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The value of early-stage phenotyping for wheat breeding in the age of genomic selection

  • Original Article
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Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

Genomic selection using data from an on-going breeding program can improve gain from selection, relative to phenotypic selection, by significantly increasing the number of lines that can be evaluated.

Abstract

The early stages of phenotyping involve few observations and can be quite inaccurate. Genomic selection (GS) could improve selection accuracy and alter resource allocation. Our objectives were (1) to compare the prediction accuracy of GS and phenotyping in stage-1 and stage-2 field evaluations and (2) to assess the value of stage-1 phenotyping for advancing lines to stage-2 testing. We built training populations from 1769 wheat breeding lines that were genotyped and phenotyped for yield, test weight, Fusarium head blight resistance, heading date, and height. The lines were in cohorts, and analyses were done by cohort. Phenotypes or GS estimated breeding values were used to determine the trait value of stage-1 lines, and these values were correlated with their phenotypes from stage-2 trials. This was repeated for stage-2 to stage-3 trials. The prediction accuracy of GS and phenotypes was similar to each other regardless of the amount (0, 50, 100%) of stage-1 data incorporated in the GS model. Ranking of stage-1 lines by GS predictions that used no stage-1 phenotypic data had marginally lower correspondence to stage-2 phenotypic rankings than rankings of stage-1 lines based on phenotypes. Stage-1 lines ranked high by GS had slightly inferior phenotypes in stage-2 trials than lines ranked high by phenotypes. Cost analysis indicated that replacing stage-1 phenotyping with GS would allow nearly three times more stage-1 candidates to be assessed and provide 0.84–2.23 times greater gain from selection. We conclude that GS can complement or replace phenotyping in early stages of phenotyping.

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Abbreviations

AST1:

Predictions and selections based on GEBVs using all stage-1 phenotypic data

FHB:

Fusarium head blight

FST1:

Predictions and selections based on GEBVs using ½ stage-1 phenotypic data-based selecting lines based on family relations

GEBV:

Genomic estimated breeding values

GS:

Genomic selection

NST1:

Predictions and selections based on GEBVs using no stage-1 phenotypic data

NST1-1K:

Same as NST1 except predictions made with a just 10% of the markers

PHEN:

Predictions and selections based on phenotypes

PS:

Phenotypic selection

RST1:

Predictions and selections based on GEBVs using ½ stage-1 phenotypic data based on random selection of lines

TP:

Training population

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Acknowledgements

We would like to thank Cassi Sewell, Duc Hua, Brian Sugerman, and all the employees of the OSU winter wheat breeding program that assisted in collecting the data used in this analysis. Without them this work would not have been possible, and for this, we are truly grateful. We acknowledge funding from Ohio Agricultural Research and Development Center, National Institute for Food and Agriculture, and the US Wheat and Barley Scab Initiative.

Funding

The funding was provided by Ohio Small Grains Marketing Program, Agricultural Research Service (Grant No. 1234567).

Author information

Authors and Affiliations

Authors

Contributions

DB executed the analyses and wrote the manuscript, MH assisted in the data analyses and editing the manuscript, EO executed the genotyping-by-sequencing, CS initiated the study, directed the project, performed some data analyses, and edited the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Clay Sneller.

Ethics declarations

Conflict of interest

The authors declare no conflicts of interest.

Additional information

Communicated by Jose Crossa.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Appendix: Prediction accuracy by trait, stage, prediction method, and cohort

