SlideShare ist ein Scribd-Unternehmen logo

Langebio 2015

•
•
jrossibarra
jrossibarra

Selection and demography talk at Langebio Nov. 2015

Wissenschaft
1 von 92
Downloaden Sie, um offline zu lesen
Selection and demography in maize evolution Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org Dept. Plant Sciences • Center for Population Biology • Genome Center University of California Davis photo by lady_lbrty
Photos: Matt Hufford, Brandon Gaut, John Doebley
maizeteosinte
Suketoshi Taba
GeographicalBreadth 0 0.02 0.04 0.06 0.08 0.1 maize potato wheat soybean sorghum barley sunflower rice groundnut rapeseed cassava millet rye sugarcane oilpalm sugarbeet Hake & Ross-Ibarra 2015 eLife
hard sweep Diversity
hard sweep multiple mutations Diversity standing variation “soft” sweeps
hard sweep multiple mutations polygenic adaptation Diversity standing variation “soft” sweeps
M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG
M T G P H R L GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG
maize origins TripsacumF1 teosinte (Z. mays ssp. parviglumis) maize (Z. mays ssp. mays)
F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
Briggs et al. 2007 Genetics 1 2 3 4 5 6 7 8 9 10
Wang et al. 2005 Nature 1 2 3 4 5 6 7 8 9 10 Figure 1. Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte e internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a m introgressed into it. d. Close-up of a single teosinte fruitcase. e. Close-up o teosinte plant with a maize allele of tga1 introgressed into it. f. Ear of maiz (Tga1-maize allele) with the cob exposed showing the small white glumes a of maize inbred W22:tga1 which carries the teosinte allele, showing enlarge h. Ear of maize inbred W22 carrying the tga1-ems1 allele, showing enlarged g NIH-PAAuthorManuscriptNIH-PAAuthorManuscriptNIH-P tga1 Wang et al. 2015 Genetics
Wang et al. 2005 Nature 1 2 3 4 5 6 7 8 9 10 Figure 1. Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte e internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a m introgressed into it. d. Close-up of a single teosinte fruitcase. e. Close-up o teosinte plant with a maize allele of tga1 introgressed into it. f. Ear of maiz (Tga1-maize allele) with the cob exposed showing the small white glumes a of maize inbred W22:tga1 which carries the teosinte allele, showing enlarge h. Ear of maize inbred W22 carrying the tga1-ems1 allele, showing enlarged g NIH-PAAuthorManuscriptNIH-PAAuthorManuscriptNIH-P tga1 Wang et al. 2015 Genetics
1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics
1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics teosinte maize Clint Whipple, BYU
1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics
1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics 5’ control region 3’ UTR
1 2 3 4 5 6 7 8 9 10 tb1 Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1gt1
1 2 3 4 5 6 7 8 9 10 tb1 Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1 GENETICS ADVANCE ONLINE PUBLICATION 3 nguish maize and teosinte. Both the maize and teosinte s for the distal component repressed luciferase expression luc luc luc luc luc luc Hopscotch mpCaMV M-dist T-prox M-prox 0 0.5 1.0 1.5 2.0 ∆M-dist ∆M-prox ProximalcontrolregionDistal Constructs and corresponding normalized luciferase expression nsient assays were performed in maize leaf protoplast. Each is drawn to scale. The construct backbone consists of the romoter from the cauliflower mosaic virus (mpCaMV, gray box), ORF (luc, white box) and the nopaline synthase terminator ). Portions of the proximal and distal components of the gion (hatched boxes) from maize and teosinte were cloned ction sites upstream of the minimal promoter. “ ” denotes on of either the Tourist or Hopscotch element from the maize Horizontal green bars show the normalized mean with s.e.m. onstruct. relative expressionconstruct gt1
1 2 3 4 5 6 7 8 9 10 tb1 Figure 2 Map of parviglumis Populations and Hopscotch allele frequency. Map showing the frequency of the Hopscotch allele in populations of parviglumis where we sampled more than 6 individuals. Size of circles reflects number of individuals sampled. The Balsas River is shown, as the Balsas River Basin is believed to be the center of domestication of maize. as our independent trait for phenotyping analyses. SAS code used for analysis is available at http://dx.doi.org/10.6084/m9.figshare.1166630. RESULTS Genotyping for the Hopscotch insertion The genotype at the Hopscotch insertion was confirmed with two PCRs for 837 individuals of the 1,100 screened (Table S1 and Table S2). Among the 247 maize landrace accessions genotyped, all but eight were homozygous for the presence of the insertion Within our parviglumis and mexicana samples we found the Hopscotch insertion segregating in 37 (n = 86) and four (n = 17) populations, respectively, and at highest frequency within populations in the states of Jalisco, Colima, and Michoac´an in central-western Mexico (Fig. 2). Using our Hopscotch genotyping, we calculated diVerentiation between populations (FST) and subspecies (FCT) for populations in which we sampled sixteen or more chromosomes. We found that FCT = 0, and levels of FST among populations within each subspecies (0.22) and among all populations (0.23) (Table 1) are similar to genome-wide estimates from previous studies Pyh¨aj¨arvi, HuVord & Ross-Ibarra, 2013. Although we found large variation in Hopscotch allele frequency among our populations, BayEnv analysis did not indicate a correlation between the Hopscotch insertion and environmental variables (all Bayes Factors < 1). Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1 GENETICS ADVANCE ONLINE PUBLICATION 3 nguish maize and teosinte. Both the maize and teosinte s for the distal component repressed luciferase expression luc luc luc luc luc luc Hopscotch mpCaMV M-dist T-prox M-prox 0 0.5 1.0 1.5 2.0 ∆M-dist ∆M-prox ProximalcontrolregionDistal Constructs and corresponding normalized luciferase expression nsient assays were performed in maize leaf protoplast. Each is drawn to scale. The construct backbone consists of the romoter from the cauliflower mosaic virus (mpCaMV, gray box), ORF (luc, white box) and the nopaline synthase terminator ). Portions of the proximal and distal components of the gion (hatched boxes) from maize and teosinte were cloned ction sites upstream of the minimal promoter. “ ” denotes on of either the Tourist or Hopscotch element from the maize Horizontal green bars show the normalized mean with s.e.m. onstruct. relative expressionconstruct gt1
hard sweep M T N P H R L GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG tga1
hard sweep M T N P H R L GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG tga1 gt1 tb1 Multiple Mutations Standing Variation M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG
Vann et al. 2015 PeerJ polygenic adaptation 30% phenotypic variance 0% phenotypic variance
Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize ~500 genes (2%) 11M shared SNPs 3,000 fixed genomes:
Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes:
Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes:
Swanson-Wagner et al. 2012 PNAS E ze network edges 6 7 2 Mb or conservation and targets of selection during improvement and/or domestication. (A) Venn diagram es, and the genes that occur in genomic regions that have evidence for selective sweeps during maize s). (B) Teosinte coexpression networks for three genes (GRMZM2G068436, GRMZM2G137947, and ned in maize coexpression networks are shown. Although the differentially expressed gene (red node) is tions are lost in maize. However, some parts of the teosinte network are still conserved in maize. (C) Cross- ExpressionGenealogy teosinte maize
nucleotidediversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
nucleotidediversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
Mexico highland6,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
Mexico highland6,000 BP S. America lowland 6,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
Mexico highland6,000 BP S. America lowland 6,000 BP S. America Highland 4,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
Mexico photobyMonthonWachirasettakul Andes photobyMattHufford
SA MEX SA MEX SA MEX SA MEX SA MEX SA MEX Ear Height Plant Height Tassel Br. Number TW Days to Anthesis SA MEX SA MEX SA MEX SA MEX LowlandHighland
95 landraces ~100K SNPs Takuno et al. 2015 Genetics
-Logp-valueFstS.America -Log p-value Fst Mexico shared SNPs unique S.America unique Mexico 95 landraces ~100K SNPs Takuno et al. 2015 Genetics
-Logp-valueFstS.America -Log p-value Fst Mexico shared SNPs unique S.America unique Mexico 39% 61% Intergenic Genic 19% 81% Standing Variation New mutation Takuno et al. 2015 Genetics
Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics
Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Z = LX i=1 ↵ipi allele freq. population breeding value effect size
Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Z = LX i=1 ↵ipi allele freq. population breeding value effect size relatednessdispersion add. genetic var. QX = ~Z0 T F 1 ~Z0 2VA
Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
Cold Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
Cold Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
masl Pyhäjärvi et al. GBE 2013
Pyhäjärvi et al. GBE 2013
Pyhäjärvi et al. GBE 2013
Pyhäjärvi et al. GBE 2013
Beissinger et al. In Prep: http://biorxiv.org/content/early/
how to adapt: Zea mays soft sweeps M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG polygenic adaptation regulatory variation
Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science
Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science
Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity
Ne diploids s selection coefficient selection is effective if 2Nes > 1
Ne diploids s selection coefficient selection is effective if 2Nes > 1 Ne ~ 150,000 Ne ~ 10,000 Ne ~ 2,000,000 Ne ~ 600,000
Ne diploids s selection coefficient selection is effective if 2Nes > 1 Ne ~ 150,000 Ne ~ 10,000 Ne ~ 2,000,000 Ne ~ 600,000 20% nonsyn. subs 10% nonsyn. subs 50% nonsyn. subs 40% nonsyn. subs
teosinte maize DATA teosinte maize MODEL Beissinger et al. In Prep: http://biorxiv.org/content/early/2015/11/13/031666 Hufford et al. 2012
teosinte maize DATA teosinte maize MODEL 0.05Na Na Na 3Na Beissinger et al. In Prep: http://biorxiv.org/content/early/2015/11/13/031666 Hufford et al. 2012
Ne ~ 150,000 Ne ~ 50,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
0.05Na Na Na 3Na Ne ~ 450,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000 Ne ~ 5,000,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
nucleotidediversity distance to gene (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
nucleotidediversity distance to gene (cM) singletondiversity distance to gene (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
singletondiversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity Ne >> 1,000,000 Ne ~ 10,000* Ne ~ 2,000,000 Ne ~ 600,000
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAGx
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAGx
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x x x x
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x
M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x x x x x
Makarevitch et al. 2014 PLoS Genetics
Makarevitch et al. 2014 PLoS Genetics single TE family, many genes
Makarevitch et al. 2014 PLoS Genetics single TE family, many genes new insertions activate expression Makarevitch et al. 2014 bioRxiv Lines with the TE insertion Lines without the TE insertion GRMZM2G071206 Log2(stress/control) -2 0 2 4 6 8 10 12 Lines with the TE insertion Lines without the TE insertion -2 0 2 4 6 8 10 12 Log2(stress/control) GRMZM2G400718 C 1.0 1.5 2.0 D GRMZM2G102447 -2 0 2 4 6 8 10 12 14 Lines with the TE insertion Lines without the TE insertion GRMZM2G108149 A B Log2(stress/control)s/control) http://biDownloaded from -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 1 2 3 4 5 6 7 8 9 10 Oh43 B73 Mo17 - - + - - + - + - - ++ - - + - - + - - + - - + - - + - - + Gene Log2(stress/control) TE presence 0% 20% 40% 60% 80% 100% alaw dagaf etug flip gyma ipiki jeli joemon naiba nihep odoj pebi raider riiryl ubel uwum Zm00346 Zm02117 Zm03238 Zm05382 Salt UV Heat Cold B A Percentofconserved genes * ** *** * * ** * single gene, many individuals
Hancock et al 2011 Science Hernandez et al. 2011 Science Fraser et al. 2013 Gen. Research enrichment intergenic<———>coding Pyhäjärvi et al. GBE 2013 enrichment intergenic<———>coding
Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1
Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1 Garud et al. 2015 PLoS Gen. Jensen 2014 Nat. Comm. Pritchard et al. 2010 Curr. Bio. Enard et al. 2014 Gen. Res. Beissinger et al. In Prep µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp µ ∝ 130 Mbp
Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1 Garud et al. 2015 PLoS Gen. Jensen 2014 Nat. Comm. Pritchard et al. 2010 Curr. Bio. Enard et al. 2014 Gen. Res. Beissinger et al. In Prep µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp µ ∝ 130 Mbp µ ∝ 220 Mbp µ ∝ 130 Mbp Williamson et al. 2014 PLoS Gen
Brandon Gaut maizeArabidopsis Kew C-Value Database log 1C genome size
• “Soft sweeps” and polygenic selection predominate in maize and teosinte • Most selection appears in noncoding sequence • Both effective population size & mutational target contribute • Large, complex genomes may mean more targets & more soft sweeps & less linked effects of selection Concluding Thoughts
Acknowledgments Maize Diversity Group Peter Bradbury Ed Buckler John Doebley Theresa Fulton Sherry Flint-Garcia Jim Holland Sharon Mitchell Qi Sun Doreen Ware Collaborators Graham Coop Nathan Springer Ruairidh Sawers Lab Alumni Tim Beissinger (USDA-ARS, Mizzou) Kate Crosby (Monsanto) Matt Hufford (Iowa State) Tanja Pyhäjärvi (Oulu) Shohei Takuno (Sokendai) Joost van Heerwaarden (Wageningen)
Langebio 2015

