Agricultural Genomics: The Rise of the Genomes

Agricultural Genomics: The Rise of the Genomes

Dr. Doreen Ware, USDA ARSAgricultural Biotechnology: Emerging Technologies and Insights

January, 27, 2021

Advancing Agriculture Through Collaborative Research on Crop & Model Species

Outline

• Agricultural Drivers• Maize genome 16 years

– What’s in a genome– Improvements in Sequencing technology we can

Continue to evaluate approaches to develop reference assembly and annotations

• Genome/Biology enabled agriculture– Sorghum EMS population

• Forward and reverse genetics – Breaking down complex trait: Yeild & Quality

• Plant architecture: flower• Response to environment: water, heat, nitrogen, disease

• Biology & “Big Data” – collaborative infrastructure– Future

NB#ARC'

LRR'CC'

Drivers for Agriculture: Sustainability and Defense

3

Population Growth

ClimateChange

20182050

Agricultural Resources

Nature Editorial, How to feed a hungry world. 2010

BREEDING FOR 2050 AND BEYOND. Prepare for plant and animal pests and disease while they are still offshore. Design plants for new environments.

CLIMATE CHANGE. Collect and preserve natural diversity.

Maize is the highest world-wide production crop

Reference genomes are foundation tools for ensuring food security & environmental sustainability

Acknowledgements

Gramene www.gramene.org ( NSF & USDA ARS) 2002- present NSF IOS-1127112PI: Doreen Ware, PI (USDA ARS, CSHL) & Pankaj Jaiswal, Co-PI (OSU), Paul Kersey (Ensembl Genomes EBI), Helen Parkinson (ATLAS EBI), Lincoln Stein (Reactome OCIR), Crispin Taylor (ASPB)Gramene @ CSHL Andrew Olson, Joshua Stein, Sharon Wei, : Marcela Karey Monaco, Institutes: Cold Spring Harbor Laboratory, Oregon State University, EMBL – European Bioinformatics Institute, Ontario Institute for Cancer Research, American Society for Plant Biologists

USDA ARS Sorghum Functional Genomics and Germplasm improvement: 2015- presentUSDA Doreen Ware, Zhanguo Xin, Chad Hayes, Yinghua Huang, Gloria Burow, Ratan Chopra, John BurkeSorghumBase: Nick Gladman, Yinping Jiao, Bo Wang, Kapeel Chougule Andrew Olson, Sharon Wei, : Marcela Karey MonacoCorteva,

B73 Genome & Annotation Improvements V4 ( NSF & USDA ARS) ~ 2015 -2017CSHL staff: Yinping Jiao, Bo Wang, Mike Campbell, Josh Stein, Sharon Wei, Doreen Ware, Dick McCombie, Eric AntinouPacBio: David Rank, Paul Peluso, Jason Chin, Tyson Clark, Ting Hong, Elizabeth TsengBioNano: Alex Hestie, Tiffany Liang, Jinghua Shi. USDA ARS Mike McMullen, Kate Guill, University of Georgia: Kelly Dawe , Jonathan Gent, University of Hawaii: Gernot Presting, Kevin Schneider, Thomas WolfgruberInstitutes: Cold Spring Harbor Laboratory, USDA ARS, Pacific BioSciences, BioNano, University of Georgia, University of Hawaii

Maize Diveristy Project ( NSF & USDA ARS) ~ 2003- presentUSD AARS Ed Buckler, Sherry Flint-Garcia, Mike McMullen, Jim Holland, Peter Bradbury, Doreen Ware Cornell QiSun, UCDavisJeff Ross-Ibarra

Transcriptome Variation (USDA ARS) 2016- 2019CSHL staff: Yinping Jiao, Bo Wang, Mike Campbell, Josh Stein, Sharon Wei, Doreen Ware, Dick McCombie, Sara GoodwinPacBio: Elizabeth Tseng, Tyson Clark, Ting Hong, Kevin Eng, Primo BaybayanInstitutes: Cold Spring Harbor Laboratory, USDA ARS, Pacific BioSciences

o

Maize Nested Association Mapping Panel Reference Assemblies (NSF & USDA ARS) 2018- presentUniversity of Georgia: Kelly Dawe, University of Iowa: Matt Hufford University Minnesota Candy HirschCSHL staff: Josh Stein, Kapeel Chougule Sharon Wei, Doreen Ware, Dick McCombie, Sara GoodwinPacBio: Emily Hatas, Paul Peluso, Jason Chin, Cortiva: Victor Llaca, Kevin Fengler, Greg May, DNA Nexus: Brent Hannigan, Chai Fungtammasan, Brittanny O’Sullivan, NIH: Adam Phillippy, Serge KorenInstitutes: Cold Spring Harbor Laboratory, USDA ARS, University of Georgia, University of Iowa, Pacific BioSciences, DNANexus, NIH

Maize Genome Project ( NSF, DOE, USDA ) ~ 2005-2010University of Washington, Rick Wilson, CSHL: Rob Martienssen, Dick McCombie, Doreen Ware, University of Arizona, Rod Wing, University of Iowa Pat Schnable

http://www.gramene.org/

Maize Genome is over 12 years old

Schnable, Ware et al. Science (2009)Maize Sequence Consortium (NSF, DOE, USDA) PI Rick Wilson

STIFF STALK

B73

Sequence genomes provides us the parts list and allows us to see what is the same or different between organisms

Genes in corn, rice, and sorghum are in similar places in the genome

Schnable, Ware et al. Science (2009)

Triceratops Genome

http://www.jurassicworld.com/creation-lab/

Genomes sequences allow us to see all the variations (mutations) that exist in nature

Letters or Single nucleotides polymorphisms (SNPs)

Gene content or parts list, known as copy number variations (CNVs)

