COPY DO NOT David Jordan Sorghum QTL Atlas€¦ · 16.06.2018 · sPb-0810 M188404 txp43M343014 txp88 sPb-0232 M343356 sPb-5358 sPb-2602 sPb-6600 sPb-7567 sPb-8492 M188582. M189251

Sorghum QTL AtlasEmma Mace

David Jordan

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Why have we developed a QTL Atlas?How users can access the Atlas?

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The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited, despite a large volume of data having been generated.

How can we better improve the rate of progress in an applied breeding program focused on quantitative traits?

Why have we developed a QTL Atlas?

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Over the last 2 decades, >150 QTL and GWAS studies have been published in sorghum, producing an enormous amount of information concerning the genetic basis of quantitative traits

• genomic location, • allelic effects, • epistatic interactions.

But making use of this information is not straight forward.

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There is no central repository of QTL studies that allows users to compare results of all current QTL and GWAS studies against a common framework

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>150 studies > 6000 QTL in sorghum for over 220 traits identified

heterogeneous nature of QTL studies leading to variable reliability of QTL identified

from one study to the next

the time investment required to integrate the information and generate a comprehensive

QTL database


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Heterogeneous nature of QTL studies…not all QTL are equal

The precision of initial QTL identification in QTL mapping studies is influenced by many factors including:

• population size and type, • precision of the phenotyping, • QTL analysis methodology • marker order, coverage and density.

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sPb-0145

sPb-2823

sPb-6061

sPb-0090 sPb-3386

sPb-0232

sPb-3798

sPb-8616

sPb-7695

sPb-4970

sPb-6434

sPb-1784

sPb-1017sPb-2075 sPb-2639sPb-4311sPb-6700

sPb-3361

sPb-3834

sPb-5737

sPb-8677

sPb-3853

sPb-9388

sPb-6857

sPb-3940

sPb-2562

sPb-8536

sPb-6882

sPb-4921

sPb-7186

sPb-4629

sPb-9894

sPb-8802

sPb-8138

sPb-4661

sPb-4734

sPb-9304

sPb-0906

sPb-5890

sPb-9312 sPb-7893

sPb-7030

sPb-9490

sPb-2551

sPb-3837

sPb-2457 sPb-8425

sPb-5030

sPb-9066

sPb-8436

sPb-1543

sPb-5230

sPb-0255

sPb-5403 sPb-7960

sPb-5765

sPb-7105

sPb-9931 sPb-8980

sPb-6825

sPb-1982

sPb-7381

sPb-8673

sPb-2630

sPb-9508

sPb-7944

sPb-7280

sPb-7086

sPb-5397 sPb-9365

sPb-6589

sPb-1503

sPb-9818

sPb-7126

sPb-5054

sPb-9372 sPb-0235sPb-0645

sPb-0380

sPb-1888

sPb-1272 sPb-5250

sPb-2846

sPb-9584

sPb-4385

sPb-2487

sPb-1323

sPb-3274sPb-1997 sPb-9449

sPb-8090sPb-8590

sPb-4011sPb-1895

sPb-0005

sPb-4156

sPb-8812 sPb-9227

sPb-8716

sPb-7460

sPb-2222

sPb-7473

sPb-9381

sPb-9999

sPb-9215 sPb-3958sPb-1722 sPb-4480sPb-8432 sPb-6875sPb-7643

sPb-9826

sPb-5834

sPb-6288

sPb-5841

sPb-6889 sPb-8201

sPb-7015

sPb-2465sPb-8208

sPb-2058

sPb-0232

sPb-0274

sPb-5358

txp58

sPb-9203 sPb-2683

sPb-4638

txp279

txp284

sPb-0277 sPb-4593sPb-0746

sPb-1984

sPb-7611

sPb-3577 sPb-1060

sPb-7984

sPb-8897

sPb-1631

txp4

txp3

sPb-3361

sPb-5737 sPb-3834

sPb-4054

sPb-1669 sPb-2055

sPb-6690

sPb-6857

sPb-1137sPb-1362 sPb-5108sPb-6122

sPb-8787

sPb-8349

txp285

sPb-6465

sPb-2521

sPb-4074

sPb-8446 sPb-2739sPb-7493 sPb-4718

sPb-1584

sPb-6741sPb-4506 sPb-2138sPb-8296 sPb-6559sPb-1811 sPb-1798sPb-9359 sPb-7310sPb-7274 sPb-5742sPb-1841 sPb-9987sPb-0867 sPb-7210sPb-9033 sPb-3903sPb-1295 sPb-8470sPb-2187