Empfohlen

Evolutionary Genetics of Complex Genome
Evolutionary Genetics of Complex GenomeEvolutionary Genetics of Complex Genome
Evolutionary Genetics of Complex Genomejrossibarra
 
Toronto 2015
Toronto 2015Toronto 2015
Toronto 2015jrossibarra
 
Historical Genomics of US Maize: Domestication and Modern Breeding
Historical Genomics of US Maize: Domestication and Modern BreedingHistorical Genomics of US Maize: Domestication and Modern Breeding
Historical Genomics of US Maize: Domestication and Modern Breedingjrossibarra
 
Bottlenecks -- some ramblings and a bit of data from maize PAGXXII
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIBottlenecks -- some ramblings and a bit of data from maize PAGXXII
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIjrossibarra
 
Danforth 2015
Danforth 2015Danforth 2015
Danforth 2015jrossibarra
 
Complex adaptation in Zea
Complex adaptation in ZeaComplex adaptation in Zea
Complex adaptation in Zeajrossibarra
 
Evolutionary genetics of hybrid maize
Evolutionary genetics of hybrid maizeEvolutionary genetics of hybrid maize
Evolutionary genetics of hybrid maizejrossibarra
 
JGI: Genome size impacts on plant adaptation
JGI: Genome size impacts on plant adaptationJGI: Genome size impacts on plant adaptation
JGI: Genome size impacts on plant adaptationjrossibarra
 

Empfohlen

Evolutionary Genetics of Complex Genome
Evolutionary Genetics of Complex GenomeEvolutionary Genetics of Complex Genome
Evolutionary Genetics of Complex Genomejrossibarra
 
Toronto 2015
Toronto 2015Toronto 2015
Toronto 2015jrossibarra
 
Historical Genomics of US Maize: Domestication and Modern Breeding
Historical Genomics of US Maize: Domestication and Modern BreedingHistorical Genomics of US Maize: Domestication and Modern Breeding
Historical Genomics of US Maize: Domestication and Modern Breedingjrossibarra
 
Bottlenecks -- some ramblings and a bit of data from maize PAGXXII
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIBottlenecks -- some ramblings and a bit of data from maize PAGXXII
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIjrossibarra
 
Danforth 2015
Danforth 2015Danforth 2015
Danforth 2015jrossibarra
 
Complex adaptation in Zea
Complex adaptation in ZeaComplex adaptation in Zea
Complex adaptation in Zeajrossibarra
 
Evolutionary genetics of hybrid maize
Evolutionary genetics of hybrid maizeEvolutionary genetics of hybrid maize
Evolutionary genetics of hybrid maizejrossibarra
 
JGI: Genome size impacts on plant adaptation
JGI: Genome size impacts on plant adaptationJGI: Genome size impacts on plant adaptation
JGI: Genome size impacts on plant adaptationjrossibarra
 
Deleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXIIDeleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXIIjrossibarra
 
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
 
Ecogen2013
Ecogen2013Ecogen2013
Ecogen2013jrossibarra
 
A bad genetic history of maize
A bad genetic history of maizeA bad genetic history of maize
A bad genetic history of maizejrossibarra
 
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
 
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
 
Genomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingGenomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingCIMMYT
 
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
 
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
 
Crop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai liCrop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai liExternalEvents
 
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
 
THEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybeanTHEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybeanICARDA
 
An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals OECD Environment
 
Genome size and adaptation in plants
Genome size and adaptation in plantsGenome size and adaptation in plants
Genome size and adaptation in plantsjrossibarra
 
Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...Premier Publishers
 
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...Pat (JS) Heslop-Harrison
 
Application of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van EenennaamApplication of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van EenennaamOECD Environment
 
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...FOODCROPS
 
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
 
Phylogenetics: Making publication-quality tree figures
Phylogenetics: Making publication-quality tree figuresPhylogenetics: Making publication-quality tree figures
Phylogenetics: Making publication-quality tree figuresBioinformatics and Computational Biosciences Branch
 
BEAST: Time-stamped data and population dynamics
BEAST: Time-stamped data and population dynamicsBEAST: Time-stamped data and population dynamics
BEAST: Time-stamped data and population dynamicsBioinformatics and Computational Biosciences Branch
 

Weitere ähnliche Inhalte

Was ist angesagt?

Deleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXIIDeleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXIIjrossibarra
 
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
 
A bad genetic history of maize
A bad genetic history of maizeA bad genetic history of maize
A bad genetic history of maizejrossibarra
 
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
 
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
 
Genomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingGenomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingCIMMYT
 
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
 
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
 
Crop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai liCrop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai liExternalEvents
 
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
 
THEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybeanTHEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybeanICARDA
 
An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals OECD Environment
 
Genome size and adaptation in plants
Genome size and adaptation in plantsGenome size and adaptation in plants
Genome size and adaptation in plantsjrossibarra
 
Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...Premier Publishers
 
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...Pat (JS) Heslop-Harrison
 
Application of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van EenennaamApplication of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van EenennaamOECD Environment
 
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...FOODCROPS
 
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
 

Was ist angesagt? (20)

Deleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXIIDeleterious Alleles in maize, talk from PAGXXII
Deleterious Alleles in maize, talk from PAGXXII
 
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
 
Ecogen2013
Ecogen2013Ecogen2013
Ecogen2013
 
A bad genetic history of maize
A bad genetic history of maizeA bad genetic history of maize
A bad genetic history of maize
 
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
 
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
 
Genomic Selection & Precision Phenotyping
Genomic Selection & Precision PhenotypingGenomic Selection & Precision Phenotyping
Genomic Selection & Precision Phenotyping
 
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
 
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...
 
Crop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai liCrop genetic improvement and utilization in china. xinhai li
Crop genetic improvement and utilization in china. xinhai li
 
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
 
THEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybeanTHEME – 4 Genomic diversity of domestication in soybean
THEME – 4 Genomic diversity of domestication in soybean
 
An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals An overview of agricultural applications of genome editing: Farm animals
An overview of agricultural applications of genome editing: Farm animals
 
Genome size and adaptation in plants
Genome size and adaptation in plantsGenome size and adaptation in plants
Genome size and adaptation in plants
 
Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...Genetic variability, heritability, genetic advance, genetic advance as percen...
Genetic variability, heritability, genetic advance, genetic advance as percen...
 
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
Banana, Ensete and Boesenbergia Genomics - Schwarzacher, Heslop-Harrison, Har...
 
Application of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van EenennaamApplication of genome editing in farm animals: Cattle - Alison Van Eenennaam
Application of genome editing in farm animals: Cattle - Alison Van Eenennaam
 
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
2015. Jesse Poland. Integration of physiological breeding and genomic selecti...
 