Appendix: Prediction accuracy by trait, stage, prediction method, and cohort

Trait

Cohort

Stages

Model

Prediction accuracy

Yield

OH12

2013 Stage-1 to 2014 Stage-2

PHEN

− 0.060

Yield

OH13

2014 Stage-1 to 2015 Stage-2

PHEN

0.098

Yield

OH12

2014 Stage-2 to 2015 Stage-3

PHEN

0.383

Yield

OH14

2015 Stage-1 to 2016 Stage-2

PHEN

0.027

Yield

OH13

2015 Stage-2 to 2016 Stage-3

PHEN

− 0.015

Yield

OH15

2016 Stage-1 to 2017 Stage-2

PHEN

0.413

Yield

OH14

2016 Stage-2 to 2017 Stage-3

PHEN

0.302

Yield

OH16

2017 Stage-1 to 2018 Stage-2

PHEN

0.210

Yield

OH15

2017 Stage-2 to 2018 Stage-3

PHEN

0.517

Yield

OH12

2013 Stage-1 to 2014 Stage-2

AST1

0.022

Yield

OH13

2014 Stage-1 to 2015 Stage-2

AST1

0.130

Yield

OH12

2014 Stage-2 to 2015 Stage-3

AST1

0.309

Yield

OH14

2015 Stage-1 to 2016 Stage-2

AST1

0.008

Yield

OH13

2015 Stage-2 to 2016 Stage-3

AST1

0.009

Yield

OH15

2016 Stage-1 to 2017 Stage-2

AST1

0.450

Yield

OH14

2016 Stage-2 to 2017 Stage-3

AST1

0.416

Yield

OH16

2017 Stage-1 to 2018 Stage-2

AST1

0.246

Yield

OH15

2017 Stage-2 to 2018 Stage-3

AST1

0.528

Yield

OH12

2013 Stage-1 to 2014 Stage-2

NST1

0.171

Yield

OH13

2014 Stage-1 to 2015 Stage-2

NST1

0.181

Yield

OH12

2014 Stage-2 to 2015 Stage-3

NST1

0.456

Yield

OH14

2015 Stage-1 to 2016 Stage-2

NST1

0.127

Yield

OH13

2015 Stage-2 to 2016 Stage-3

NST1

− 0.039

Yield

OH15

2016 Stage-1 to 2017 Stage-2

NST1

0.219

Yield

OH14

2016 Stage-2 to 2017 Stage-3

NST1

0.444

Yield

OH16

2017 Stage-1 to 2018 Stage-2

NST1

0.127

Yield

OH15

2017 Stage-2 to 2018 Stage-3

NST1

0.536

Yield

OH12

2013 Stage-1 to 2014 Stage-2

RST1

0.053

Yield

OH13

2014 Stage-1 to 2015 Stage-2

RST1

0.108

Yield

OH14

2015 Stage-1 to 2016 Stage-2

RST1

0.010

Yield

OH15

2016 Stage-1 to 2017 Stage-2

RST1

0.360

Yield

OH16

2017 Stage-1 to 2018 Stage-2

RST1

0.272

Yield

OH12

2013 Stage-1 to 2014 Stage-2

FST1

0.053

Yield

OH13

2014 Stage-1 to 2015 Stage-2

FST1

0.108

Yield

OH14

2015 Stage-1 to 2016 Stage-2

FST1

0.015

Yield

OH15

2016 Stage-1 to 2017 Stage-2

FST1

0.356

Yield

OH16

2017 Stage-1 to 2018 Stage-2

FST1

0.266

Yield

OH12

2013 Stage-1 to 2014 Stage-2

NST1-1K

0.267

Yield

OH13

2014 Stage-1 to 2015 Stage-2

NST1-1K

0.163

Yield

OH12

2014 Stage-2 to 2015 Stage-3

NST1-1K

0.429

Yield

OH14

2015 Stage-1 to 2016 Stage-2

NST1-1K

0.141

Yield

OH13

2015 Stage-2 to 2016 Stage-3

NST1-1K

0.026

Yield

OH15

2016 Stage-1 to 2017 Stage-2

NST1-1K

0.071

Yield

OH14

2016 Stage-2 to 2017 Stage-3

NST1-1K

0.296

Yield

OH16

2017 Stage-1 to 2018 Stage-2

NST1-1K

0.074

Yield

OH15

2017 Stage-2 to 2018 Stage-3

NST1-1K

0.490

Yield

OH12

2013 Stage-1 to 2014 Stage-2

NST1-0.5

0.147

Yield

OH13

2014 Stage-1 to 2015 Stage-2

NST1-0.5

0.039

Yield

OH12

2014 Stage-2 to 2015 Stage-3

NST1-0.5

