in plants
Genome size and adaptation in plantsGenome size and adaptation in plants
Genome size and adaptation in plants
 
Adaptive evolution of genome size across altitudinal clines in maize
Adaptive evolution of genome size across altitudinal clines in maizeAdaptive evolution of genome size across altitudinal clines in maize
Adaptive evolution of genome size across altitudinal clines in maize
 
Gene flow and cross-incompatibility in maize and teosinte
Gene flow and cross-incompatibility in maize and teosinteGene flow and cross-incompatibility in maize and teosinte
Gene flow and cross-incompatibility in maize and teosinte
 
Demography and deleterious alleles in maize
Demography and deleterious alleles in maizeDemography and deleterious alleles in maize
Demography and deleterious alleles in maize
 
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"
2015 SF Exploratorium Lecture: "Corn: Diversity and Origins"
 
Presentation at SMBEBA
Presentation at SMBEBAPresentation at SMBEBA
Presentation at SMBEBA
 
FIsherOrr_maize
FIsherOrr_maizeFIsherOrr_maize
FIsherOrr_maize
 
Advice for getting into grad school (in the biological sciences)
Advice for getting into grad school (in the biological sciences)Advice for getting into grad school (in the biological sciences)
Advice for getting into grad school (in the biological sciences)
 
Drift
DriftDrift
Drift
 

Recently uploaded

INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdf
INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdfINU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdf
INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdfbu07226
 
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45MysoreMuleSoftMeetup
 
IATP How-to Foreign Travel May 2024.pdff
IATP How-to Foreign Travel May 2024.pdffIATP How-to Foreign Travel May 2024.pdff
IATP How-to Foreign Travel May 2024.pdff17thcssbs2
 
Navigating the Misinformation Minefield: The Role of Higher Education in the ...
Navigating the Misinformation Minefield: The Role of Higher Education in the ...Navigating the Misinformation Minefield: The Role of Higher Education in the ...
Navigating the Misinformation Minefield: The Role of Higher Education in the ...Mark Carrigan
 
ppt your views.ppt your views of your college in your eyes
ppt your views.ppt your views of your college in your eyesppt your views.ppt your views of your college in your eyes
ppt your views.ppt your views of your college in your eyesashishpaul799
 
Mbaye_Astou.Education Civica_Human Rights.pptx
Mbaye_Astou.Education Civica_Human Rights.pptxMbaye_Astou.Education Civica_Human Rights.pptx
Mbaye_Astou.Education Civica_Human Rights.pptxnuriaiuzzolino1
 
Matatag-Curriculum and the 21st Century Skills Presentation.pptx
Matatag-Curriculum and the 21st Century Skills Presentation.pptxMatatag-Curriculum and the 21st Century Skills Presentation.pptx
Matatag-Curriculum and the 21st Century Skills Presentation.pptxJenilouCasareno
 
size separation d pharm 1st year pharmaceutics
size separation d pharm 1st year pharmaceuticssize separation d pharm 1st year pharmaceutics
size separation d pharm 1st year pharmaceuticspragatimahajan3
 
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General Quiz
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General QuizPragya Champions Chalice 2024 Prelims & Finals Q/A set, General Quiz
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General QuizPragya - UEM Kolkata Quiz Club
 
Championnat de France de Tennis de table/
Championnat de France de Tennis de table/Championnat de France de Tennis de table/
Championnat de France de Tennis de table/siemaillard
 
Essential Safety precautions during monsoon season
Essential Safety precautions during monsoon seasonEssential Safety precautions during monsoon season
Essential Safety precautions during monsoon seasonMayur Khatri
 
Morse OER Some Benefits and Challenges.pptx
Morse OER Some Benefits and Challenges.pptxMorse OER Some Benefits and Challenges.pptx
Morse OER Some Benefits and Challenges.pptxjmorse8
 
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...Sayali Powar
 
Basic Civil Engg Notes_Chapter-6_Environment Pollution & Engineering
Basic Civil Engg Notes_Chapter-6_Environment Pollution & EngineeringBasic Civil Engg Notes_Chapter-6_Environment Pollution & Engineering
Basic Civil Engg Notes_Chapter-6_Environment Pollution & EngineeringDenish Jangid
 