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
 

Andere mochten auch

Liceo fernández madrid prueba inf aplic,
Liceo fernández madrid prueba inf aplic,Liceo fernández madrid prueba inf aplic,
Liceo fernández madrid prueba inf aplic,Martín Rojas
 
Agenda barcelona www.mundoespiritual.net
Agenda barcelona www.mundoespiritual.netAgenda barcelona www.mundoespiritual.net
Agenda barcelona www.mundoespiritual.netdenivel
 
Bases del Concurso Público para el Otorgamiento de Autorizaciones
Bases del Concurso Público para el Otorgamiento de Autorizaciones Bases del Concurso Público para el Otorgamiento de Autorizaciones
Bases del Concurso Público para el Otorgamiento de Autorizaciones Carlos Mena
 
Manual sistema de gestión de calida1
Manual sistema de gestión de calida1Manual sistema de gestión de calida1
Manual sistema de gestión de calida1tiburoneza
 
La dematerializzazione dei contratti
La dematerializzazione dei contrattiLa dematerializzazione dei contratti
La dematerializzazione dei contrattiGiovanni Maria Riccio
 
Wellness Plus+ Power Point Version 2003
Wellness Plus+ Power Point Version 2003Wellness Plus+ Power Point Version 2003
Wellness Plus+ Power Point Version 2003guest1780bbf
 
Fundamentos TSO para una barrica de calidad (1. selección de madera)
Fundamentos TSO para una barrica de calidad (1. selección de madera)Fundamentos TSO para una barrica de calidad (1. selección de madera)
Fundamentos TSO para una barrica de calidad (1. selección de madera)Juan C.T. López-Cano
 
Estudiantes primaria 4. animales, animalitos y animalotes
Estudiantes primaria 4. animales, animalitos y animalotesEstudiantes primaria 4. animales, animalitos y animalotes
Estudiantes primaria 4. animales, animalitos y animalotesRossyPalmaM Palma M
 

Andere mochten auch (17)

Phylogenetics: Making publication-quality tree figures
Phylogenetics: Making publication-quality tree figuresPhylogenetics: Making publication-quality tree figures
Phylogenetics: Making publication-quality tree figures
 
BEAST: Time-stamped data and population dynamics
BEAST: Time-stamped data and population dynamicsBEAST: Time-stamped data and population dynamics
BEAST: Time-stamped data and population dynamics
 
Pathogen phylogenetics using BEAST
Pathogen phylogenetics using BEASTPathogen phylogenetics using BEAST
Pathogen phylogenetics using BEAST
 
Tree building 2
Tree building 2Tree building 2
Tree building 2
 
Selection analysis using HyPhy
Selection analysis using HyPhySelection analysis using HyPhy
Selection analysis using HyPhy
 
Business Voice January 2011
Business Voice January 2011Business Voice January 2011
Business Voice January 2011
 
Liceo fernández madrid prueba inf aplic,
Liceo fernández madrid prueba inf aplic,Liceo fernández madrid prueba inf aplic,
Liceo fernández madrid prueba inf aplic,
 
Program 2016
Program 2016Program 2016
Program 2016
 
Presentacion bienestar2
Presentacion bienestar2Presentacion bienestar2
Presentacion bienestar2
 
Agenda barcelona www.mundoespiritual.net
Agenda barcelona www.mundoespiritual.netAgenda barcelona www.mundoespiritual.net
Agenda barcelona www.mundoespiritual.net
 
Bases del Concurso Público para el Otorgamiento de Autorizaciones
Bases del Concurso Público para el Otorgamiento de Autorizaciones Bases del Concurso Público para el Otorgamiento de Autorizaciones
Bases del Concurso Público para el Otorgamiento de Autorizaciones
 
Manual sistema de gestión de calida1
Manual sistema de gestión de calida1Manual sistema de gestión de calida1
Manual sistema de gestión de calida1
 
The Five Sentence E-mail
The Five Sentence E-mailThe Five Sentence E-mail
The Five Sentence E-mail
 
La dematerializzazione dei contratti
La dematerializzazione dei contrattiLa dematerializzazione dei contratti
La dematerializzazione dei contratti
 
Wellness Plus+ Power Point Version 2003
Wellness Plus+ Power Point Version 2003Wellness Plus+ Power Point Version 2003
Wellness Plus+ Power Point Version 2003
 
Fundamentos TSO para una barrica de calidad (1. selección de madera)
Fundamentos TSO para una barrica de calidad (1. selección de madera)Fundamentos TSO para una barrica de calidad (1. selección de madera)
Fundamentos TSO para una barrica de calidad (1. selección de madera)
 
Estudiantes primaria 4. animales, animalitos y animalotes
Estudiantes primaria 4. animales, animalitos y animalotesEstudiantes primaria 4. animales, animalitos y animalotes
Estudiantes primaria 4. animales, animalitos y animalotes
 

Ähnlich wie Langebio 2015

Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison Malaysia
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison MalaysiaChromosomes, Crops and Superdomestication - Pat Heslop-Harrison Malaysia
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison MalaysiaPat (JS) Heslop-Harrison
 
Experimental validation, genetic map saturation and gene flow pilot study in ...
Experimental validation, genetic map saturation and gene flow pilot study in ...Experimental validation, genetic map saturation and gene flow pilot study in ...
Experimental validation, genetic map saturation and gene flow pilot study in ...CIAT
 
Genome Evolution Chromosomes Heslop-Harrison ICC Prague
Genome Evolution Chromosomes Heslop-Harrison ICC PragueGenome Evolution Chromosomes Heslop-Harrison ICC Prague
Genome Evolution Chromosomes Heslop-Harrison ICC PraguePat (JS) Heslop-Harrison
 
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013Pat (JS) Heslop-Harrison
 
Poster Presentation PPT Jia Cheong draft 1 (1)
Poster Presentation PPT Jia Cheong draft 1 (1)Poster Presentation PPT Jia Cheong draft 1 (1)
Poster Presentation PPT Jia Cheong draft 1 (1)Jia Cheong
 
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...Peter Vos
 
Temporal dynamics in microbial soil communities at anthrax carcass sites
Temporal dynamics in microbial soil communities at anthrax carcass sitesTemporal dynamics in microbial soil communities at anthrax carcass sites
Temporal dynamics in microbial soil communities at anthrax carcass sitesThomas Haverkamp
 
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...Avjinder (Avi) Kaler
 
Tropical maize genome: what do we know so far and how to use that information
Tropical maize genome: what do we know so far and how to use that informationTropical maize genome: what do we know so far and how to use that information
Tropical maize genome: what do we know so far and how to use that informationCIMMYT
 