sPb-2842

sPb-5220

txp343

SB1-10

sPb-9303 sPb-6115

sPb-5119 sPb-9544sPb-5408

sPb-9009

txp303

sPb-5892

sPb-9642

sPb-8149

sPb-6323

sPb-7203

sPb-1454

sPb-6287

sPb-1396sPb-2874 sPb-0873

sPb-7892

sPb-5603 sPb-0017sPb-4732 sPb-1486

sPb-5101

sPb-8316 sPb-7064sPb-4740 sPb-9309sPb-2034

sPb-1414 sPb-2757sPb-1244 sPb-0571

sPb-2774

sPb-8673

sPb-6577

sPb-9007 sPb-8251sPb-4179

sPb-2491

sPb-6248

sPb-0703

sPb-7126

sPb-9818 sPb-7843

sPb-3396

sPb-9242

sPb-4432

sPb-0258

sPb-9700

sPb-1661sPb-7889

sPb-7312

sPb-1881

sPb-2228sPb-9743 sPb-4546sPb-0833sPb-3954

sPb-7823

sPb-6918 sPb-1825

sPb-5401 sPb-1291sPb-1051

sPb-1272 sPb-7082sPb-5250sPb-7648

sPb-2290sPb-5420sPb-4385

sPb-3434

sPb-7855

sPb-1991

sPb-8812 sPb-9227

sPb-3253

sPb-9538

sPb-7105

sPb-7905

sPb-1239 sPb-0771sPb-8338

sPb-6667

txp230

txp67

txp258

sPb-4156

sPb-6515

sPb-8306sPb-2735

sPb-2193sPb-3432 sPb-0248sPb-5005

sPb-8357

sPb-9592

sPb-0817

sPb-8150 sPb-6292

sPb-5917

sPb-7473

sPb-1962

sPb-5841

sPb-9064 sPb-8201

sPb-6889sPb-9215 sPb-1722sPb-3958 sPb-8432sPb-7643 sPb-4944sPb-6875sPb-4480

sPb-1040

M188427

umc84

sPb-8325

sPb-7161sPb-5521 sPb-0623sPb-2583 txp208SbRPG837

msbcir268

HVHGA1 HVGAD1umc107 msbcir347txp302 sPb-3891msbcir242msbcir228

M340904

M342631

sbAGFO8umc140

sPb-6917

sPb-6577

sPb-4329SbRPG873 um7

M189295

sPb-5315

M340898sPb-8041

sPb-6176

txp182 sPb-3618

umc83

sPb-4793

gpsb089

sPb-3727sPb-1191sPb-3525sPb-4234

M187880

M187200

sPb-2684sPb-2412 sPb-9216sPb-0810

M188404txp43 M343014txp88

sPb-0232M343356

sPb-5358

sPb-2602

sPb-6600

sPb-7567sPb-8492

M188582

M189251

msbcir304b

sPb-3311

msbcir286 gpsb173

sPb-3801

gap57sPb-8423sPb-7958sPb-6083gpsb051txp75M187238

M343241 M187616

gap36

msbcir336

bnl5.09

sPb-0233

M343279

SbRPG80

txp340 M342904M340364

msbcir306sPb-7611

sPb-4435

gpsb129 M340373

sPb-8743

sPb-7549 sPb-7657sPb-4855

M200042 M341662M341592 msbcir266

sPb-2754 gpsb011

gpsb174

M187772 sPb-0333

sPb-3103

txp25gpsb178 M342927M342711 sPb-8345M340957M341741

msbcir223 sPb-7668bsPb-7668txp211OPA7sPb-3086 sPb-1764sPb-9687M188881 M343289sPb-1127

M342329 M340416M342090SbRPG136sPb-3798

sPb-5347 sPb-8376

M342380

sPb-7177 sPb-8897sPb-5643

umc55

sPb-0364

sPb-5224sPb-4081msbcir238sPb-8616 sPb-4419gpsb087M187382M340431 M342471sPb-7695sPb-1920sPb-6434sPb-6288sPb-4970

M340888M343120 M343067

sPb-7882

M343086 M188424M342358M188643M188479 M342759M342673sPb-0350M340532

M342498

sbAGBO3

msbcir312

M341108 M188174

M187697 M188348

sPb-1970M187871 M187894

M188335

msbcir339 M189020

txp1

M342762

sPb-3917

sPb-2568

sPb-3361M340414 M342409M340589sPb-4862sPb-2229

sPb-6424sPb-1925

sPb-8706

SSmsbcir78

sPb-8568

sPb-0363

M342700 M189270sPb-5454M199861M340963

M340747 M342200

M188917 M342283

gpsb012sPb-2309 sPb-6714sPb-2461 sPb-5594M341408umc124 M342808sPb-1906 sPb-4915sPb-6982sPb-2055 sPb-1669sPb-0656 M188933M188681 M340763M188657M341540SBRPG846M342547sPb-0319M341223sPb-5409txp215sPb-9135

M187276

sPb-6857

M340732sPb-9388

SbRPG106

sPb-4226

gpsb086

sPb-2562

sPb-9076

sPb-7688sPb-5108 sPb-1362sPb-6122

sPb-1137

msbcir224 txp33

gap236sPb-9779 M187546

sPb-5922

csu58M340384 M341885M340852 M342663M340802 M188114txp31

msbcir276

sPb-2209

sPb-3965sPb-1496

sPb-9139 msbcir314

sPb-1725

sbAGEO1

sPb-1480

M341446 M341571

M188311

msbcir225

txp38

M188846 M342704sPb-6013

txp34

bnl5.37sPb-3228 sPb-6925M340973 M342779

M342567 M188347M188920 M342305

sPb-9894

sPb-6770

sPb-4074sPb-7493sPb-8446sPb-2739msbcir340sPb-4718

sPb-4233

sPb-7042

gpsb050

sPb-1853 msbcir323M187763

sPb-1932

M187985

M188323

M200413

RZ599

M188005 M188903

sPb-2944 sPb-6547

sPb-2842

M340930

M187716

M187502

sPb-8488

M343007sPb-7534txp12

M187661

sbAGGO2RZ166 M340886M341851 M340482

M340990 sPb-2084sPb-0854 sPb-9041

M200347

umc68sPb-4649M340664 M342464M342470 M187539gpsb073txp24

M340375 M341949csu26

M342928M342010M342065

txp327 txp60

msbcir232

sPb-8100M187223 M340952M187170 M187207M188305 M342916M188710

gpsb045

M342320 M342191M341902 M342643M187461M187118sPb-4692 M340433

gpsb028

txp21sPb-0110M341593M341500

msbcir329 M188451

gpsb159M341693 sPb-4041sPb-0906

txp65

sPb-0381

sPb-7047 sPb-5256

gpsb84 M188102M340916 sPb-5692bgpsb005M342865 sPb-4131sPb-3977sPb-5317 sPb-1282M188898 msbcir248sPb-5390sPb-8247 sPb-0510umc8 gpsb017gpsb165