Jumping genes, Transposable Elements (TEs) associated with the regulatory sequence between the Genes

Barbara McClintock1983 Nobel Prize in Physiology & Medicine

Maize is a “Tale of Two Genomes”

A

B

n = 10

n = 10

X AB

n = 20

C

Chromosome breakage and re-fusion

Gene loss

n = 10

Return to 10 chromosomes

Ancestors

Evolutionary History of the Maize Genome

A

B

n = 10

n = 10

X AB

n = 20

C

Chromosome breakage and re-fusion

Gene loss

n = 10

Return to 10 chromosomes

Ancestors

Red = “strong”, dominant genomeBlue = “weak”

Schnable, Ware et.al, Science 2009

Maize is a “Tale of Two Genomes”

Maize, also known as corn experienced a whole genome duplications and then lost many of the genes

The genes that were kept by corn can tell us about how corn is adapting

Transcription factors, kinases, chromatin modifiers

Not all genomes have the same potential

Schnable, Ware et.al, Science 2009

Humans Have Limited Molecular Diversity

0.09%

Silent Diversity; Zhao, et al. (2001) PNAS

1.34%

Maize diversity is greater than the difference between human and chimps

Silent Diversity; Tenallion, et al. (2001) PNAS

1.42%

Individual Maize lines are very different from each other

The SNPs and gene differences affect how corn plants grow

Access to these sequences can accelerate the time it takes to make new lines of corn

Differences come from locally duplicated genes

Images Bo Wang

10/19/2017 fe9228_008f5b8700b54c5590404beccdc6c171.webp (845×552)

http://static.wixstatic.com/media/fe9228_008f5b8700b54c5590404beccdc6c171.jpg/v1/fill/w_845,h_552,al_c,q_85,usm_0.66_1.00_0.01/fe9228_008f5b8700b54c559… 1/1

An additional copy of gene confers tolerance to acidic soil

Maron et. al, PNAS, 2013

Maize genomes are highly variable

Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC et al: Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 2012, 44(7):803-807.

• High rate of SNP and structure variation in the population

• Structure variations are highly associated with phenotypic variation

• Structural variation in non coding region was enriched for phenotypic variation

• One genome is not enough to represent the diversity of the population

MAIZE DIVERSITY PROJECTMeet the Family (2002 - present)

www.panzea.org

COURTESY SHERRY FLINT-GARCIA

http://www.panzea.org/

NC33

B115I137TN

81-1MEF 156-55-2IL677A

Ia5125

IA2132

IL101

F2EP1F7

CO255

NC366B52

SC213R

NC238

GT112

Mp339GA209

D940Y

T232

U267Y

CI28AB2

F2834TMo24WMS1334

IDS28

I-29

SA24

4722

SG18Sg1533

IDS91IDS69

F6F44

Ab28A

CML328Oh603

A441-5

CML323

SC55

NC264NC370

NC320NC318NC334NC332

CML92

CML220

CML218A272

Tzi9

CML77

TZI10

CML311

CML349CML158Q

CML154Q

CML281

CML91

parvi-14

parvi-36

parvi-03

parvi-49parvi-30

NC356

TX601

NC340NC300

NC304

NC338NC302

NC354TZI18

A6

Ki44Ki43

Ki2007Ki21

Ki2021Ki14

CML238CML321

CML157Q

CML332CML331CML261CML341CML45CML11CML10Q6199

CML314

CML258

CML5CML254CML61

CML264

CML9

CML108CML287Tzi11

CML38CML14

SC357L578T234

N6E2558WK64

CI64

CI44CI31A NC230

CI66 K55R109BMoGL317NC232

VaW6CH701-30

Va85CI90C M14

H99Va99 PA91

Ky226

H95Oh40B

VA26 Pa762 OH43

A619

Va22Va17Va14 Va59

Va102Va35

T8

A654

Pa880SD44CH9

Pa875H49

W64A

WF9

Mo1WOs420

R168

38-11NC260

Mo44

CI21E

HyA661

ND246

WDA554

CO125CO109

B75

DE-3

DE-2

DE1

B57C123

C103

NC360

NC364NC362

NC342NC290A

NC262

NC344

NC258CI91B

CI187-2

A682K4

NC222

NC236

CI3A

K148

Mt42

MS153

W401A556B77

CM37

CMV3

W117HT

CM7

CO106

B103

R4

Ky228

B164

Mo46Mo47

Mo45

Hi27Yu796-NS

I205

Tzi16Tzi25

B79

B105

N7ASD40N28HT

A641

DE811

H105W

A214NH100

A635A632

A634B14AH91B68

B64

CM174CM105B104

B84

NC250H84

B76

B37

N192A679

B109 NC294NC368 NC326NC314

NC308NC312NC306NC268B46 B10

A239C49AC49

A188

W153RA659R177

W22W182B

33-16

4226

26 Reference Assemblies for the Maize Nested Association Mapping (NAM) Population

B97, KY21, MO17, MS71, M162W, OH43, OH7B

NON STIFF STALK

TROPICAL-SUBTROPICAL

CML52, CML69, CML103, CML228, CML247,CML27, CML322, CML333, KI3, KI11, NC350, NC358, TX303, TZI8

STIFF STALK

B73

SWEET CORN

IL14H, P39

POPCORN

HP301

MIXED

MO18W, M37W

Adapted from McMullen et al. Science 2009

• 25 Parental lines selected to represent the diversity in maize

• From these, 25 families of 200 recombinant inbred lines were generated

• Rich collection of phenotypes

• Resource for joint linkage, association mapping studies

Maize Nested Association Mapping (NAM) Population

Yu, et al. (2008) Genetics

25 DL

× B73

F1s

Ä

Ä

Ä

Ä

Ä

Ä

Ä

Ä

ÄSSD

NAM

1

2

200

.