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...Premier Publishers
 
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...Premier Publishers
 
Evaluation of viable selection criteria at the seedling stage in corn genotyp...
Evaluation of viable selection criteria at the seedling stage in corn genotyp...Evaluation of viable selection criteria at the seedling stage in corn genotyp...
Evaluation of viable selection criteria at the seedling stage in corn genotyp...Innspub Net
 
Science 2013-schuenemann-179-83 leprosy önemli
Science 2013-schuenemann-179-83 leprosy önemliScience 2013-schuenemann-179-83 leprosy önemli
Science 2013-schuenemann-179-83 leprosy önemliHazal Sav
 
1. MMLS 3 23Feb Sudhir Navathe.pdf
1. MMLS 3 23Feb Sudhir Navathe.pdf1. MMLS 3 23Feb Sudhir Navathe.pdf
1. MMLS 3 23Feb Sudhir Navathe.pdfSudhirNavathe
 
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...Integrated Breeding Platform
 

Ähnlich wie Langebio 2015 (20)

Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison Malaysia
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison MalaysiaChromosomes, Crops and Superdomestication - Pat Heslop-Harrison Malaysia
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison Malaysia
 
Experimental validation, genetic map saturation and gene flow pilot study in ...
Experimental validation, genetic map saturation and gene flow pilot study in ...Experimental validation, genetic map saturation and gene flow pilot study in ...
Experimental validation, genetic map saturation and gene flow pilot study in ...
 
Genome Evolution Chromosomes Heslop-Harrison ICC Prague
Genome Evolution Chromosomes Heslop-Harrison ICC PragueGenome Evolution Chromosomes Heslop-Harrison ICC Prague
Genome Evolution Chromosomes Heslop-Harrison ICC Prague
 
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013
Polyploidy and molecular cytogenetics in crops: ECA conference Dublin July 2013
 
Poster Presentation PPT Jia Cheong draft 1 (1)
Poster Presentation PPT Jia Cheong draft 1 (1)Poster Presentation PPT Jia Cheong draft 1 (1)
Poster Presentation PPT Jia Cheong draft 1 (1)
 
Tom_Adrianna-1
Tom_Adrianna-1Tom_Adrianna-1
Tom_Adrianna-1
 
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...
Development and anlysis of a 20K SNP array for potato (Solanum tuberosum) an ...
 
Temporal dynamics in microbial soil communities at anthrax carcass sites
Temporal dynamics in microbial soil communities at anthrax carcass sitesTemporal dynamics in microbial soil communities at anthrax carcass sites
Temporal dynamics in microbial soil communities at anthrax carcass sites
 
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...
Genome-Wide Association Mapping of Carbon Isotope and Oxygen Isotope Ratios i...
 
My publication-1
My publication-1My publication-1
My publication-1
 
Heslopharrisonassisiweb
HeslopharrisonassisiwebHeslopharrisonassisiweb
Heslopharrisonassisiweb
 
Cereal genomics
Cereal genomicsCereal genomics
Cereal genomics
 
Tropical maize genome: what do we know so far and how to use that information
Tropical maize genome: what do we know so far and how to use that informationTropical maize genome: what do we know so far and how to use that information
Tropical maize genome: what do we know so far and how to use that information
 
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...
Genetic Variability, Heritability and Genetic Advance of Kabuli Chickpea (Cic...
 
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...
Genetic Variability, Heritability and Genetic Advance in Potato (Solanum Tube...
 
Evaluation of viable selection criteria at the seedling stage in corn genotyp...
Evaluation of viable selection criteria at the seedling stage in corn genotyp...Evaluation of viable selection criteria at the seedling stage in corn genotyp...
Evaluation of viable selection criteria at the seedling stage in corn genotyp...
 
Science 2013-schuenemann-179-83 leprosy önemli
Science 2013-schuenemann-179-83 leprosy önemliScience 2013-schuenemann-179-83 leprosy önemli
Science 2013-schuenemann-179-83 leprosy önemli
 
Transposable elements
Transposable elementsTransposable elements
Transposable elements
 
1. MMLS 3 23Feb Sudhir Navathe.pdf
1. MMLS 3 23Feb Sudhir Navathe.pdf1. MMLS 3 23Feb Sudhir Navathe.pdf
1. MMLS 3 23Feb Sudhir Navathe.pdf
 
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...
Our PAG XXVI Presentations: Integrating Marker-Assisted Selection into a Popu...
 

Mehr von jrossibarra

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
 
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
 

Mehr von jrossibarra (9)

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
 
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
 

Kürzlich hochgeladen

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b
Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 bAsymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b
Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 bSérgio Sacani
 
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...ssifa0344
 
Disentangling the origin of chemical differences using GHOST
Disentangling the origin of chemical differences using GHOSTDisentangling the origin of chemical differences using GHOST
Disentangling the origin of chemical differences using GHOSTSérgio Sacani
 
Green chemistry and Sustainable development.pptx
Green chemistry and Sustainable development.pptxGreen chemistry and Sustainable development.pptx
Green chemistry and Sustainable development.pptxRajatChauhan518211
 
Physiochemical properties of nanomaterials and its nanotoxicity.pptx
Physiochemical properties of nanomaterials and its nanotoxicity.pptxPhysiochemical properties of nanomaterials and its nanotoxicity.pptx
Physiochemical properties of nanomaterials and its nanotoxicity.pptxAArockiyaNisha
 
Botany 4th semester series (krishna).pdf
Botany 4th semester series (krishna).pdfBotany 4th semester series (krishna).pdf
Botany 4th semester series (krishna).pdfSumit Kumar yadav
 
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.Nitya salvi
 
Spermiogenesis or Spermateleosis or metamorphosis of spermatid
Spermiogenesis or Spermateleosis or metamorphosis of spermatidSpermiogenesis or Spermateleosis or metamorphosis of spermatid
Spermiogenesis or Spermateleosis or metamorphosis of spermatidSarthak Sekhar Mondal
 
Hubble Asteroid Hunter III. Physical properties of newly found asteroids
Hubble Asteroid Hunter III. Physical properties of newly found asteroidsHubble Asteroid Hunter III. Physical properties of newly found asteroids
Hubble Asteroid Hunter III. Physical properties of newly found asteroidsSérgio Sacani
 
Presentation Vikram Lander by Vedansh Gupta.pptx
Presentation Vikram Lander by Vedansh Gupta.pptxPresentation Vikram Lander by Vedansh Gupta.pptx
Presentation Vikram Lander by Vedansh Gupta.pptxgindu3009
 
Biopesticide (2).pptx .This slides helps to know the different types of biop...
Biopesticide (2).pptx .This slides helps to know the different types of biop...Biopesticide (2).pptx .This slides helps to know the different types of biop...
Biopesticide (2).pptx .This slides helps to know the different types of biop...RohitNehra6
 