....................Muslim-Law notes.pdf
....................Muslim-Law notes.pdf....................Muslim-Law notes.pdf
....................Muslim-Law notes.pdfVikramadityaRaj
 
Behavioral-sciences-dr-mowadat rana (1).pdf
Behavioral-sciences-dr-mowadat rana (1).pdfBehavioral-sciences-dr-mowadat rana (1).pdf
Behavioral-sciences-dr-mowadat rana (1).pdfaedhbteg
 
Features of Video Calls in the Discuss Module in Odoo 17
Features of Video Calls in the Discuss Module in Odoo 17Features of Video Calls in the Discuss Module in Odoo 17
Features of Video Calls in the Discuss Module in Odoo 17Celine George
 
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...Nguyen Thanh Tu Collection
 
REPRODUCTIVE TOXICITY STUDIE OF MALE AND FEMALEpptx
REPRODUCTIVE TOXICITY  STUDIE OF MALE AND FEMALEpptxREPRODUCTIVE TOXICITY  STUDIE OF MALE AND FEMALEpptx
REPRODUCTIVE TOXICITY STUDIE OF MALE AND FEMALEpptxmanishaJyala2
 

Recently uploaded (20)

INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdf
INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdfINU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdf
INU_CAPSTONEDESIGN_비밀번호486_업로드용 발표자료.pdf
 
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45
Exploring Gemini AI and Integration with MuleSoft | MuleSoft Mysore Meetup #45
 
IATP How-to Foreign Travel May 2024.pdff
IATP How-to Foreign Travel May 2024.pdffIATP How-to Foreign Travel May 2024.pdff
IATP How-to Foreign Travel May 2024.pdff
 
Navigating the Misinformation Minefield: The Role of Higher Education in the ...
Navigating the Misinformation Minefield: The Role of Higher Education in the ...Navigating the Misinformation Minefield: The Role of Higher Education in the ...
Navigating the Misinformation Minefield: The Role of Higher Education in the ...
 
ppt your views.ppt your views of your college in your eyes
ppt your views.ppt your views of your college in your eyesppt your views.ppt your views of your college in your eyes
ppt your views.ppt your views of your college in your eyes
 
Mbaye_Astou.Education Civica_Human Rights.pptx
Mbaye_Astou.Education Civica_Human Rights.pptxMbaye_Astou.Education Civica_Human Rights.pptx
Mbaye_Astou.Education Civica_Human Rights.pptx
 
Matatag-Curriculum and the 21st Century Skills Presentation.pptx
Matatag-Curriculum and the 21st Century Skills Presentation.pptxMatatag-Curriculum and the 21st Century Skills Presentation.pptx
Matatag-Curriculum and the 21st Century Skills Presentation.pptx
 
size separation d pharm 1st year pharmaceutics
size separation d pharm 1st year pharmaceuticssize separation d pharm 1st year pharmaceutics
size separation d pharm 1st year pharmaceutics
 
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General Quiz
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General QuizPragya Champions Chalice 2024 Prelims & Finals Q/A set, General Quiz
Pragya Champions Chalice 2024 Prelims & Finals Q/A set, General Quiz
 
Championnat de France de Tennis de table/
Championnat de France de Tennis de table/Championnat de France de Tennis de table/
Championnat de France de Tennis de table/
 
Essential Safety precautions during monsoon season
Essential Safety precautions during monsoon seasonEssential Safety precautions during monsoon season
Essential Safety precautions during monsoon season
 
Morse OER Some Benefits and Challenges.pptx
Morse OER Some Benefits and Challenges.pptxMorse OER Some Benefits and Challenges.pptx
Morse OER Some Benefits and Challenges.pptx
 
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...
UNIT – IV_PCI Complaints: Complaints and evaluation of complaints, Handling o...
 