.

.

. . . . . .

B97

CML1

03

CML2

28

CML2

47

CML2

77

CML3

22

CML3

33

CML5

2

CML6

9

Hp30

1

Il14H Ki11 Ki

3

Ky21

M16

2W

M37

W

Mo1

8W

MS7

1

NC3

50

NC3

58

Oh4

3

Oh7

B

P39

Tx30

3

Tzi8

5000 RILs

Arun Seetharam -ISUMargaret Woodhouse – MaizeGDBKapeel Chougule -CSHLShujun Ou -ISUJianing Liu -UGAXuehong Wei –CSHLZhenyuan Lu –CSHL Andrew Olson –CSHLBo Wang -CSHL Sharon Wei -CSHLTingTing Guo -ISURafael Della Coletta -UMXianran Li -ISUJohn Portwood –MaizeGDBKevin Fengler -CortevaVictor Llaca -CortevaAmanda Gilbert -UMNancy Manchanda -ISUSamantha Snodgrass -ISUDavid Hufnagel -ISUSarah Pedersen -ISUMichael Syring –ISUEthy Cannon - MaizeGDBCarson Andorf -MaizeGDBJonathan Gent –UGATodd Michael - JCVIJianming Yu –ISUCandice Hirsch -UMDoreen Ware –CSHLMatthew B. Hufford -ISUR. Kelly Dawe -UGA

Victor Llacas

Kelly DaweU. Georgia

Doreen WareUSDA-ARSCSHL

Matt HuffordIowa State U.

Candy HirschU. Minnesota

Zhenyuan Lu

26 Maize NAM founders reference assemblies (2019- 2021)

Bo Warg

Andrew Olson

New assemblies have a vast improvement in the contiguity of the sequence

StiffStalkNonStiffStalkMixedPopCornSweetCornTropical

Matrices Assembled Contigs

Total Bases in Assembly

2,180,413,054

Contig Contiguity (NG50)

52,409,415

Number of Contigs 811

Longest Contig 161,290,055

Kevin Fengler

Victor Llaca

N50 is the shortest contig length needed to cover 50% of the genome. -> Half of the genome sequence is covered by contigs larger than or equal the N50 contig size. Hufford et, al, bioRxiv, 2021

More than 100, 000 genes found in the 26 maize accession

Hufford et, al, bioRxiv, 2021

Maize Pan Gene Set



Maize Pan Gene SetCore genes are more likely to be Syntenic



The bulk of the genes in maize are found in other species


Genome contains life history of the speciesTeosinte

Zea mays L. ssp. parviglumis Landraces

Maize, Modern InbredsZea mays L. ssp. mays

Biology Enabled Agriculture

Complex Traits: Yield & Quality Phenomes

Regulatory NetworksMetabolic Pathways

Genome EditingGenomic SelectionMarker Assisted Breeding

QTLGWAS

MetabolomicsExpressionEpigenetic

Genomes

Gene Networks

G X (environment +management) = P

Profiling new sorghum genetic & phenotypic variation

• Parental line: BTX 623• >10,000 individual M2 seed

pools• >6,400 M3 seeds obtained and • Phenotyping is on-going and

need to be expanded• High quality DNA prepared for

all linesEMS Mutagenesis-Random- Single nucleotide change- >99% GCàAT

Zhanguo XinCropping Systems Research Lab,

USDA-ARS, Lubbock TX

Jiao et al. The Plant Cell, 2016

Mutation Detection by whole genome sequencing of 256

mutants for forward genetics• Sequencing summary

- 20 M3 plants pooled together for sequence to averagely 16X - Average whole genome coverage – 86%; gene space coverage -95%

• Quality control of the population: 2 contamination lines + 2 sibling lines• Mutation detection:

- 1,862,560 EMS-induced mutations- Sanger sequencing validation rate >98%- 7,660 mutation/mutant = 1,798 homozygous + 5,862 heterozygous

• Mutation Effect:- 22% of mutations are located in genes, covering 95% of Sorghum genes - 57% (18,684) of the genes harbor >35,000 disruptive mutations, ~2

disruptive mutations per gene.

Yinping Jiao


Multiseeded (msd1, msd2, msd3)

BTX623 msd2PS

SS

~50% Fertility 100% Fertility

Collaborator Zhanguo Xin USDA ARS, Lubbock


Regulatory Networks

EMS population

ExpressionMetabolites

Genomes

Transcription factor


Zhanguo XinYoung Koung LeeYinping Jiao Nick Gladman

MSD1 TCP transcription factor

Jiao et al., Nature Comm. (2018)

Yield > Flower development > grain number > fertility/branching


Regulatory Networks

EMS population


Genomes



Teosinte BranchedDoebley et al., Geneitics (1995)

TCP transcription factor



Regulatory NetworksMetabolic Pathways

Genome EditingMarker Assisted Breeding

EMS population


Genomes

Transcription factor, Plant hormones


Ahmad, et al. 2016. Frontiers

MSD2

MSD3

MSD1 TCP transctiption factor

Jasmonic Acid (JA) Pathway

Jiao et al., Nature Comm. (2018)Gladman et al., Int. J. Mol. Science (2019)Dampanaboina, L., Int. J. Mol. Science (2019)


Nitrogen, soil, and agricultural sustainability

October 2011. Credit, USGS, NASA.Nitrogen deficiencies, LSU (courtesy, Dr. Brenda Tubana)