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls Agency
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls AgencyHire 💕 9907093804 Hooghly Call Girls Service Call Girls Agency
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls AgencySheetal Arora
 
Pests of mustard_Identification_Management_Dr.UPR.pdf
Pests of mustard_Identification_Management_Dr.UPR.pdfPests of mustard_Identification_Management_Dr.UPR.pdf
Pests of mustard_Identification_Management_Dr.UPR.pdfPirithiRaju
 
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...anilsa9823
 
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptx
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptxUnlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptx
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptxanandsmhk
 
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡anilsa9823
 
Chemistry 4th semester series (krishna).pdf
Chemistry 4th semester series (krishna).pdfChemistry 4th semester series (krishna).pdf
Chemistry 4th semester series (krishna).pdfSumit Kumar yadav
 
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral Analysis
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral AnalysisRaman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral Analysis
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral AnalysisDiwakar Mishra
 
Botany 4th semester file By Sumit Kumar yadav.pdf
Botany 4th semester file By Sumit Kumar yadav.pdfBotany 4th semester file By Sumit Kumar yadav.pdf
Botany 4th semester file By Sumit Kumar yadav.pdfSumit Kumar yadav
 

Kürzlich hochgeladen (20)

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b
Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 bAsymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b
Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b
 
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...
TEST BANK For Radiologic Science for Technologists, 12th Edition by Stewart C...
 
Disentangling the origin of chemical differences using GHOST
Disentangling the origin of chemical differences using GHOSTDisentangling the origin of chemical differences using GHOST
Disentangling the origin of chemical differences using GHOST
 
Green chemistry and Sustainable development.pptx
Green chemistry and Sustainable development.pptxGreen chemistry and Sustainable development.pptx
Green chemistry and Sustainable development.pptx
 
Physiochemical properties of nanomaterials and its nanotoxicity.pptx
Physiochemical properties of nanomaterials and its nanotoxicity.pptxPhysiochemical properties of nanomaterials and its nanotoxicity.pptx
Physiochemical properties of nanomaterials and its nanotoxicity.pptx
 
Botany 4th semester series (krishna).pdf
Botany 4th semester series (krishna).pdfBotany 4th semester series (krishna).pdf
Botany 4th semester series (krishna).pdf
 
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.
❤Jammu Kashmir Call Girls 8617697112 Personal Whatsapp Number 💦✅.
 
Spermiogenesis or Spermateleosis or metamorphosis of spermatid
Spermiogenesis or Spermateleosis or metamorphosis of spermatidSpermiogenesis or Spermateleosis or metamorphosis of spermatid
Spermiogenesis or Spermateleosis or metamorphosis of spermatid
 
Hubble Asteroid Hunter III. Physical properties of newly found asteroids
Hubble Asteroid Hunter III. Physical properties of newly found asteroidsHubble Asteroid Hunter III. Physical properties of newly found asteroids
Hubble Asteroid Hunter III. Physical properties of newly found asteroids
 
Presentation Vikram Lander by Vedansh Gupta.pptx
Presentation Vikram Lander by Vedansh Gupta.pptxPresentation Vikram Lander by Vedansh Gupta.pptx
Presentation Vikram Lander by Vedansh Gupta.pptx
 
Biopesticide (2).pptx .This slides helps to know the different types of biop...
Biopesticide (2).pptx .This slides helps to know the different types of biop...Biopesticide (2).pptx .This slides helps to know the different types of biop...
Biopesticide (2).pptx .This slides helps to know the different types of biop...
 
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls Agency
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls AgencyHire 💕 9907093804 Hooghly Call Girls Service Call Girls Agency
Hire 💕 9907093804 Hooghly Call Girls Service Call Girls Agency
 
Pests of mustard_Identification_Management_Dr.UPR.pdf
Pests of mustard_Identification_Management_Dr.UPR.pdfPests of mustard_Identification_Management_Dr.UPR.pdf
Pests of mustard_Identification_Management_Dr.UPR.pdf
 
The Philosophy of Science
The Philosophy of ScienceThe Philosophy of Science
The Philosophy of Science
 
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...
Lucknow 💋 Russian Call Girls Lucknow Finest Escorts Service 8923113531 Availa...
 
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptx
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptxUnlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptx
Unlocking the Potential: Deep dive into ocean of Ceramic Magnets.pptx
 
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡
CALL ON ➥8923113531 🔝Call Girls Kesar Bagh Lucknow best Night Fun service 🪡
 
Chemistry 4th semester series (krishna).pdf
Chemistry 4th semester series (krishna).pdfChemistry 4th semester series (krishna).pdf
Chemistry 4th semester series (krishna).pdf
 
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral Analysis
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral AnalysisRaman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral Analysis
Raman spectroscopy.pptx M Pharm, M Sc, Advanced Spectral Analysis
 
Botany 4th semester file By Sumit Kumar yadav.pdf
Botany 4th semester file By Sumit Kumar yadav.pdfBotany 4th semester file By Sumit Kumar yadav.pdf
Botany 4th semester file By Sumit Kumar yadav.pdf
 