sPb-5408 sPb-9080

sPb-3995

sPb-0932

sPb-1989

M187365

M340444 M340397sPb-6787 M340953sPb-5399 M189058sPb-6861txp15 M340502M340464 M341521sPb-6341M188512M341155sPb-7893 sPb-9312sPb-2187 M341517sPb-8470M188205 sPb-9054

M343065M188878sPb-4086 M342398csu166

sPb-6855

sPb-7106

gpsb003

txp23

M188834

gpsb176

SbRPG608

sPb-9490

sbKAFGK1

sPb-2570 sPb-9858

sPb-1181

sPb-2161 M342033M343312 M341274M342046 M340547sPb-3418sPb-5562 sPb-7892msbcir222

SSmsbcir120

gpsb032

sPb-1677 sPb-9772

sPb-1491

msbcir211 M342640

sPb-8793sPb-3644cdo456

sPb-9511

sPb-8963

txp6

M340448

M187805

sPb-8362 sPb-5564sPb-6017 M342664

gap7 gap72

sPb-5506 sPb-7660M187589M342089 M340758SSmsbcir92 M341530

sPb-4947

sPb-4503 sPb-3019

M341635

sPb-5030

txp145 sPb-4324

txp265 txp274sPb-1755 sPb-7777

gpsb127 M188023

sPb-7290

M341712 M340945M341047M342581M342391M342764gpsb069M341192

sPb-5802 sPb-7581

umc44

sPb-0255

bnl10.13

sPb-1721M187824M189179M343162 sPb-3962txp95sPb-6526M342082

sPb-5086 M340415sPb-9830sPb-5212 sPb-8954sPb-9422sPb-0581 sPb-7627sPb-1657sPb-8410

sPb-9667

M187362

gpsb169SbRPG225M340483 M188251M341110gpsb019 M188096M341392 M342492M343304M342678

gpsb148msbcir348

umc85M341299

sPb-1311

sPb-4878sPb-2566

M342381 gpsb114

sPb-5277M341472

sPb-8296

SbRPG22

sPb-1244sPb-0508 sPb-3708sPb-7531sPb-0571sPb-6252 sPb-2757sPb-1414sPb-7992

gap342gpsb010

M343313sPb-6863 sPb-7687sPb-3541sPb-9206 sPb-8340

gpsb031

msbcir246

sPb-8251 sPb-4179sPb-9007

msbcir300 M340509

sPb-9351txp295

sPb-6927

sPb-3258sbAGBO2sPb-5688sPb-9750 M341979bnl5.59

sPb-6798

sPb-8608

sPb-9299

txp273

gpsb041

gpsb104

gpsb023

M188849

SbRPG931

sPb-1130sPb-5054M341589

sPb-7630

sPb-5825

sPb-3247

sPb-8260

M341597

M343025 M343001

sPb-9279

M341867

sPb-7856 msbcir240

sPb-4768a

M340629 M340408M341359sPb-2140 sPb-4200sPb-2474 sPb-8057sPb-3195SbRPG125

sPb-9242M342657gpsb067sPb-4934sPb-5980sPb-2271 sPb-4432sPb-8059 M187350sPb-0435

sPb-3014

sPb-9762 sPb-3236sPb-5886 sPb-0325sPb-0441 sPb-6807sPb-3312 sPb-1265

sPb-3189

txp354

sPb-0258

gpsb103

msbcir337a sPb-0856

sPb-7375

txp18 txp321msbcir304asPb-6935sPb-3715

gpsb002

txp105

gpsb123

M343181

M188408M188523M342880 M188830M340454sPb-8363sPb-7220sPb-0289 sPb-2487sPb-6960 sPb-8384sPb-6918M187818sPb-5401sPb-1051

sPb-1291

sPb-4614

SbRPG950

sPb-0445

sbAGEO3umc62M187494M343363

M188061sPb-7460sPb-7686 gpsb020

M343231 sPb-2968sPb-1732 sPb-0852sPb-4006

M189112 M188652M342540

M342839sPb-6089 gpsb079M340730 M340810sPb-1991

umc38

sPb-4933

M341480SbRPG743 M188412sPb-0975 sPb-4416M340974

sPb-8542

sPb-8777M340536

sPb-3298sPb-6748M188560

sPb-9306

sPb-8764

sPb-1324 sPb-8873sPb-4786 sPb-6852sPb-6280 sPb-6043sPb-5055 M188501M342028 M341817sPb-5312 sPb-3158sPb-9272SbRPG821

M342543M341251M342741 M341021M342494M187902msbcir337b msbcir317M188207

sPb-7193

sPb-0005

gap42

M340587M342280 M341115umc64sPb-6515

sPb-0303sPb-7367 sPb-7955sPb-8368 sPb-9091M340964 sPb-9410sPb-4787 sPb-9962sPb-6506