Insufficient Nitrogen fertilizer Excess Nitrogen fertilizer


NUE

Metabolic NetworkExpression

Genomes


Complex Traits: Yield> Fitness> Limiting Nitrogen

ChristopheLiseron-MonfilsAndrew OlsonLifang Zhang

Guardinier et al, Nature 2017

Siobhan Brady UC DAVIS

Allie GaudinierUC DAVIS


AT4G24620

AT1G12110

AT3G61830

AT5G60910

AT3G47340

AT3G14180

AT5G54680

AT5G15210

AT3G53340

AT2G44730

AT5G39760

AT5G05410

AT1G13960

AT4G31550 AT1G76510

AT1G61730

AT3G01970

AT2G47890

AT3G28920

AT5G63790

AT5G66320

AT3G49940

AT2G46830

AT3G11580

AT5G53460

AT1G51600

AT4G29080

AT2G31230

AT4G01250

AT2G35530

AT1G53910

AT1G20700

AT2G40950

AT2G27300

AT1G54060

AT5G54930

AT2G02540

AT1G73730

AT1G21910

AT5G61590

AT2G22840

AT1G71130

AT5G57390

AT5G13330

AT4G23980

AT4G37260

AT1G12630

AT1G12610

AT5G56860

AT1G04880

AT2G23290

AT1G76880

AT3G07650

AT1G68360

AT5G60850

AT2G40620

AT3G54810

AT3G55730

AT1G78600

AT1G32450

AT1G19220

AT2G46310

AT3G08590

AT1G75540

AT5G07440

AT2G33480

AT1G47270

AT5G59820

AT3G17609

AT3G51910

AT5G10140

AT1G05380

AT3G57480

AT2G21320

AT4G30410

AT5G25830

AT4G23750

AT1G22810

AT1G79180

AT5G07700

AT5G07690

AT5G60770

AT3G62100

AT3G24050

AT5G22570

AT4G32890

AT3G60530

AT2G22430

AT5G51990

AT5G16770

AT1G22070

AT1G69170

AT1G01010

AT1G56170

AT3G58120

AT1G14510

AT4G25470

AT5G25810

AT2G44940

AT1G28470

AT2G40740

AT1G22190

TMO5/LHW

AT2G46680

AT1G10120

AT1G69490

AT1G68640

AT3G61890

AT4G28140

AT3G16770

AT5G06710

AT1G31320

AT1G75240

AT4G37790

AT1G72360

AT3G04070

AT5G44080

AT1G22640

AT3G46600

AT2G22900

AT1G29280

AT4G34990

AT5G43170

AT3G58710

AT3G45610

AT4G34610

AT2G30590

AT1G34190

AT1G24280

AT2G15620

AT1G78050

AT5G52020

AT1G47870

AT1G77450

AT1G24625

AT5G40850

AT4G24400

AT4G35260

AT1G14580

AT4G16750

AT5G67190

AT2G38290

AT3G60490

AT5G18170

AT1G03840

AT5G44160

AT4G18880

AT4G35550

AT1G35560

AT2G23320

AT5G41410

AT1G08090

AT5G65010

AT4G24020

AT2G46270

AT2G20880

AT2G04240

AT1G77760

AT1G64530

AT5G13110

AT1G02860

AT5G49620

AT5G09330

AT1G54830

AT2G37630

AT5G12840

AT3G19860

AT5G14340

AT3G03200

AT5G10280

AT3G19580

AT4G14550

AT3G50260

AT5G60890

AT5G26660

AT3G06490

AT1G78080

AT2G04880

AT3G57230

AT2G37430

AT4G39070

AT5G41920

AT4G05390

AT5G24800

AT1G37130

AT4G40060

AT3G23240

AT5G03510

AT1G69310

AT3G42790

AT2G47900

AT1G20910

AT3G08500

AT1G22710

AT3G14940

AT3G22760

AT1G73870

AT1G63910

AT5G60450

AT1G02340

AT3G17100

AT1G48000

AT4G36900

AT4G32800

AT4G04955

AT2G25930

AT3G60750

AT1G72330

AT4G37540

AT5G35630

AT1G30510

AT1G30270

AT2G26940

AT1G26610

AT1G64780

AT1G76350

AT1G16530

AT2G31955

AT5G67420

AT5G11260

AT5G14570

AT5G23090

AT1G34180

AT5G22290

AT4G28500

AT1G32870

AT5G49520

AT1G01060

AT1G29160

AT2G38470

AT1G02220

AT5G08520

AT1G16490

AT5G18270

AT4G01680

AT4G36160

AT1G09540

AT1G66230

AT1G34670

AT5G54470

AT4G22680

AT1G43860

AT1G12860

AT2G18380

AT4G00940

AT5G45710

AT1G31050

AT4G29410

AT3G50410

AT2G42830

AT3G24490

AT1G18570

AT1G77570

AT5G51230

AT2G46530

AT2G38340

AT2G22850

AT1G77640

AT5G65210

AT3G17820

AT3G22830

AT3G56400

AT5G47220

AT1G69010

AT1G22985

AT4G17490

AT1G12260

AT2G36400

AT3G10500

AT2G18280

AT5G02840

AT2G24500

AT2G47270

AT2G48100

AT2G36720

AT3G05800

AT4G36620

AT5G63280

AT1G49720

AT3G10470

AT1G76900

AT3G06120

AT5G67580

AT5G39660

AT4G35040

AT1G75710

AT2G16400

AT2G26150

AT5G50820

AT1G07980

AT5G47230

AT5G43700

AT1G05805

AT1G53170

AT5G05790

AT2G41070

AT3G04730

AT5G13910

AT1G14350

AT1G25560

AT5G62380

AT2G21230

AT1G44830

AT5G01380

AT5G61600

AT5G62020

AT5G28040

AT3G10040

AT3G49760

AT4G38900

AT5G12870

AT1G13260

AT1G68130

AT3G60580

AT5G51190