Langebio 2015

  • 1. Selection and demography in maize evolution Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org Dept. Plant Sciences • Center for Population Biology • Genome Center University of California Davis photo by lady_lbrty
  • 2.
  • 3. Photos: Matt Hufford, Brandon Gaut, John Doebley
  • 9. hard sweep multiple mutations polygenic adaptation Diversity standing variation “soft” sweeps
  • 10. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
  • 11. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG
  • 12. M T G P H R L GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG
  • 13. maize origins TripsacumF1 teosinte (Z. mays ssp. parviglumis) maize (Z. mays ssp. mays)
  • 14. F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
  • 15. F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
  • 16. F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
  • 17. F1 Beadle 1979 Field Museum of Nat. Hist. Bull.
  • 18. Briggs et al. 2007 Genetics 1 2 3 4 5 6 7 8 9 10
  • 19. Wang et al. 2005 Nature 1 2 3 4 5 6 7 8 9 10 Figure 1. Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte e internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a m introgressed into it. d. Close-up of a single teosinte fruitcase. e. Close-up o teosinte plant with a maize allele of tga1 introgressed into it. f. Ear of maiz (Tga1-maize allele) with the cob exposed showing the small white glumes a of maize inbred W22:tga1 which carries the teosinte allele, showing enlarge h. Ear of maize inbred W22 carrying the tga1-ems1 allele, showing enlarged g NIH-PAAuthorManuscriptNIH-PAAuthorManuscriptNIH-P tga1 Wang et al. 2015 Genetics
  • 20. Wang et al. 2005 Nature 1 2 3 4 5 6 7 8 9 10 Figure 1. Phenotypes. a. Maize ear showing the cob (cb) exposed at top. b. Teosinte e internode (in) and glume (gl) labeled. c. Teosinte ear from a plant with a m introgressed into it. d. Close-up of a single teosinte fruitcase. e. Close-up o teosinte plant with a maize allele of tga1 introgressed into it. f. Ear of maiz (Tga1-maize allele) with the cob exposed showing the small white glumes a of maize inbred W22:tga1 which carries the teosinte allele, showing enlarge h. Ear of maize inbred W22 carrying the tga1-ems1 allele, showing enlarged g NIH-PAAuthorManuscriptNIH-PAAuthorManuscriptNIH-P tga1 Wang et al. 2015 Genetics
  • 21. 1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics
  • 22. 1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics teosinte maize Clint Whipple, BYU
  • 23. 1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics
  • 24. 1 2 3 4 5 6 7 8 9 10 gt1 tga1 Wills et al. 2013 PLoS Genetics 5’ control region 3’ UTR
  • 25. 1 2 3 4 5 6 7 8 9 10 tb1 Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1gt1
  • 26. 1 2 3 4 5 6 7 8 9 10 tb1 Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1 GENETICS ADVANCE ONLINE PUBLICATION 3 nguish maize and teosinte. Both the maize and teosinte s for the distal component repressed luciferase expression luc luc luc luc luc luc Hopscotch mpCaMV M-dist T-prox M-prox 0 0.5 1.0 1.5 2.0 ∆M-dist ∆M-prox ProximalcontrolregionDistal Constructs and corresponding normalized luciferase expression nsient assays were performed in maize leaf protoplast. Each is drawn to scale. The construct backbone consists of the romoter from the cauliflower mosaic virus (mpCaMV, gray box), ORF (luc, white box) and the nopaline synthase terminator ). Portions of the proximal and distal components of the gion (hatched boxes) from maize and teosinte were cloned ction sites upstream of the minimal promoter. “ ” denotes on of either the Tourist or Hopscotch element from the maize Horizontal green bars show the normalized mean with s.e.m. onstruct. relative expressionconstruct gt1
  • 27. 1 2 3 4 5 6 7 8 9 10 tb1 Figure 2 Map of parviglumis Populations and Hopscotch allele frequency. Map showing the frequency of the Hopscotch allele in populations of parviglumis where we sampled more than 6 individuals. Size of circles reflects number of individuals sampled. The Balsas River is shown, as the Balsas River Basin is believed to be the center of domestication of maize. as our independent trait for phenotyping analyses. SAS code used for analysis is available at http://dx.doi.org/10.6084/m9.figshare.1166630. RESULTS Genotyping for the Hopscotch insertion The genotype at the Hopscotch insertion was confirmed with two PCRs for 837 individuals of the 1,100 screened (Table S1 and Table S2). Among the 247 maize landrace accessions genotyped, all but eight were homozygous for the presence of the insertion Within our parviglumis and mexicana samples we found the Hopscotch insertion segregating in 37 (n = 86) and four (n = 17) populations, respectively, and at highest frequency within populations in the states of Jalisco, Colima, and Michoac´an in central-western Mexico (Fig. 2). Using our Hopscotch genotyping, we calculated diVerentiation between populations (FST) and subspecies (FCT) for populations in which we sampled sixteen or more chromosomes. We found that FCT = 0, and levels of FST among populations within each subspecies (0.22) and among all populations (0.23) (Table 1) are similar to genome-wide estimates from previous studies Pyh¨aj¨arvi, HuVord & Ross-Ibarra, 2013. Although we found large variation in Hopscotch allele frequency among our populations, BayEnv analysis did not indicate a correlation between the Hopscotch insertion and environmental variables (all Bayes Factors < 1). Studer et al. 2011 Nat. Gen.; Vann et al. 2015 PeerJ tga1 GENETICS ADVANCE ONLINE PUBLICATION 3 nguish maize and teosinte. Both the maize and teosinte s for the distal component repressed luciferase expression luc luc luc luc luc luc Hopscotch mpCaMV M-dist T-prox M-prox 0 0.5 1.0 1.5 2.0 ∆M-dist ∆M-prox ProximalcontrolregionDistal Constructs and corresponding normalized luciferase expression nsient assays were performed in maize leaf protoplast. Each is drawn to scale. The construct backbone consists of the romoter from the cauliflower mosaic virus (mpCaMV, gray box), ORF (luc, white box) and the nopaline synthase terminator ). Portions of the proximal and distal components of the gion (hatched boxes) from maize and teosinte were cloned ction sites upstream of the minimal promoter. “ ” denotes on of either the Tourist or Hopscotch element from the maize Horizontal green bars show the normalized mean with s.e.m. onstruct. relative expressionconstruct gt1
  • 28. hard sweep M T N P H R L GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG tga1
  • 29. hard sweep M T N P H R L GGTCGA ATG ACT GAT CCA CAT CGA CTG TAG tga1 gt1 tb1 Multiple Mutations Standing Variation M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG
  • 30. Vann et al. 2015 PeerJ polygenic adaptation 30% phenotypic variance 0% phenotypic variance
  • 31. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize ~500 genes (2%) 11M shared SNPs 3,000 fixed genomes:
  • 32. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes:
  • 33. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen 13 teosinte 23 maize genomes:
  • 34. Swanson-Wagner et al. 2012 PNAS E ze network edges 6 7 2 Mb or conservation and targets of selection during improvement and/or domestication. (A) Venn diagram es, and the genes that occur in genomic regions that have evidence for selective sweeps during maize s). (B) Teosinte coexpression networks for three genes (GRMZM2G068436, GRMZM2G137947, and ned in maize coexpression networks are shown. Although the differentially expressed gene (red node) is tions are lost in maize. However, some parts of the teosinte network are still conserved in maize. (C) Cross- ExpressionGenealogy teosinte maize