M188934 M341036gap85sPb-8366

SbRPG917sPb-5281 sPb-8306M340704

sPb-1945

W AXY6msbcir331 msbcir324M189136

M342557

M187940 sPb-6720

gpsb027

SbRPG921

sPb-9517asPb-8357

umc113

sPb-3828 M341294

sPb-1104

sPb-5917

sPb-2149

sPb-0494

sPb-1962M340774 M342244M340871 M188983sPb-9999

sPb-6331

M341606M341123

M187142

txp217 sPb-4121bnl7.24msbcir283 sPb-6271

M340333

sPb-3696

sPb-9682

sPb-8019

sPb-2935 sPb-8232

SbRPG742

M342842

M342954 M340856M340712 M340495gap1

sPb-0859

msbcir262 msbcir227sPb-0162

M343252 M342053M342566

RZ143

sPb-4588 sPb-5814gpsb145


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SBI-01 SBI-02 SBI-03 SBI-04 SBI-05 SBI-06 SBI-07 SBI-08 SBI-09 SBI-10

Some QTL have a large confidence interval (CI), others have a small CI.

Some are highly significant, others less significant.

Some are detected from a single source (bi-parental mapping population), whereas others are detected in multiple sources (from a diversity panel)***

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QTL

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QTL

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our-c

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The resulting complexity of the QTL landscape means that delimiting the QTL confidence

intervals identified across multiple highly diverse studies is a major challenge


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Any attempt to project QTL locations from multiple experiments onto a single genetic or physical map

must take into account factors on which the reliability of the initial QTL study depends.


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QTL database


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QTL database

This consisted of: • 44 QTL studies• 771 QTL• 161 unique traitsAll 771 QTL were aligned to• Version 1 of the sorghum genome assembly• The sorghum consensus genetic linkage map


We have estimated the CIs for projected QTL following:CI = 530/(NR2) for F2 (described by Darvasi & Soller 1997)CI = 163/(NR2) for RI (described by Guo et al. 2006) where N is the number of lines in the mapping population and R2 is the proportion of phenotypic variation explained by the identified QTL. DO

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QTL database

The updated Sorghum QTL Atlas currently consists of: • >150 QTL and GWAS studies• ~6000 QTL and significant marker-trait

associations• >220 unique traitsAll 6000 QTL are aligned to• All 3 versions of the sorghum genome assembly• The sorghum consensus genetic linkage map• Zea mays genome (agpv2)• Oryza sativa genome (release 7)


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• What other QTL are nearby my trait of interest that could be effected by any selection I apply?

• In what populations have QTL for my trait(s) of interest been identified?

• How often has a particular QTL been identified in other studies/populations?

• What is the largest effect size QTL that has been identified for my trait(s) of interest?

• How many GWAS studies versus standard QTL mapping studies have been undertaken for my trait of interest?

• Which genes are within the QTL CI for my target trait in sorghum and also in the syntenic locations in maize and rice?

QTL atlas we have developed will enable researchers to answer the following sorts of questions:

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csu5870.0MT3670.7txp3171.1txp33673.2txp18375.2msbcir27676.3sPb-878777.4

txp44480.2

txs58485.4txp50387.5txS143987.6umc6387.8R87.9txp12088.4txp43589.2sPb-220991.6

sPb-224695.7

cdo116098.9txp231101.1sPb-3965102.8txp59103.2sPb-1496104.0

txS307106.7txS545108.9bcd828110.2isu121111.5msbcir314112.0txp114113.7txp437115.8sPb-1725116.5ST458117.1

sPb-6121121.6M341446125.3txs1927126.0txp440127.1sPb-8349128.2bcd738129.0M342704130.6txp442131.9S1329132.5sPb-4921133.7isu166134.5txs1226135.4msbcir225136.0txp285136.6txp421137.4txp38138.1txp448138.7sPb-9977140.8txp420141.4txS301144.0sPb-4629144.9txp34147.8txp424148.9bnl5.37149.1sPb-6925149.9isu68150.6AltSB152.0sPb-9894153.7txS1075154.6ms3155.3sPb-6770158.0A159.8txp69160.2txp425162.1Str58162.6CUa1163.2txp426164.2sPb-1642168.3sPb-8802172.3

Pericarp colour (R)

Awns (A)

Scenario 1: No selection

Scenario 2: Selection for red grain (R_)

Scenario 3: Selection for lemon yellow grain (rr)

Scenario 4: Selection for red grain (R_) and no awns (A_)

Scenario 5: Selection for lemon yellow grain (rr) and awns (aa)

0.0

0.2

0.4

0.6

0.8

1.0

Frequency of the senescent parent allele

stg2stg1

stg2stg1

Awnless

A_

Awned

aa

98.4% of progeny with stg2 favourable alleles

90.6% of progeny with stg1 favourable alleles

csu5870.0MT3670.7txp3171.1txp33673.2txp18375.2msbcir27676.3sPb-878777.4

txp44480.2

txs58485.4txp50387.5txS143987.6umc6387.8R87.9txp12088.4txp43589.2sPb-220991.6

sPb-224695.7

cdo116098.9txp231101.1sPb-3965102.8txp59103.2sPb-1496104.0

txS307106.7txS545108.9bcd828110.2isu121111.5msbcir314112.0txp114113.7txp437115.8sPb-1725116.5ST458117.1

sPb-6121121.6M341446125.3txs1927126.0txp440127.1sPb-8349128.2bcd738129.0M342704130.6txp442131.9S1329132.5sPb-4921133.7isu166134.5txs1226135.4msbcir225136.0txp285136.6txp421137.4txp38138.1txp448138.7sPb-9977140.8txp420141.4txS301144.0sPb-4629144.9txp34147.8txp424148.9bnl5.37149.1sPb-6925149.9isu68150.6AltSB152.0sPb-9894153.7txS1075154.6ms3155.3sPb-6770158.0A159.8txp69160.2txp425162.1Str58162.6CUa1163.2txp426164.2sPb-1642168.3sPb-8802172.3