AT5G13080

AT4G25210

AT2G24570

AT5G53980

AT5G44210

AT5G17800

AT1G68840

AT1G43700

AT5G62610

AT4G36730

AT3G45650

AT3G25730

AT2G45680

AT3G54390

AT1G68920

AT1G66200

AT3G19290

AT5G06960

AT1G69850

AT5G50200

AT4G01120

AT3G55370

AT1G17520

AT4G14770

AT1G07520

AT4G37850

AT1G34310

AT1G30490

AT5G10510

AT3G47520

AT3G15210

AT2G14210

AT4G37740

AT1G50640


NUE

Regulatory NetworksMetabolic Network

ExpressionGene regulation

Genomes








Limiting N1mM NO3

AT4G24620

AT1G12110

AT3G61830

AT5G60910

AT3G47340

AT3G14180

AT5G54680

AT5G15210

AT3G53340

AT2G44730

AT5G39760

AT5G05410

AT1G13960

AT4G31550 AT1G76510

AT1G61730

AT3G01970

AT2G47890

AT3G28920

AT5G63790

AT5G66320

AT3G49940

AT2G46830

AT3G11580

AT5G53460

AT1G51600

AT4G29080

AT2G31230

AT4G01250

AT2G35530

AT1G53910

AT1G20700

AT2G40950

AT2G27300

AT1G54060

AT5G54930

AT2G02540

AT1G73730

AT1G21910

AT5G61590

AT2G22840

AT1G71130

AT5G57390

AT5G13330

AT4G23980

AT4G37260

AT1G12630

AT1G12610

AT5G56860

AT1G04880

AT2G23290

AT1G76880

AT3G07650

AT1G68360

AT5G60850

AT2G40620

AT3G54810

AT3G55730

AT1G78600

AT1G32450

AT1G19220

AT2G46310

AT3G08590

AT1G75540

AT5G07440

AT2G33480

AT1G47270

AT5G59820

AT3G17609

AT3G51910

AT5G10140

AT1G05380

AT3G57480

AT2G21320

AT4G30410

AT5G25830

AT4G23750

AT1G22810

AT1G79180

AT5G07700

AT5G07690

AT5G60770

AT3G62100

AT3G24050

AT5G22570

AT4G32890

AT3G60530

AT2G22430

AT5G51990

AT5G16770

AT1G22070

AT1G69170

AT1G01010

AT1G56170

AT3G58120

AT1G14510

AT4G25470

AT5G25810

AT2G44940

AT1G28470

AT2G40740

AT1G22190

TMO5/LHW

AT2G46680

AT1G10120

AT1G69490

AT1G68640

AT3G61890

AT4G28140

AT3G16770

AT5G06710

AT1G31320

AT1G75240

AT4G37790

AT1G72360

AT3G04070

AT5G44080

AT1G22640

AT3G46600

AT2G22900

AT1G29280

AT4G34990

AT5G43170

AT3G58710

AT3G45610

AT4G34610

AT2G30590

AT1G34190

AT1G24280

AT2G15620

AT1G78050

AT5G52020

AT1G47870

AT1G77450

AT1G24625

AT5G40850

AT4G24400

AT4G35260

AT1G14580

AT4G16750

AT5G67190

AT2G38290

AT3G60490

AT5G18170

AT1G03840

AT5G44160

AT4G18880

AT4G35550

AT1G35560

AT2G23320

AT5G41410

AT1G08090

AT5G65010

AT4G24020

AT2G46270

AT2G20880

AT2G04240

AT1G77760

AT1G64530

AT5G13110

AT1G02860

AT5G49620

AT5G09330

AT1G54830

AT2G37630

AT5G12840

AT3G19860

AT5G14340

AT3G03200

AT5G10280

AT3G19580

AT4G14550

AT3G50260

AT5G60890

AT5G26660

AT3G06490

AT1G78080

AT2G04880

AT3G57230

AT2G37430

AT4G39070

AT5G41920

AT4G05390

AT5G24800

AT1G37130

AT4G40060

AT3G23240

AT5G03510

AT1G69310

AT3G42790

AT2G47900

AT1G20910

AT3G08500

AT1G22710

AT3G14940

AT3G22760

AT1G73870

AT1G63910

AT5G60450

AT1G02340

AT3G17100

AT1G48000

AT4G36900

AT4G32800

AT4G04955

AT2G25930

AT3G60750

AT1G72330

AT4G37540

AT5G35630

AT1G30510

AT1G30270

AT2G26940

AT1G26610

AT1G64780

AT1G76350

AT1G16530

AT2G31955

AT5G67420

AT5G11260

AT5G14570

AT5G23090

AT1G34180

AT5G22290

AT4G28500

AT1G32870

AT5G49520

AT1G01060

AT1G29160

AT2G38470

AT1G02220

AT5G08520

AT1G16490

AT5G18270

AT4G01680

AT4G36160

AT1G09540

AT1G66230

AT1G34670

AT5G54470

AT4G22680

AT1G43860

AT1G12860

AT2G18380

AT4G00940

AT5G45710

AT1G31050

AT4G29410

AT3G50410

AT2G42830

AT3G24490

AT1G18570

AT1G77570

AT5G51230

AT2G46530

AT2G38340

AT2G22850

AT1G77640

AT5G65210

AT3G17820

AT3G22830

AT3G56400

AT5G47220

AT1G69010

AT1G22985

AT4G17490

AT1G12260

AT2G36400

AT3G10500

AT2G18280

AT5G02840

AT2G24500

AT2G47270

AT2G48100

AT2G36720

AT3G05800

AT4G36620

AT5G63280

AT1G49720

AT3G10470

AT1G76900

AT3G06120

AT5G67580

AT5G39660

AT4G35040

AT1G75710

AT2G16400

AT2G26150

AT5G50820

AT1G07980

AT5G47230

AT5G43700

AT1G05805

AT1G53170

AT5G05790

AT2G41070

AT3G04730

