The Future of Wheat Genomics to Accelerate Wheat

60% Increase in demand for wheat by 2050 - 20% Potential yield decrease from

Trends in Population, Production & Acres 10 900 9 800 8 700 7 600

The Breeding Funnel Elite Un-adapted Exotic Crossing Years Early Generation Testing Prelim Yield testing

Plant Breeding – It’s a numbers game 300, 000 plants Bulk populations 3, 000

The Breeding Cycle Crossing Evaluation Selection

The breeder’s (favorite) equation: selection intensity selection accuracy genetic gain over time genetic variance

more to chose from = increasing selection intensity

Genomic Selection Prediction of total genetic value using dense genome-wide markers üEstimate Kinship (realized

DNA markers… A T G G C T G A A 600, 000 DNA

DNA markers…. A T G G C T G A A Variety A A

Hybridization Events Forming Bread Wheat Triticum urartu Triticum turgidum (2 n=2 x=14, AA) (2

Wheat Genome Arabidopsis Rice Sorghum Soybean Barley Maize 16, 000, 000 base pairs Wheat

Wheat genome sequence nearing completion….

Genomic prediction models…. A T G G C T G A A Line #1

Wheat Quality Phenotypes • Grain • thousand kernel weight • protein content • hardness

CIMMYT Bread Wheat Breeding Year • Preliminary yield trials of CIMMYT bread wheat breeding

GS: Prediction of wheat quality TRAIT Test Weight Grain Hardness Grain Protein Flour SDS

Yield Prediction Models: Central Plains Southern Regional Performance Nursery

Genomic Prediction Models for Yield: genomic prediction accuracy average yield testing accuracy

Accelerating The Breeding Cycle Inbreeding Seed Increase Multi-location Multi-year testing Crossing PREDICTION Selection Evaluation

Shuangye Wu Byron Evers Haley Ahlers Mark Lucas Jared Crain Sandra Dunckel Trevor Rife

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The Future of Wheat: Genomics to Accelerate Wheat Breeding Jesse Poland Wheat Genetics Resource Center Kansas State University

60% Increase in demand for wheat by 2050 - 20% Potential yield decrease from climate change 2% Rate of gain needed to meet projections < 1% Current rate of gain

Trends in Population, Production & Acres 10 900 9 800 8 700 7 600 6 500 5 Acreage Production Demand Population 400 300 200 100 0 4 3 Population (bil) MH, MMT 1, 000 2 1 0 1950 1960 1970 1980 1990 2000 2010 2020 2030 2040 2050 Source – USDA and UN Population Database Slide: Dalton Henry Mark Tester and Peter Langridge (2010) Breeding Technologies to Increase Crop Production in a Changing World, Science 12: 327 pp. 818 -822

The Breeding Funnel Elite Un-adapted Exotic Crossing Years Early Generation Testing Prelim Yield testing (thousands) Replicated Yield testing (hundreds) Advanced Yield testing (tens) Varieties (one)

Plant Breeding – It’s a numbers game 300, 000 plants Bulk populations 3, 000 plots Small plot yield test 300 Prelim yield trial Advanced yield trial Kansas Interstate Nursery New Variety 30 -40 10 -12 1

The Breeding Cycle Crossing Evaluation Selection

The breeder’s (favorite) equation: selection intensity selection accuracy genetic gain over time genetic variance Crossing Evaluation Selection Intensity ü Increase (to a limit) ü Need bigger populations Selection Accuracy ü Increase ü More precise measurements ü Reduce Errors ü Correct for environment years per cycle Genetic Variance (Diversity) ü Increase ü Mixed bag (not all good) ü A must have Years per Cycle ü Decrease! ü Constant ‘rate’ of return

more to chose from = increasing selection intensity

Genomic Selection Prediction of total genetic value using dense genome-wide markers üEstimate Kinship (realized relationship) with markers DNA markers prediction model phenotypic prediction

DNA markers… A T G G C T G A A 600, 000 DNA base pairs Variety A

DNA markers…. A T G G C T G A A Variety A A T A G C T G A A Variety B

The wheat genome….

Hybridization Events Forming Bread Wheat Triticum urartu Triticum turgidum (2 n=2 x=14, AA) (2 n=4 x=28, AABB) ~ Aegilops speltoides Aegilops tauschii (2 n=2 x=14, SS) Triticum aestivum (2 n=6 x=42, AABBDD) (2 n=2 x=14, DD) 13

Genome sequencing and assembly….

Wheat Genome Arabidopsis Rice Sorghum Soybean Barley Maize 16, 000, 000 base pairs Wheat

Wheat genome sequence nearing completion….

DNA markers…. A T G G C T G A A Variety A A T A G C T G A A Variety B

Genomic prediction models…. A T G G C T G A A Line #1 A T A G C T G A A Line #2 A T G G C T G A A Line #3 PREDICTION MODEL A T G G C T G A A New Breeding Line PREDICTION

Genomic Predictions: Wheat Quality

Wheat Quality Phenotypes • Grain • thousand kernel weight • protein content • hardness • Milling • flour protien • flour yield • Mixograph & Alveograph • Loaf volume

CIMMYT Bread Wheat Breeding Year • Preliminary yield trials of CIMMYT bread wheat breeding program 2010 • Ciudad Obregon, MX • 6 years data • 1 Rep/Year Total in Quality Tested & Yield Trial Genotyped 4, 956 250 2011 6, 685 995 2012 10, 196 850 2013 9, 436 886 2014 7, 672 1, 114 2015 8, 872 1, 425 Total 47, 817 5, 520

GS: Prediction of wheat quality TRAIT Test Weight Grain Hardness Grain Protein Flour SDS Mixograph Mix Time Alveograph W Alveograph P/L Loaf Volume Sarah Battenfield, KSU PREDICTION ACCURACY (r) 0. 725*** 0. 513*** 0. 630*** 0. 604*** 0. 666*** 0. 718*** 0. 697*** 0. 476*** 0. 638***

Yield Prediction Models: Central Plains Southern Regional Performance Nursery

Genomic Prediction Models for Yield: genomic prediction accuracy average yield testing accuracy

Accelerating The Breeding Cycle Inbreeding Seed Increase Multi-location Multi-year testing Crossing PREDICTION Selection Evaluation $ genotyping < $ phenotyping

Shuangye Wu Byron Evers Haley Ahlers Mark Lucas Jared Crain Sandra Dunckel Trevor Rife Daljit Singh Narinder Singh Traci Kantarski Xu (Kevin) Wang Atena Haghighattalab Mokhles Rahman Emily Delorean Allan Fritz ★ Andy Auld Shaun Winnie Chris Gaynor Sarah Battenfield ★ Ravi Singh ★ Susanne Dreisigacker Matthew Reynolds Carlos Guzman ★ Roberto J. Peña Suchismita Mondal Ravi Vallaru Uttam Kumar Mark Sorells Jessica Rutkoski ★ Yue Jin www. wheatgenetics. org 27