0.418

Yield

OH14

2015 Stage-1 to 2016 Stage-2

NST1-0.5

0.104

Yield

OH13

2015 Stage-2 to 2016 Stage-3

NST1-0.5

− 0.077

Yield

OH15

2016 Stage-1 to 2017 Stage-2

NST1-0.5

0.190

Yield

OH14

2016 Stage-2 to 2017 Stage-3

NST1-0.5

0.339

Yield

OH16

2017 Stage-1 to 2018 Stage-2

NST1-0.5

0.088

Yield

OH15

2017 Stage-2 to 2018 Stage-3

NST1-0.5

0.542

Yield

OH12

2013 Stage-1 to 2014 Stage-2

NST1-1.5

0.126

Yield

OH13

2014 Stage-1 to 2015 Stage-2

NST1-1.5

0.112

Yield

OH12

2014 Stage-2 to 2015 Stage-3

NST1-1.5

0.416

Yield

OH14

2015 Stage-1 to 2016 Stage-2

NST1-1.5

0.126

Yield

OH13

2015 Stage-2 to 2016 Stage-3

NST1-1.5

− 0.058

Yield

OH15

2016 Stage-1 to 2017 Stage-2

NST1-1.5

0.225

Yield

OH14

2016 Stage-2 to 2017 Stage-3

NST1-1.5

0.419

Yield

OH16

2017 Stage-1 to 2018 Stage-2

NST1-1.5

0.088

Yield

OH15

2017 Stage-2 to 2018 Stage-3

NST1-1.5

0.529

Test Weight

OH12

2014 Stage-2 to 2015 Stage-3

PHEN

0.352

Test Weight

OH13

2015 Stage-2 to 2016 Stage-3

PHEN

0.477

Test Weight

OH14

2016 Stage-2 to 2017 Stage-3

PHEN

0.558

Test Weight

OH15

2017 Stage-2 to 2018 Stage-3

PHEN

− 0.170

Test Weight

OH12

2014 Stage-2 to 2015 Stage-3

AST1

0.141

Test Weight

OH13

2015 Stage-2 to 2016 Stage-3

AST1

0.316

Test Weight

OH14

2016 Stage-2 to 2017 Stage-3

AST1

0.583

Test Weight

OH15

2017 Stage-2 to 2018 Stage-3

AST1

− 0.178

Test Weight

OH12

2014 Stage-2 to 2015 Stage-3

NST1

0.157

Test Weight

OH13

2015 Stage-2 to 2016 Stage-3

NST1

0.338

Test Weight

OH14

2016 Stage-2 to 2017 Stage-3

NST1

0.469

Test Weight

OH15

2017 Stage-2 to 2018 Stage-3

NST1

− 0.145

Height

OH12

2013 Stage-1 to 2014 Stage-2

PHEN

0.572

Height

OH13

2014 Stage-1 to 2015 Stage-2

PHEN

0.285

Height

OH12

2014 Stage-2 to 2015 Stage-3

PHEN

0.395

Height

OH14

2015 Stage-1 to 2016 Stage-2

PHEN

 

Height

OH13

2015 Stage-2 to 2016 Stage-3

PHEN

0.472

Height

OH15

2016 Stage-1 to 2017 Stage-2

PHEN

0.520

Height

OH14

2016 Stage-2 to 2017 Stage-3

PHEN

0.488

Height

OH16

2017 Stage-1 to 2018 Stage-2

PHEN

0.376

Height

OH15

2017 Stage-2 to 2018 Stage-3

PHEN

0.646

Height

OH12

2013 Stage-1 to 2014 Stage-2

AST1

0.281

Height

OH13

2014 Stage-1 to 2015 Stage-2

AST1

0.312

Height

OH12

2014 Stage-2 to 2015 Stage-3

AST1

0.321

Height

OH14

2015 Stage-1 to 2016 Stage-2

AST1

 

Height

OH13

2015 Stage-2 to 2016 Stage-3

AST1

0.436

Height

OH15

2016 Stage-1 to 2017 Stage-2

AST1

0.494

Height

OH14

2016 Stage-2 to 2017 Stage-3

AST1

0.409

Height

OH16

2017 Stage-1 to 2018 Stage-2

AST1

0.283

Height

OH15

2017 Stage-2 to 2018 Stage-3

AST1

0.499

Height

OH12

2013 Stage-1 to 2014 Stage-2

NST1

0.057

Height

OH13

2014 Stage-1 to 2015 Stage-2

NST1

0.281

Height

OH12

2014 Stage-2 to 2015 Stage-3

NST1

0.353

Height

OH14

2015 Stage-1 to 2016 Stage-2

NST1

 