AT5G13910

AT1G14350

AT1G25560

AT5G62380

AT2G21230

AT1G44830

AT5G01380

AT5G61600

AT5G62020

AT5G28040

AT3G10040

AT3G49760

AT4G38900

AT5G12870

AT1G13260

AT1G68130

AT3G60580

AT5G51190

AT5G13080

AT4G25210

AT2G24570

AT5G53980

AT5G44210

AT5G17800

AT1G68840

AT1G43700

AT5G62610

AT4G36730

AT3G45650

AT3G25730

AT2G45680

AT3G54390

AT1G68920

AT1G66200

AT3G19290

AT5G06960

AT1G69850

AT5G50200

AT4G01120

AT3G55370

AT1G17520

AT4G14770

AT1G07520

AT4G37850

AT1G34310

AT1G30490

AT5G10510

AT3G47520

AT3G15210

AT2G14210

AT4G37740

AT1G50640

Sufficient N10mM NO3


NUE


tDNA population


Genomes








Limiting N1mM NO3

AT4G24620

AT1G12110

AT3G61830

AT5G60910

AT3G47340

AT3G14180

AT5G54680

AT5G15210

AT3G53340

AT2G44730

AT5G39760

AT5G05410

AT1G13960

AT4G31550 AT1G76510

AT1G61730

AT3G01970

AT2G47890

AT3G28920

AT5G63790

AT5G66320

AT3G49940

AT2G46830

AT3G11580

AT5G53460

AT1G51600

AT4G29080

AT2G31230

AT4G01250

AT2G35530

AT1G53910

AT1G20700

AT2G40950

AT2G27300

AT1G54060

AT5G54930

AT2G02540

AT1G73730

AT1G21910

AT5G61590

AT2G22840

AT1G71130

AT5G57390

AT5G13330

AT4G23980

AT4G37260

AT1G12630

AT1G12610

AT5G56860

AT1G04880

AT2G23290

AT1G76880

AT3G07650

AT1G68360

AT5G60850

AT2G40620

AT3G54810

AT3G55730

AT1G78600

AT1G32450

AT1G19220

AT2G46310

AT3G08590

AT1G75540

AT5G07440

AT2G33480

AT1G47270

AT5G59820

AT3G17609

AT3G51910

AT5G10140

AT1G05380

AT3G57480

AT2G21320

AT4G30410

AT5G25830

AT4G23750

AT1G22810

AT1G79180

AT5G07700

AT5G07690

AT5G60770

AT3G62100

AT3G24050

AT5G22570

AT4G32890

AT3G60530

AT2G22430

AT5G51990

AT5G16770

AT1G22070

AT1G69170

AT1G01010

AT1G56170

AT3G58120

AT1G14510

AT4G25470

AT5G25810

AT2G44940

AT1G28470

AT2G40740

AT1G22190

TMO5/LHW

AT2G46680

AT1G10120

AT1G69490

AT1G68640

AT3G61890

AT4G28140

AT3G16770

AT5G06710

AT1G31320

AT1G75240

AT4G37790

AT1G72360

AT3G04070

AT5G44080

AT1G22640

AT3G46600

AT2G22900

AT1G29280

AT4G34990

AT5G43170

AT3G58710

AT3G45610

AT4G34610

AT2G30590

AT1G34190

AT1G24280

AT2G15620

AT1G78050

AT5G52020

AT1G47870

AT1G77450

AT1G24625

AT5G40850

AT4G24400

AT4G35260

AT1G14580

AT4G16750

AT5G67190

AT2G38290

AT3G60490

AT5G18170

AT1G03840

AT5G44160

AT4G18880

AT4G35550

AT1G35560

AT2G23320

AT5G41410

AT1G08090

AT5G65010

AT4G24020

AT2G46270

AT2G20880

AT2G04240

AT1G77760

AT1G64530

AT5G13110

AT1G02860

AT5G49620

AT5G09330

AT1G54830

AT2G37630

AT5G12840

AT3G19860

AT5G14340

AT3G03200

AT5G10280

AT3G19580

AT4G14550

AT3G50260

AT5G60890

AT5G26660

AT3G06490

AT1G78080

AT2G04880

AT3G57230

AT2G37430

AT4G39070

AT5G41920

AT4G05390

AT5G24800

AT1G37130

AT4G40060

AT3G23240

AT5G03510

AT1G69310

AT3G42790

AT2G47900

AT1G20910

AT3G08500

AT1G22710

AT3G14940

AT3G22760

AT1G73870

AT1G63910

AT5G60450

AT1G02340

AT3G17100

AT1G48000

AT4G36900

AT4G32800

AT4G04955

AT2G25930

AT3G60750

AT1G72330

AT4G37540

AT5G35630

AT1G30510

AT1G30270

AT2G26940

AT1G26610

AT1G64780

AT1G76350

AT1G16530

AT2G31955

AT5G67420

AT5G11260

AT5G14570

AT5G23090

AT1G34180

AT5G22290

AT4G28500

AT1G32870

AT5G49520

AT1G01060

AT1G29160

AT2G38470

AT1G02220

AT5G08520

AT1G16490

AT5G18270

AT4G01680

AT4G36160

AT1G09540

AT1G66230

AT1G34670

AT5G54470

AT4G22680

AT1G43860

AT1G12860

AT2G18380

AT4G00940

AT5G45710

AT1G31050

AT4G29410

AT3G50410

AT2G42830

AT3G24490

AT1G18570

AT1G77570

AT5G51230

AT2G46530

AT2G38340

AT2G22850

AT1G77640

AT5G65210

AT3G17820

AT3G22830

AT3G56400

AT5G47220

AT1G69010

AT1G22985

AT4G17490

AT1G12260

AT2G36400

AT3G10500

AT2G18280

AT5G02840

AT2G24500

AT2G47270

AT2G48100

AT2G36720

AT3G05800

AT4G36620

AT5G63280

AT1G49720

AT3G10470

AT1G76900

AT3G06120