Pericarp colour (R)

Awns (A)

stg2stg1

stg2stg1

Using QTL information to inform breeding strategy

Highlights the importance of knowing what other QTL are nearby the trait of interest that could be impacted by any selection applied

DO N

OT C

OPY

050

100150

200

1 2 3 4 5 6 7 8 9 10

020

4060

80100

120140

QTL distribution heat-map

Highlights the importance of knowing what other QTL are nearby the trait of interest that could be impacted by any selection applied

DO N

OT C

OPY

050

100150

200

1 2 3 4 5 6 7 8 9 10

020

4060

80100

120140

QTL distribution heat-map

DO N

OT C

OPY

SM SC BR AB P M L10 8 2 5 7 2 110 8 2 5 6 2 111 8 2 8 7 2 112 8 2 10 7 2 113 7 6 11 6 2 112 7 8 12 6 2 113 9 7 13 7 4 114 10 7 11 5 4 116 10 3 11 6 4 116 10 2 7 7 4 118 9 2 7 10 4 123 9 1 7 10 4 123 10 1 7 9 4 124 10 0 6 8 4 133 10 0 6 10 4 140 10 2 6 10 4 145 10 9 8 16 4 147 10 20 8 18 4 140 11 20 8 18 4 133 12 21 8 18 4 127 12 18 6 12 4 027 11 7 5 10 4 026 11 7 3 10 4 024 10 4 3 10 4 020 10 0 9 10 4 016 8 1 9 9 4 016 8 5 9 10 5 016 10 5 9 11 4 016 10 5 3 11 4 016 9 5 3 12 4 016 8 1 3 9 4 016 9 1 3 10 4 018 11 1 3 10 4 017 11 1 3 9 4 017 14 1 3 8 5 017 14 1 4 7 5 014 17 1 4 6 5 014 21 1 3 7 5 012 21 1 5 8 7 012 23 1 4 7 8 012 23 1 4 7 12 0

Abbreviation Trait category Number of QTL/significancesL Leaf 441M Maturity 401P Panicle 1660AB Resistance abiotic 1753BR Resistance biotic 388SC Stem composition 421SM Stem morphology 750

DO N

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OPY

SM SC BR AB P M L10 8 2 5 7 2 110 8 2 5 6 2 111 8 2 8 7 2 112 8 2 10 7 2 113 7 6 11 6 2 112 7 8 12 6 2 113 9 7 13 7 4 114 10 7 11 5 4 116 10 3 11 6 4 116 10 2 7 7 4 118 9 2 7 10 4 123 9 1 7 10 4 123 10 1 7 9 4 124 10 0 6 8 4 133 10 0 6 10 4 140 10 2 6 10 4 145 10 9 8 16 4 147 10 20 8 18 4 140 11 20 8 18 4 133 12 21 8 18 4 127 12 18 6 12 4 027 11 7 5 10 4 026 11 7 3 10 4 024 10 4 3 10 4 020 10 0 9 10 4 016 8 1 9 9 4 016 8 5 9 10 5 016 10 5 9 11 4 016 10 5 3 11 4 016 9 5 3 12 4 016 8 1 3 9 4 016 9 1 3 10 4 018 11 1 3 10 4 017 11 1 3 9 4 017 14 1 3 8 5 017 14 1 4 7 5 014 17 1 4 6 5 014 21 1 3 7 5 012 21 1 5 8 7 012 23 1 4 7 8 012 23 1 4 7 12 0


1122724392365

DO N

OT C

OPY

SM SC BR AB P M L10 8 2 5 7 2 110 8 2 5 6 2 111 8 2 8 7 2 112 8 2 10 7 2 113 7 6 11 6 2 112 7 8 12 6 2 113 9 7 13 7 4 114 10 7 11 5 4 116 10 3 11 6 4 116 10 2 7 7 4 118 9 2 7 10 4 123 9 1 7 10 4 123 10 1 7 9 4 124 10 0 6 8 4 133 10 0 6 10 4 140 10 2 6 10 4 145 10 9 8 16 4 147 10 20 8 18 4 140 11 20 8 18 4 133 12 21 8 18 4 127 12 18 6 12 4 027 11 7 5 10 4 026 11 7 3 10 4 024 10 4 3 10 4 020 10 0 9 10 4 016 8 1 9 9 4 016 8 5 9 10 5 016 10 5 9 11 4 016 10 5 3 11 4 016 9 5 3 12 4 016 8 1 3 9 4 016 9 1 3 10 4 018 11 1 3 10 4 017 11 1 3 9 4 017 14 1 3 8 5 017 14 1 4 7 5 014 17 1 4 6 5 014 21 1 3 7 5 012 21 1 5 8 7 012 23 1 4 7 8 012 23 1 4 7 12 0