Height

OH13

2015 Stage-2 to 2016 Stage-3

NST1

0.288

Height

OH15

2016 Stage-1 to 2017 Stage-2

NST1

0.042

Height

OH14

2016 Stage-2 to 2017 Stage-3

NST1

0.492

Height

OH16

2017 Stage-1 to 2018 Stage-2

NST1

0.209

Height

OH15

2017 Stage-2 to 2018 Stage-3

NST1

0.439

Height

OH12

2013 Stage-1 to 2014 Stage-2

RST1

0.433

Height

OH13

2014 Stage-1 to 2015 Stage-2

RST1

0.350

Height

OH14

2015 Stage-1 to 2016 Stage-2

RST1

− 0.015

Height

OH15

2016 Stage-1 to 2017 Stage-2

RST1

0.353

Height

OH16

2017 Stage-1 to 2018 Stage-2

RST1

0.228

Height

OH12

2013 Stage-1 to 2014 Stage-2

FST1

0.433

Height

OH13

2014 Stage-1 to 2015 Stage-2

FST1

0.350

Height

OH14

2015 Stage-1 to 2016 Stage-2

FST1

− 0.015

Height

OH15

2016 Stage-1 to 2017 Stage-2

FST1

0.356

Height

OH16

2017 Stage-1 to 2018 Stage-2

FST1

0.225

Heading Date

OH12

2013 Stage-1 to 2014 Stage-2

PHEN

0.434

Heading Date

OH13

2014 Stage-1 to 2015 Stage-2

PHEN

0.686

Heading Date

OH12

2014 Stage-2 to 2015 Stage-3

PHEN

0.664

Heading Date

OH14

2015 Stage-1 to 2016 Stage-2

PHEN

0.588

Heading Date

OH13

2015 Stage-2 to 2016 Stage-3

PHEN

0.726

Heading Date

OH15

2016 Stage-1 to 2017 Stage-2

PHEN

0.607

Heading Date

OH14

2016 Stage-2 to 2017 Stage-3

PHEN

0.752

Heading Date

OH16

2017 Stage-1 to 2018 Stage-2

PHEN

0.619

Heading Date

OH15

2017 Stage-2 to 2018 Stage-3

PHEN

0.744

Heading Date

OH12

2013 Stage-1 to 2014 Stage-2

AST1

0.471

Heading Date

OH13

2014 Stage-1 to 2015 Stage-2

AST1

0.660

Heading Date

OH12

2014 Stage-2 to 2015 Stage-3

AST1

0.614

Heading Date

OH14

2015 Stage-1 to 2016 Stage-2

AST1

0.564

Heading Date

OH13

2015 Stage-2 to 2016 Stage-3

AST1

0.681

Heading Date

OH15

2016 Stage-1 to 2017 Stage-2

AST1

0.621

Heading Date

OH14

2016 Stage-2 to 2017 Stage-3

AST1

0.720

Heading Date

OH16

2017 Stage-1 to 2018 Stage-2

AST1

0.645

Heading Date

OH15

2017 Stage-2 to 2018 Stage-3

AST1

0.734

Heading Date

OH12

2013 Stage-1 to 2014 Stage-2

NST1

0.282

Heading Date

OH13

2014 Stage-1 to 2015 Stage-2

NST1

0.576

Heading Date

OH12

2014 Stage-2 to 2015 Stage-3

NST1

0.670

Heading Date

OH14

2015 Stage-1 to 2016 Stage-2

NST1

0.191

Heading Date

OH13

2015 Stage-2 to 2016 Stage-3

NST1

0.643

Heading Date

OH15

2016 Stage-1 to 2017 Stage-2

NST1

0.284

Heading Date

OH14

2016 Stage-2 to 2017 Stage-3

NST1

0.707

Heading Date

OH16

2017 Stage-1 to 2018 Stage-2

NST1

0.502

Heading Date

OH15

2017 Stage-2 to 2018 Stage-3

NST1

0.774

Heading Date

OH12

2013 Stage-1 to 2014 Stage-2

RST1

0.496

Heading Date

OH13

2014 Stage-1 to 2015 Stage-2

RST1

0.698

Heading Date

OH14

2015 Stage-1 to 2016 Stage-2

RST1

0.418

Heading Date

OH15

2016 Stage-1 to 2017 Stage-2

RST1

0.519

Heading Date

OH16

2017 Stage-1 to 2018 Stage-2

RST1

0.559

Heading Date

OH12

2013 Stage-1 to 2014 Stage-2

FST1

0.496

Heading Date

OH13

2014 Stage-1 to 2015 Stage-2

FST1

0.698

Heading Date

OH14

2015 Stage-1 to 2016 Stage-2

FST1

0.435

Heading Date

OH15

2016 Stage-1 to 2017 Stage-2

FST1

0.516

Heading Date

OH16

2017 Stage-1 to 2018 Stage-2

FST1

0.573

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

PHEN

0.155

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

PHEN

 

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

PHEN

0.402

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

PHEN

0.027

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

PHEN

0.543

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

PHEN

0.494

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

PHEN

0.454

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

PHEN

0.566

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

PHEN

0.556

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

AST1

0.280

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

AST1

 

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

AST1

0.343

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

AST1

0.066

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

AST1

0.408

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

AST1

0.536

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

AST1

0.448

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

AST1

0.588