AT5G67580

AT5G39660

AT4G35040

AT1G75710

AT2G16400

AT2G26150

AT5G50820

AT1G07980

AT5G47230

AT5G43700

AT1G05805

AT1G53170

AT5G05790

AT2G41070

AT3G04730

AT5G13910

AT1G14350

AT1G25560

AT5G62380

AT2G21230

AT1G44830

AT5G01380

AT5G61600

AT5G62020

AT5G28040

AT3G10040

AT3G49760

AT4G38900

AT5G12870

AT1G13260

AT1G68130

AT3G60580

AT5G51190

AT5G13080

AT4G25210

AT2G24570

AT5G53980

AT5G44210

AT5G17800

AT1G68840

AT1G43700

AT5G62610

AT4G36730

AT3G45650

AT3G25730

AT2G45680

AT3G54390

AT1G68920

AT1G66200

AT3G19290

AT5G06960

AT1G69850

AT5G50200

AT4G01120

AT3G55370

AT1G17520

AT4G14770

AT1G07520

AT4G37850

AT1G34310

AT1G30490

AT5G10510

AT3G47520

AT3G15210

AT2G14210

AT4G37740

AT1G50640

Sufficient N10mM NO3


NUE


tDNA population


Genomes








Changing climate increasing temperature and drought

Reverse Genetics: From Gene to Phenotype

GeneinArabidopsis Sorghumgene Aminoacid

change MutantId

CER6 Sobic.001G453200 E159K ARS20KCS12 Sobic.004G341300 R189C ARS73CER5 Sobic.009G083300 P581L ARS73

CER5 Sobic.009G083300 L244F ARS20

CER6 Sobic.006G020600 A133T ARS205KCS7 Sobic.002G268300 P449S ARS31KCS4 Sobic.002G268500 A49V ARS31KCS20 Sobic.005G168700 R303Q ARS185CER1 Sobic.001G222700 L100F ARS185


Epicuticular wax (bloom) of sorghum plays important roles in tolerance of environmental stress.


Heat tolerance

Regulatory Networks

EMS populationFitness impact

Genomes

ATP dependent protease

Complex Traits: Yeild > Stress > Heat tolerance

Ftsh11 identified in a model plant

USDA-ARS, Lubbock TX Zhanguo Xin, Gloria Burow, Ratan Chopra, John Burke, Chad Hayes

Jiao et al. Plant Cell 2016


Yinping Jiao Zhanguo Xin


Metabolic Pathways


Genomes

Long chain fatty acid, ATP dependent protease

Complex Traits: Stress Resilience> Water Use efficiency

Jiao et al. Front. Plant Science 2018

Mass Spec

USDA-ARS, Lubbock TX Zhanguo Xin, Gloria Burow, Ratan Chopra, John Burke, Chad Hayes


Yinping Jiao Zhanguo XinNick Gladman

EMS population

Resistance to Southern Leaf BlightKump et al. Nat Genet 2011

Climate change impacts disease pressures

• Yield loss: Pesticide spraying increases direct cost and impacts to the environment, and human health

• Disease resistance “R”genes (NLR) are rapidly evolving and often seen in cluster. Good candidate for structural variation

• Pan Genomes: High quality reference assemblies to support characterization of core and dispensible (adaptive) genes

Sorghum Leaf spothttp://texassorghum.org/wp-content/uploads/2015/10/Fig.-2.jpg

R gene

http://texassorghum.org/wp-content/uploads/2015/10/Fig.-2.jpg

Sugarcane aphids

https://www.myfields.info/pests/sugarcane-aphid

• Since 2013 in the US sugarcane aphids have been causing enormous damage to sorghum crop

• Tx2783 has high resistance to SCA

Tx2783SCA locus mapped to the top of chromosojme 6

Collaborators:Yinghua Huang (USDA-ARS), Zhanguo Xin (USDA-ARS) Chad Hayes (USDA-ARS)

Wang et al., bioRxiv, 2021

Sorghum sugarcane aphid tolerant TX2783 reference assembly

447 PacBio contigs (25.6 Mb contig N50)


Chr. 06

Chr. 06

1. Tx2783 191KB insertion black box2. All of the genes in the cluster are disease resistance genes3. Complex region with local duplications 4. Inversion

Chr. 10

Sorghum Pan Genomes site: TX2783, BTX623, TX436, TX430, RIOAssembly Gene Neighborhood conservation view

Andrew Olson Sharon Wei Kapeel Chougule

Biology Enabled AgricultureYield> Biotic Stress > Disease Resistance

Signaling pathway


Expression

Genomes

NLR R Genes



Yinping Jiao Zhanguo Xin Bo Wang

TX2783 191 kb structural variant (SV) containing a cluster of R Genes

Resequencing data from 62 accessions identified the SV is segregating at a low frequency in these lines. Liya Wang