QC

ldEmer9.11

QBrix9.1

QD

BMsA9.1

QPanBrLg9.3

New

13

QC

ldChl9.25

QC

ldChl9.26

New

80

New

679

New

705

New

1690

New

1689

QSTKR

9.1

QSTKR

9.2

QSTKR

9.3

QSTKR

9.4

QH

gt9.9

QH

gt9.10

QSTKR

9.5

QSTKR

9.6

QC

ldEmer9.12

QC

ldEmer9.13

QC

ldDM

GR

9.17

QC

ldChl9.27

New

1556

QSalt_W

gt9.1

QSalt_W

gt9.2

QSD

W9.4

New

495

QH

gt9.13 QSTKR9.7

QG

rnWgt9.5

QH

gt9.14

QPanLgth9.4

QH

gt9.15

QH

gt9.16

QH

gt9.17

QH

gt9.18

QH

gt9.19

QH

gt9.20

New

1645

New

1653 QStJYld9.1

QH

gt9.21

QH

gt9.22

QH

gt9.23

QBrix9.2

New

1596

New

799

QH

gt9.24

QH

gt9.25

QH

gt9.26

QH

gt9.27

QH

gt9.28

QH

gt9.29

QH

gt9.30

QH

gt9.31

QH

gt9.32

QH

gt9.33

QSTKR

9.8

QSTKR

9.9

QH

gt9.70

QH

gt9.34

QH

gt9.35

QH

gt9.36

QH

gt9.37

QH

gt9.38

QH

gt9.39

QH

gt9.40

QH

gt9.41

QG

rnPrA9.5

QG

rnPrA9.6

QPanW

gt9.4

QH

gt9.42

QH

gt9.43

QH

gt9.44

QPanLgth9.5

QSTKR

9.10

QSTKR

9.11

QSTKR

9.12

QSTKR

9.13

New

971

New

1104

QG

rnPrA9.7

QH

gt9.71

QG

rnPrA9.8

QG

rnPrA9.9

QSTKR

9.14

QSTKR

9.15

QSTKR

9.16

QG

rnPrA9.10

QSTKR

9.17

QSTKR

9.18

QSTKR

9.19

QSTKR

9.20

QSTKR

9.21

QSTKR

9.22

QSTKR

9.23

QSTKR

9.24

QSTKR

9.25

QSTKR

9.26

QSTKR

9.27

QG

rnPrA9.11

QG

rnPrA9.12

QH

gt9.45

QPanW

gt9.2

QG

rnWgt9.4

QH

gt9.46

QH

gt9.47

QYld9.3

QYld9.4

QPanW

th9.2

QH

gt9.48

QD

BMsB9.1

QBrix9.3

QH

gt9.49

QSTKR

9.28

QSTKR

9.29

QSTKR

9.30

QSugYld9.3

QStJYld9.2

QH

gt9.64

QH

gt9.65

QH

gt9.66

QH

gt9.67

QG

LA9.3

QSTKR

9.31

QSTKR

9.32

QSTKR

9.33

QSTKR

9.34

QH

gt9.50 QHgt9.51

QG

LA9.4

QH

gt9.52

QSD

W9.6

New

972

New

1105

New

1169

New

973

New

1106

New

1170

QTN

9.7

New

1496

New

1497

New

1498

QTN

9.8

QD

TFl9.34

QD

TFl9.35

QSTKR

9.35

QSTKR

9.36

QSTKR

9.37

QSTKR

9.38

QH

gt9.72

QPanExr9.2

QSD

W9.7

New

1583

QH

gt9.73

QPanExr9.3

QSFW

9.3

QStJYld9.3

QH

gt9.53

QG

rnPrA9.13

QD

TFl9.18

QH

gt9.54

QH

gt9.55

QH

gt9.56

QH

gt9.57

QH

gt9.58 New552

QSFW

9.4

QM

dgAN9.1

QH

rvYld9.1

QH

gt9.59 New

416 QVYld9.1

QVYld9.2

QH

rvYld9.2

QD

BMsA9.2

QD

BMsA9.3

QG

rnPrA9.14

Height (Dw1) Stalk rot resistance Tillering Maturity

23 QTL studies16 GWAS studiesDO

NOT

COP

Y








DO N

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Study Number of QTL Population Analysis Burrell et al 2015 2 BTx623/SC748-5 QTLFelderhoff et al 2016 2 Bk7/Early-Hegari-Sart QTLKlein et al 2001 1 RTx430/Sureno QTLMohan et al 2010 4 296B/IS18551 QTLPerumal et al 2009 1 SC748-5/BTx623 QTLUpadhyaya et al 2013 8 mini-core set GWAS

Anthracnose resistance

DO N

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OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

DO N

OT C

OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

One of oldest and largest gene families known in plants. Involved in detection and response to diverse pathogens (bacteria, viruses, fungi, nematodes,

insects and oomycetes)

DO N

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OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

• Co-locating QTL for anthracnose resistance from same source (SC748-5) across 2 studies

• Co-locating with known NBS-LRR genes• Very near major effect gene for striga

resistance (lgs)• Highly significant (LOD>20 and R2 72%

in Burrell et al 2015)

DO N

OT C

OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

R2=10.3%LOD = 3.8

R2=8.6%LOD = 3.2

R2=6.9%LOD = 3.1

R2=39.5%LOD = 12.5 R2=55.1%

LOD = 20.3

R2=35%-log10P = 20.3

R2=54%-log10P = 9.3

DO N

OT C

OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

Genetic architecture of the trait• Number of QTL/significant SNPs• Distribution• Significance/effect size• Sources of resistance

DO N

OT C

OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10Additional information critical for molecular breeding strategy development• Proximity to known disease resistance genes• Proximity to major effect genes• Proximity to large effect QTL for other traits