Basic Civil Engg Notes_Chapter-6_Environment Pollution & Engineering
Basic Civil Engg Notes_Chapter-6_Environment Pollution & EngineeringBasic Civil Engg Notes_Chapter-6_Environment Pollution & Engineering
Basic Civil Engg Notes_Chapter-6_Environment Pollution & Engineering
 
....................Muslim-Law notes.pdf
....................Muslim-Law notes.pdf....................Muslim-Law notes.pdf
....................Muslim-Law notes.pdf
 
Operations Management - Book1.p - Dr. Abdulfatah A. Salem
Operations Management - Book1.p  - Dr. Abdulfatah A. SalemOperations Management - Book1.p  - Dr. Abdulfatah A. Salem
Operations Management - Book1.p - Dr. Abdulfatah A. Salem
 
Behavioral-sciences-dr-mowadat rana (1).pdf
Behavioral-sciences-dr-mowadat rana (1).pdfBehavioral-sciences-dr-mowadat rana (1).pdf
Behavioral-sciences-dr-mowadat rana (1).pdf
 
Features of Video Calls in the Discuss Module in Odoo 17
Features of Video Calls in the Discuss Module in Odoo 17Features of Video Calls in the Discuss Module in Odoo 17
Features of Video Calls in the Discuss Module in Odoo 17
 
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...
TỔNG HỢP HƠN 100 ĐỀ THI THỬ TỐT NGHIỆP THPT VẬT LÝ 2024 - TỪ CÁC TRƯỜNG, TRƯ...
 
REPRODUCTIVE TOXICITY STUDIE OF MALE AND FEMALEpptx
REPRODUCTIVE TOXICITY  STUDIE OF MALE AND FEMALEpptxREPRODUCTIVE TOXICITY  STUDIE OF MALE AND FEMALEpptx
REPRODUCTIVE TOXICITY STUDIE OF MALE AND FEMALEpptx
 