  • 35. nucleotidediversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 36. nucleotidediversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 37. Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
  • 38. Mexico highland6,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
  • 39. Mexico highland6,000 BP S. America lowland 6,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
  • 40. Mexico highland6,000 BP S. America lowland 6,000 BP S. America Highland 4,000 BP Mexico lowland 9,000 BP Matsuoka et al. 2002; Piperno 2006 Perry et al. 2006; Piperno et al. 2009
  • 42. SA MEX SA MEX SA MEX SA MEX SA MEX SA MEX Ear Height Plant Height Tassel Br. Number TW Days to Anthesis SA MEX SA MEX SA MEX SA MEX LowlandHighland
  • 43. 95 landraces ~100K SNPs Takuno et al. 2015 Genetics
  • 44. -Logp-valueFstS.America -Log p-value Fst Mexico shared SNPs unique S.America unique Mexico 95 landraces ~100K SNPs Takuno et al. 2015 Genetics
  • 45. -Logp-valueFstS.America -Log p-value Fst Mexico shared SNPs unique S.America unique Mexico 39% 61% Intergenic Genic 19% 81% Standing Variation New mutation Takuno et al. 2015 Genetics
  • 46. Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics
  • 47. Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Z = LX i=1 ↵ipi allele freq. population breeding value effect size
  • 48. Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Z = LX i=1 ↵ipi allele freq. population breeding value effect size relatednessdispersion add. genetic var. QX = ~Z0 T F 1 ~Z0 2VA
  • 49. Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
  • 50. Cold Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
  • 51. Cold Beissinger et al. In Prep (b) Berg & Coop 2014 PLoS Genetics Warm
  • 53. Pyhäjärvi et al. GBE 2013
  • 54. Pyhäjärvi et al. GBE 2013
  • 55. Pyhäjärvi et al. GBE 2013
  • 56. Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 57. how to adapt: Zea mays soft sweeps M T G P H R L GGTAAA ATG ACT GGT CCA CAT CGA CTG TAG polygenic adaptation regulatory variation
  • 58. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science
  • 59. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science
  • 60. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity
  • 61. Ne diploids s selection coefficient selection is effective if 2Nes > 1
  • 62. Ne diploids s selection coefficient selection is effective if 2Nes > 1 Ne ~ 150,000 Ne ~ 10,000 Ne ~ 2,000,000 Ne ~ 600,000
  • 63. Ne diploids s selection coefficient selection is effective if 2Nes > 1 Ne ~ 150,000 Ne ~ 10,000 Ne ~ 2,000,000 Ne ~ 600,000 20% nonsyn. subs 10% nonsyn. subs 50% nonsyn. subs 40% nonsyn. subs
  • 64. teosinte maize DATA teosinte maize MODEL Beissinger et al. In Prep: http://biorxiv.org/content/early/2015/11/13/031666 Hufford et al. 2012
  • 65. teosinte maize DATA teosinte maize MODEL 0.05Na Na Na 3Na Beissinger et al. In Prep: http://biorxiv.org/content/early/2015/11/13/031666 Hufford et al. 2012
  • 66. Ne ~ 150,000 Ne ~ 50,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 67. 0.05Na Na Na 3Na Ne ~ 450,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 68. 0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 69. 0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 70. 0.05Na Na Na 3Na Ne ~ 450,000 Ne ~ 1,000,000 1e+05 1e+07 1e+09 1e+03 1e+042e+04 1e+05 years(u=3e−8, generation=1) effectivepopulationsize pop BKN_4Hap BKN_6Hap TIL_4Hap_Jalisco TIL_6Hap Ne ~ 1,000,000,000 Ne ~ 5,000,000,000 Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 71. nucleotidediversity distance to gene (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 72. nucleotidediversity distance to gene (cM) singletondiversity distance to gene (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 73. singletondiversity distance to nearest substitution (cM) Beissinger et al. In Prep: http://biorxiv.org/content/early/
  • 74. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science diversity Ne >> 1,000,000 Ne ~ 10,000* Ne ~ 2,000,000 Ne ~ 600,000
  • 75. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG
  • 76. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAGx
  • 77. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAGx
  • 78. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x x x x
  • 79. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x
  • 80. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x
  • 81. M T G P H R L ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L ATG ACT GAT CCA CAT CGA CTG TAG x xx x x x x x x
  • 82. Makarevitch et al. 2014 PLoS Genetics
  • 83. Makarevitch et al. 2014 PLoS Genetics single TE family, many genes
  • 84. Makarevitch et al. 2014 PLoS Genetics single TE family, many genes new insertions activate expression Makarevitch et al. 2014 bioRxiv Lines with the TE insertion Lines without the TE insertion GRMZM2G071206 Log2(stress/control) -2 0 2 4 6 8 10 12 Lines with the TE insertion Lines without the TE insertion -2 0 2 4 6 8 10 12 Log2(stress/control) GRMZM2G400718 C 1.0 1.5 2.0 D GRMZM2G102447 -2 0 2 4 6 8 10 12 14 Lines with the TE insertion Lines without the TE insertion GRMZM2G108149 A B Log2(stress/control)s/control) http://biDownloaded from -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 1 2 3 4 5 6 7 8 9 10 Oh43 B73 Mo17 - - + - - + - + - - ++ - - + - - + - - + - - + - - + - - + Gene Log2(stress/control) TE presence 0% 20% 40% 60% 80% 100% alaw dagaf etug flip gyma ipiki jeli joemon naiba nihep odoj pebi raider riiryl ubel uwum Zm00346 Zm02117 Zm03238 Zm05382 Salt UV Heat Cold B A Percentofconserved genes * ** *** * * ** * single gene, many individuals
  • 85. Hancock et al 2011 Science Hernandez et al. 2011 Science Fraser et al. 2013 Gen. Research enrichment intergenic<———>coding Pyhäjärvi et al. GBE 2013 enrichment intergenic<———>coding
  • 86. Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1
  • 87. Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1 Garud et al. 2015 PLoS Gen. Jensen 2014 Nat. Comm. Pritchard et al. 2010 Curr. Bio. Enard et al. 2014 Gen. Res. Beissinger et al. In Prep µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp µ ∝ 130 Mbp
  • 88. Ne diploids µ beneficial mutation rate per trait selection from standing variation when 2Neµ > 1 Garud et al. 2015 PLoS Gen. Jensen 2014 Nat. Comm. Pritchard et al. 2010 Curr. Bio. Enard et al. 2014 Gen. Res. Beissinger et al. In Prep µ ∝ 2,500 Mbp µ ∝ 3,100 Mbp µ ∝ 130 Mbp µ ∝ 220 Mbp µ ∝ 130 Mbp Williamson et al. 2014 PLoS Gen
  • 89. Brandon Gaut maizeArabidopsis Kew C-Value Database log 1C genome size
  • 90. • “Soft sweeps” and polygenic selection predominate in maize and teosinte • Most selection appears in noncoding sequence • Both effective population size & mutational target contribute • Large, complex genomes may mean more targets & more soft sweeps & less linked effects of selection Concluding Thoughts
  • 91. Acknowledgments Maize Diversity Group Peter Bradbury Ed Buckler John Doebley Theresa Fulton Sherry Flint-Garcia Jim Holland Sharon Mitchell Qi Sun Doreen Ware Collaborators Graham Coop Nathan Springer Ruairidh Sawers Lab Alumni Tim Beissinger (USDA-ARS, Mizzou) Kate Crosby (Monsanto) Matt Hufford (Iowa State) Tanja Pyhäjärvi (Oulu) Shohei Takuno (Sokendai) Joost van Heerwaarden (Wageningen)