DO N

OT C

OPY

Tb1Sh1

Ma3Y

QAnth1.1

QAnth1.2

QAnth1.3

QAnth1.4

SBI-01

Rf2

B2

Z

Ma5

SBI-02

Pla

R

AltSBms3

A

SBI-03

bmr6

QAnth4.1

SBI-04

opr

lgs

QAnth5.2

QAnth5.3

QAnth5.1

SBI-05

Ma6

Ma1

dw2

gc

d

Rs1

Lg

P

QAnth6.1

QAnth6.2

QAnth6.3

QAnth6.4

QAnth6.5

QAnth6.6

SBI-06

bmr12

I

dw3

QAnth7.1

SBI-07

Pu

Rf1

Shs1

QAnth8.1

SBI-08

Dw1

QAnth9.1

SBI-09

bmrlf

wxma4Rs2

Trit

QAnth10.1

SBI-10

lgs

New

796

New

92

New

98 QD

TFl5.14

QD

TFl5.15

QC

ldLAR5.8

QC

ldLAR5.9

QC

ldLAR5.10

QC

ldChl5.31

QC

ldChl5.32

New

885

New

886 QTN5.7

MaturityGrain yieldLeaf appearance rate Chlorophyll contentTranspiration rateTillering

QTL co-locating with the anthracnose QTL on SBI-05

Additional information critical for molecular breeding strategy development• Proximity to known disease resistance genes• Proximity to major effect genes• Proximity to large effect QTL for other traits

DO N

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OPY








DO N

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QTL database resource developed to enable researchers to answer the following sorts of questions:


DO N

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OPY


Target QTL location in sorghum

Syntenic location in maize and rice


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• How many QTL have been identified for my trait(s) of interest in a specific genotype?



• How many highly significant QTL have been identified for my trait(s) of interest?





Syntenic location in maize and rice

Identify all predicted gene models in QTL CI in maize and rice

Linking to whole genome assembly resources for both species

DO N

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OPY










Os03g20020Os03g19990Os03g19970Os03g19940Os03g19920Os03g19900Os03g19890Os03g19820Os03g19780Os03g19760Os03g19720Os03g19700Os03g19690Os03g19670PhyBOs03g19580Os03g19540Os03g19520Os03g19410Os03g19380Os03g19370Os03g19310Os03g19300Os03g19290

Sobic.001G391600Sobic.001G392000Sobic.001G392100Sobic.001G392200Sobic.001G392300Sobic.001G392400Sobic.001G392600Sobic.001G392700Sobic.001G392800Sobic.001G393000Sobic.001G393200Sobic.001G393300Sobic.001G393401Sobic.001G393500Sobic.001G393600Sobic.001G393700Sobic.001G393900Sobic.001G394000PhyB Sobic.001G394600Sobic.001G394800Sobic.001G394900Sobic.001G395000Sobic.001G395100Sobic.001G395200Sobic.001G395500Sobic.001G395600Sobic.001G395700Sobic.001G395900Sobic.001G396000Sobic.001G396100Sobic.001G396300Sobic.001G396400Sobic.001G396500Sobic.001G396600Sobic.001G396700Sobic.001G396800Sobic.001G396900

GRMZM2G084940GRMZM2G385931GRMZM2G030794GRMZM2G317160GRMZM2G018941GRMZM2G550861

GRMZM2G008490

GRMZM2G089720GRMZM2G135968

PhyB

GRMZM2G013639GRMZM2G422295 GRMZM2G422295GRMZM2G011483

GRMZM2G140432GRMZM2G301823GRMZM2G038015

GRMZM2G383790 GRMZM2G383790GRMZM2G084389

48,8

76,6

94 –

51,3

18,9

93

10,8

48,4

74 –

11,2

83,3

40


Maize chromosome 1Rice chromosome 3

Genes within the predicted location of the QTL in riceand maize

DO N

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OPY










Os03g20020Os03g19990Os03g19970Os03g19940Os03g19920Os03g19900Os03g19890Os03g19820Os03g19780Os03g19760Os03g19720Os03g19700Os03g19690Os03g19670PhyBOs03g19580Os03g19540Os03g19520Os03g19410Os03g19380Os03g19370Os03g19310Os03g19300Os03g19290

Sobic.001G391600Sobic.001G392000Sobic.001G392100Sobic.001G392200Sobic.001G392300Sobic.001G392400Sobic.001G392600Sobic.001G392700Sobic.001G392800Sobic.001G393000Sobic.001G393200Sobic.001G393300Sobic.001G393401Sobic.001G393500Sobic.001G393600Sobic.001G393700Sobic.001G393900Sobic.001G394000PhyB Sobic.001G394600Sobic.001G394800Sobic.001G394900Sobic.001G395000Sobic.001G395100Sobic.001G395200Sobic.001G395500Sobic.001G395600Sobic.001G395700Sobic.001G395900Sobic.001G396000Sobic.001G396100Sobic.001G396300Sobic.001G396400Sobic.001G396500Sobic.001G396600Sobic.001G396700Sobic.001G396800Sobic.001G396900

GRMZM2G084940GRMZM2G385931GRMZM2G030794GRMZM2G317160GRMZM2G018941GRMZM2G550861

GRMZM2G008490

GRMZM2G089720GRMZM2G135968

PhyB

GRMZM2G013639GRMZM2G422295 GRMZM2G422295GRMZM2G011483

GRMZM2G140432GRMZM2G301823GRMZM2G038015

GRMZM2G383790 GRMZM2G383790GRMZM2G084389


The atlas provides links to external resources to further interrogate the genes in rice and maize

DO N

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OPY










Identify all predicted gene models in maize and riceIdentify which genes within the QTL CI are under selection in sorghum, maize and rice