Deleterious Alleles in maize, talk from PAGXXII

  • 1. Deleterious Alleles in Maize Jeffrey Ross-Ibarra www.rilab.org @jrossibarra rossibarra January 11, 2014
  • 2. Many new mutations, most deleterious ≈90 mutations per meiosis1 Maize HapMap2 : new mutations of large effect: 2Ne s > 100 1 2 Clark et al. 2005 MBE, Jiao et al. 2012 Nature Genetics Hufford et al. 2012 Nat. Genetics, Stoletzki & Eyre-Walker 2011 MBE
  • 3. Many new mutations, most deleterious Nongenic Genic 15000 3000 10000 2000 maize teo 5000 Taxa count count Taxa maize teo 1000 0 0 −2 0 Tajima's D 2 4 −2 0 2 Tajima's D ≈90 mutations per meiosis1 Maize HapMap2 : new mutations of large effect: 2Ne s > 100 Purifying selection retards recovery of diversity in genic regions 1 2 Clark et al. 2005 MBE, Jiao et al. 2012 Nature Genetics Hufford et al. 2012 Nat. Genetics, Stoletzki & Eyre-Walker 2011 MBE
  • 4. Inbreeding depression and segregating deleterious variants Likely cause of inbreeding depression in Zea3 Purging: fewer, lower frequency premature stops in maize4 ≈8% filtered genes ≥ 1 premature stop codon segregating Exponential growth since domestication increases number of weakly deleterious mutations 3 4 Jones 1924 Genetics; Hufford & Gepts Unpublished Chia et al. 2012 Nature Genetics
  • 5. Residual heterozygosity suggests complementation Residual heterozygosity in RILs correlates negatively with recombination5,6 5 6 Gore et al. 2009 Science McMullen et al. 2009 Science
  • 6. Residual heterozygosity suggests complementation 5 6 Gore et al. 2009 Science McMullen et al. 2009 Science
  • 7. Deleterious alleles in the 282 association panel Explore patterns of deleterious alleles and associations with agronomic phenotypes (heterosis)7 GBS data8 for 282 inbreds Inbred and hybrid yield data9 from crosses to B73 and Mo17 A priori identify putatively deleterious alleles10 7 Mezmouk & Ross-Ibarra 2014 G3 Romay et al. 2013 Genome Biology 9 Flint-Garcia et al. 2009 PLoS ONE 10 Ng & Henikoff 2003 Nucl. Acids Res., Stone & Sidow 2005 Gen. Res. 8
  • 8. Deleterious alleles in the 282 association panel Explore patterns of deleterious alleles and associations with agronomic phenotypes (heterosis)7 GBS data8 for 282 inbreds Inbred and hybrid yield data9 from crosses to B73 and Mo17 A priori identify putatively deleterious alleles10 Physicochemical properties of amino acids Amino acid conservation across plant genomes 7 Mezmouk & Ross-Ibarra 2014 G3 Romay et al. 2013 Genome Biology 9 Flint-Garcia et al. 2009 PLoS ONE 10 Ng & Henikoff 2003 Nucl. Acids Res., Stone & Sidow 2005 Gen. Res. 8
  • 9. Deleterious alleles at lower frequencies
  • 10. Constraint, not positive selection patterns deleterious SNPs 0.5 0.4 del KN KS 0.3 Deleterious None 0.2 0.1 NotC C 0.0 Not selected: 4% at high freq, 9% significant PHS11 No hitchhiking: <3% of these are in domestication features12 Genes with deleterious SNPs have higher mean 11 12 Toomajian et al. 2006 PLoS Biology Hufford et al. 2012 Nature Genetics KN KS
  • 11. Deleterious alleles not correlated with recombination No relationship of abundance or frequency with recombination Low recombination is effective over long time scales13 13 Haddrill et al. 2007 Genome Biology
  • 12. Low FST and few fixed deleterious variants among groups
  • 13. Deleterious allele frequencies consistent with BPH BPH increases with distance from B73 tester Significant BPH even among stiff-stalk lines
  • 14. GWA hits enriched for genes with deleterious alleles No enrichment for individual deleterious SNPs (too rare) All traits show enrichment at the gene level No gene enrichment for synonymous SNPs
  • 15. Higher % VA and more causal SNPs under growth Number of causal variants A 250 ● ● ● 200 150 ● ● ● ● ● 100 ● 50 BN BN+growth Old growth Number of causal variants B 250 200 Exponential growth leads to more rare causal variants14 , and these explain a larger proportion of VA ● ● ● ● ● 150 ● ● ● ● ● 100 ● 50 14 Lohmueller 2013 arXivOld growth BN BN+growth
  • 16. Allele frequency change in Iowa RRS Significant increase in yield over time15 15 16 Rouse, Hinze, Lamkey, Unpublished Gerke, Edwards, Guill, Ross-Ibarra, McMullen In Review
  • 17. Allele frequency change in Iowa RRS Significant increase in yield over time15 Allele frequency change over time using 55K16 15 16 Rouse, Hinze, Lamkey, Unpublished Gerke, Edwards, Guill, Ross-Ibarra, McMullen In Review
  • 18. No overlap in selected haplotypes: complementation
  • 19. No overlap in selected haplotypes: complementation
  • 20. Consistent with QTL for heterosis QTL for heterosis enriched in centromeric regions17 17 Lari`pe et al. 2012 Genetics e
  • 21. Consistent with change in inbred and hybrid yield? GENETIC PROGRESS IN YIELD OF U.S. MAIZE 199 om 98 SSR loci distributed cal series of widely grown s of change in allele frer of alleles per group is t al. (2004a). Copyright © material is used by permis- FIGURE 7 - Yields of single crosses (SX) and their inbred parent Selection means (MP), and heterosis as SX – MP.regions pedigrees are inbreds? in high recombination Single-cross improve based on heterotic inbred combinations in the Era hybrids during Haplotype blocks in1930s through 1980s, 12 inbreds maintain heterosis?18 the six decades, low recombination and six single 18 crosses per decade. Means of trials grown in three locations in 1992 and two locations in 1993 at three densities (30, 54, and 79 thousand plants/ha) with one replication per density. From DUVICK et al. (2004b). Copyright © 2004 by John Wiley & Sons, Inc. This material is used by permission of John Wiley & Sons, Inc. Duvick 205 Advances in Agronomy
  • 22. Conclusions Deleterious mutations common in maize. Large effect mutations likely removed by inbreeding. Weak-intermediate effect mutations abundant, but low frequency Deleterious mutations enriched in GWAS for heterosis Simple complementation consistent with patterns of evolution in Iowa RRS, QTL for heterosis, and perhaps inbred and hybrid yield trends
  • 23. Acknowledgements People Sofiane Mezmouk Justin Gerke UC Davis U. Missouri Funding Jode Edwards (Iowa State) Mike McMullen (U. Missouri)