AT1G31320

AT2G42300 bZIP29

ANAC102

AT2G21230

CUC1

CUC2

HDG1

bZIP17

AT3G05760

AT1G20910

PHV

MGP

IAA2ARF6

SHR

miR393aIAA7

SCRIAA14

RGA1HSL1DREB2A

ARF9

AT5G08520

ERF104HSFA5

GATA9

AT2G44730

miR169emiR169d

ERF4

NF-YA10

EDF1

AT1G76510 WOX14

OBP2

AT2G44940 WRKY6

HB21

TRB2

bHLH121

GBF3ILR3

ANAC092

miR169nm PLT3GBF2

HB30

IAA19

IAA3

AT3G11280

IAA11

CBF4

IAA9 IAA4

IAA18

AT1G12630

IAA26

AT5G52020

AT5G63090 NF-YA8

miR169lHAP2B

HAP2C

miR169f

miR169b

NF-YA5HAP2A AT1G68360

NF-YA6 E2FCNF-YA9DDF1

AT1G76880

AT1G61730

AT1G04880

ARF18

DOF6

AT1G44830

ANT

miR169cAT1G54060

TMO6

bZIP69

AT5G62940

AT4G39070

TOE1

AT5G40330

AT2G46400 AT1G16490

AT4G23810

AT1G53230

ARF7

AT5G13790 AT3G55370

REV GAI

ARF11

IAA10IAA1

IAA31

IAA8

Exploring Genomes with an eye toward breedingBiology Enabled Agriculture

Phenomes

Metabolic PathwaysProtein ComplexesRegulatory Networks

Genome EditingGenomic SelectionMarker Assisted BreedingQTL

GWAS

MetabolomicsExpressionEpigenetic

Genomes

Gene Networks

Association AnalysesGenes with major affect

Comparative analysisTransfer information across species

Regulatory and Inference NetworksMany genes with minor contributions associated with a complex trait

Improved understanding of biological mechanisms & systems will improve breeding models and support for genetic engineering

Genomes X (Environment +Management) = Phenotypes

MetabolitesProteinsTranscripts Chromatin

Decreasing cost of sequencing leads to increasing computes and data management

$50 million (2009) Sequencing CentersBAC library, Sanger sequencing library, finishing libraries,computes

$250- 180 thousand (2016) Sequencing Centers PacBio long single molecule, Optical map, illumina short read High quality DNA, Library prep, access sequencer & ***compute

$90- 50 thousand (2017) Sequencing CentersPacBio long single molecule, Optical map, 10X illumina short read High quality DNA, Library prep, access sequencer & ***compute

$45- 25 thousand (2018) Local/ Sequencing Centers$2-6 thousand (2021) Long single molecule

DecreaseSequence

Cost

Increase Compute

Cost

Improve Assembly

Quality

Schnable, Ware et al, Science 2009Jiao et al., Nature, 2017Ou et. al, Genome Biology 2020Liu et al, Nature Comm 2020Wang et. al, submitted 2021Hufford et. al, submitted 2021

Sensors & MetadataSequencers, Microscopy, Imaging, Mass spec, Metadata & Ontologies

IO SystemsHardrives, Networking, Databases, Compression, LIMS

Compute SystemsCPU, GPU, Distributed, Clouds, Workflows

Scalable AlgorithmsStreaming, Sampling, Indexing, Parallel

Machine Learningclassification, modeling,

visualization & data Integration

ResultsDomain

Knowledge

Biology has transitioned to an Information Science

Keystone Big Data in Biology 2014 Stein, Schatz, Ware

Big Data” Biology PyramidQuantitative Biology Technologies

Artificial Inteligence (AI) is allowing us to reimagine how we approach science

Artificial Inteligence (AI) is allowing us to reimagine how we approach science

“AlphaFold is a once in a generation advance, predicting protein structures with incredible speed and precision. This leap forward demonstrates how

computational methods are poised to transform research in biology and hold much promise for

accelerating the drug discovery process.”

ARTHUR D. LEVINSONPHD, FOUNDER & CEO CALICO, FORMER CHAIRMAN

& CEO, GENENTECH

Wild Grapes have natural resistance to disease

10/18/2017 severe PM at MHRI 2013 (21).JPG (3648×2736)

https://www.agric.wa.gov.au/sites/gateway/files/severe%20PM%20at%20MHRI%202013%20%2821%29.JPG 1/1

Wild Grapes come with baggage they have shed with domestication

Wild: Male and Female

Domesticated:Hermaphrodite

Unpleasant taste

This, (2006); Feechan, et.al (2015)

Fig. 3

Plant NLR R-genes

Tyler B. (2001). Trends in Genetics. 17(11):611-614

Pathogen elicitor

NB#ARC'

LRR'CC'

coil-coil ATP-binding

Gene-for-gene hypothesis

Imagine a world where you can begin to model protein ligand models for disease resitance genes!

The Next Green Revolution will be “Data” and “Design” driven

Agriculture has transition to a Data Science. Massive data generation—genotypes, phenotypes, soil & environment.

Data now exceeds human capacity to formulate and test hypotheses about gene function, regulatory networks, and predictive agriculture.

Develop new approaches and systems that can supply new hypotheses for researchers for crop breeding, fermentation systems, solar energy capture, pest and disease management.

Adapt what has evolved in nature and design the space nature missed Norman Borlaug

Nobel Peace Prize 1970

While CRISPR has the power to enhance breeding byrapidly customizing and optimizing crop productivity

Genome Biology provides the insights to drive the translation

Unraveling Complex Traits using Genomic, Genetic, Systems & Computational Approaches

Advancing Agriculture Through Collaborative Research on Crop & Model Species

Ware LabKapeel ChouguleNick GladmanYInping JiaoVivek KumarSunita KumariForrest LiAugusto Lima DinzZhenyuan LuAndrew OlsonMichael RegulskiBo WangLiya WangXiaofei WangMarcela Tello RuizSharon WeiPeter Van BurenLifang ZhangCarol Hu

CSHL Dick McCombieRob MartienssenDave JacksonTom GingerasDave Micklos

Uplands FarmTim MulliganKyle Schlecht

HPCC resourcesTodd Heywood

Documents

Agricultural Genomics: The Rise of the Genomes