Previously published studies identifying genes under selection

SorghumRice Maize

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OPY

The utility of comparative genomics

Take advantage of known gene order conservation (synteny)

QTL

>4x as many QTL and GWAS studies in rice and maize compared to sorghum

• Make use of information gained in other species• Compare locations of QTL for specific traits

across species• Compare genes underlying QTL across species

• Functional characterisation in other species • Selection signals on the same gene in other

species

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OPY








DO N

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OPY

Why have we developed a QTL Atlas?How users can access the Atlas?

https://aussorgm.org.au/sorghum-qtl-atlas/

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OPY

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OPY

223 unique traits have been classified into 7 broad trait categories, modified from Mace and Jordan (2011): • Leaf• Maturity• Panicle• Resistance abiotic• Resistance biotic• Stem composition• Stem morphology DO

NOT

COP

Y

223 unique traits have been classified into 7 broad trait categories, modified from Mace and Jordan (2011): • Leaf• Maturity• Panicle• Resistance abiotic• Resistance biotic• Stem composition• Stem morphology

Leaf Age-related leaf sensecence Leaf composition Leaf morphology Leaf yield Photosynthesis Stomata Sugar-related traits

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OPY


Panicle Germination Glume morphology Grain & Panicle Yield Grain Composition Panicle Architecture Pollen Fertility

DO N

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OPY


Resistance abiotic Cold tolerance Drought tolerance Heat tolerance Phosphorus tolerance Salt tolerance

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Resistance biotic Anthracnose resistance Aphid resistance Bacterial leaf stripe Drechstera leaf blight resistance Ergot resistance Grain mold resistance Green bug resistance Head bug resistance Leaf scorch Midge resistance Milo disease resistance Rice weevil resistance Rust resistance Shoot fly resistance Southern root-knot nematode resistance Stalk rot resistance Striga resistance Target leaf spot resistance Zonate leaf spot resistance

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Stem composition Stem biomass yield Stem composition Sugar-related traits

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Stem morphology Height Lodging tolerance Plant colour Regrowth Rhizomatousness Roots Stem morphology Tillering

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Version 1.4Version 2.0Version 3.0

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cM locations of the sorghum consensus map

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Felderhoff

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e.g. txp302, Dsenhsbm64, S1_10629136DO N

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Users can search for QTL in sorghum based on the syntenic location in either maize or rice

Users can specify the location in:

• the maize genome assembly (B73 RefGen_v1; Schnable et al 2009) or

• the rice genome assembly, O. sativa subsp. japonica (Release 7; Goff et al 2002; Yu et al 2002), or

• provide a candidate gene ID from either species (e.g. GRMZM2G108663; LOC_Os01g01080.1).

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LOC_Os09g26840

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Users can further modify their original search to limit to specific populations, publications, genome locations and export the output in a variety of formats

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In summary:This is the first database resource that has integrated all existing QTL and GWAS studies for sorghum used parameters from the original studies to take into account factors influencing the reliability of the initial

QTL study aligned to all current genome assemblies, predicted the syntenic locations in maize and rice, and provided

links to the underlying genes across species, as well as details of any signatures of selection previously identified.

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In summary:The database provides researchers with a new tool to integrate data across multiple studies and types of studies (QTL, GWAS) and across species to compare positions across studies and to determine allelic relationships among QTL. This will allow for: more comprehensive dissection of the genetic architecture of complex traits, identification of suitable targets for molecular breeding strategies

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AcknowledgementsConcept David JordanProgramming and database development support David Innes Michael Hassall Jared BaxterHelp with QTL projection Xuemin Wang Yongfu TaoStatistics support Colleen Hunt Adrian Hathorn

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@EmmaOmics

@SorgGuy

@AusSORGM

[email protected]

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Sorghum QTL AtlasSlide Number 2Why have we developed a QTL Atlas?Why have we developed a QTL Atlas?Why have we developed a QTL Atlas?Why have we developed a QTL Atlas?Heterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalHeterogeneous nature of QTL studies…not all QTL are equalWhy have we developed a QTL Atlas?Why have we developed a QTL Atlas?Why have we developed a QTL Atlas?Why have we developed a QTL Atlas?Slide Number 19Slide Number 20Slide Number 21Slide Number 22Slide Number 23Slide Number 24Slide Number 25Slide Number 26Slide Number 27Slide Number 28Slide Number 29Slide Number 30Slide Number 31Slide Number 32Slide Number 33Slide Number 34Slide Number 35Slide Number 36Slide Number 37Slide Number 38Slide Number 39Slide Number 40Slide Number 41Slide Number 42Slide Number 43The utility of comparative genomicsSlide Number 45Slide Number 46Slide Number 47Slide Number 48Slide Number 49Slide Number 50Slide Number 51Slide Number 52Slide Number 53Slide Number 54Slide Number 55Slide Number 56Slide Number 57Slide Number 58Slide Number 59Slide Number 60Slide Number 61Slide Number 62Slide Number 63Slide Number 64Slide Number 65Slide Number 66Slide Number 67Slide Number 68Slide Number 69Slide Number 70Slide Number 71Slide Number 72Slide Number 73Slide Number 74Slide Number 75Slide Number 76Slide Number 77Slide Number 78Slide Number 79Slide Number 80Slide Number 81AcknowledgementsSlide Number 83

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COPY DO NOT David Jordan Sorghum QTL Atlas€¦ · 16.06.2018 · sPb-0810 M188404 txp43M343014 txp88 sPb-0232 M343356 sPb-5358 sPb-2602 sPb-6600 sPb-7567 sPb-8492 M188582. M189251