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

AST1

0.604

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

NST1

0.271

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

NST1

 

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

NST1

0.197

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

NST1

0.280

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

NST1

0.444

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

NST1

0.282

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

NST1

0.512

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

NST1

0.356

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

NST1

0.530

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

RST1

0.230

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

RST1

0.382

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

RST1

0.065

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

RST1

0.463

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

RST1

0.525

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

FST1

0.230

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

FST1

0.382

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

FST1

0.065

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

FST1

0.444

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

FST1

0.534

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

1RPHEN

0.169

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

1RPHEN

0.473

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

1RPHEN

0.030

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

1RPHEN

0.401

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

1RPHEN

0.497

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

1RST1

0.276

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

1RST1

0.407

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

1RST1

0.052

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

1RST1

0.442

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

1RST1

0.555

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

NST1-1K

0.234

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

NST1-1K

0.237

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

NST1-1K

0.166

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

NST1-1K

0.232

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

NST1-1K

0.491

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

NST1-1K

0.285

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

NST1-1K

0.488

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

NST1-1K

0.262

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

NST1-1K

0.480

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

NST1-0.5

0.237

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

NST1-0.5

− 0.058

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

NST1-0.5

0.184

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

NST1-0.5

0.317

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

NST1-0.5

0.299

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

NST1-0.5

0.249

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

NST1-0.5

0.457

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

NST1-0.5

0.264

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

NST1-0.5

0.512

FHB Index

OH12

2013 Stage-1 to 2014 Stage-2

NST1-1.5

0.281

FHB Index

OH13

2014 Stage-1 to 2015 Stage-2

NST1-1.5

0.063

FHB Index

OH12

2014 Stage-2 to 2015 Stage-3

NST1-1.5

0.189

FHB Index

OH14

2015 Stage-1 to 2016 Stage-2

NST1-1.5

0.278

FHB Index

OH13

2015 Stage-2 to 2016 Stage-3

NST1-1.5

0.299

FHB Index

OH15

2016 Stage-1 to 2017 Stage-2

NST1-1.5

0.282

FHB Index

OH14

2016 Stage-2 to 2017 Stage-3

NST1-1.5

0.501

FHB Index

OH16

2017 Stage-1 to 2018 Stage-2

NST1-1.5

0.326

FHB Index

OH15

2017 Stage-2 to 2018 Stage-3

NST1-1.5

0.520

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Borrenpohl, D., Huang, M., Olson, E. et al. The value of early-stage phenotyping for wheat breeding in the age of genomic selection. Theor Appl Genet 133, 2499–2520 (2020). https://doi.org/10.1007/s00122-020-03613-0

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  • DOI: https://doi.org/10.1007/s00122-020-03613-0

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