Institute for Ag Professionals

Institute for Ag Professionals Proceedings 2016 Crop Pest Management Short Course & Minnesota Crop Production Retailers Association Trade Show http://www.extension.umn.edu/agriculture/ag-professionals/ Do not reproduce or redistribute without the written consent of author(s).

Fundamentals of and Current Trends in Soybean Variety Development Aaron Lorenz CPM Workshop December 12, 2016

Soybeans in the 21 st Century

Soybeans in the 21 st Century 83 million acres in the U.S.!

Soybeans in the 21 st Century 303 million acres across the world.!

Soybeans in the 21 st Century Average U.S. yield of 52 bu/a! 73 bu/a in parts of IL and NE!

Soybeans in the 21 st Century Broad adaptation Herbicide resistance SCN resistance SDA Omega-3 Phytophthora resistance High oleic oil High yield IDC resistance

Glycine soja soybean s wild ancestor Image credit: Dr. Tommy Carter, USDA

Pace of variety development 1942 1972 94 varieties were registered 3 per year 1970 2008 2242 varieties were registered 57 per year Specht et al. (2014) Mikel et al. (2010)

Soybean breeding Plant breeding is the genetic improvement of plants for human benefit. --Rex Bernardo, UMN Parent 1 x Parent 2

Recycling germplasm Parent 1 x Parent 2 Inbreeding Singlerow eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Parent selection High yield, maturity, pest resistance, quality

Genetic gain Rincker et al. 2015

Maximizing genetic gain via breeding Useful and adequate genetic variation Precise evaluations to allow accurate selections Efficient evaluations and breeding program design to allow testing of large numbers of candidates Reducing time to choosing and recycling parents

Introducing a new trait Parent 1 x Parent 2 Inbreeding Single-row eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Parent selection High yield, maturity, pest resistance, quality Search/access germplasm for novel trait

USDA Soybean Germplasm Collection Urbana, IL Dates back to 1895 ~22,000 accessions Randall Nelson W.J. Morse Large part of collection dates back to P.H. Dorsett and W.J. Morse expeditions, 1924-1932.

Trait genetic architecture Complex/polygenic (many genes, interactions) Oligogenic (few genes) Simple (single gene) Native traits Transgenic Yield Protein SCN res. Maturity Fatty acid comp. Race-specific Phyto res. Herbicide resistance Fatty acid comp. Aphid resistance Worm resistance

Example of a simple trait Race-specific Phytophthora resistance Gene Races Rps1-a 1, 2, 10, 11, 13, 15-18, 24, 26, 27 Rps1-b 1, 3-9, 13-15, 17, 18, 21, 22 Rps1-c 1-3, 6-11, 13, 15, 17, 21, 23, 24, 26 Rps1-k 1-11, 13-15, 17, 18, 21, 22, 24, 26 Rps3-a 1-5, 8, 9, 11, 13, 14, 16, 18, 23, 25 Rps4 1-4, 10, 12-16, 18-21, 25 Rps6 1-4, 10, 12, 14-16, 18-21, 25 Image credit: Berlin Nelson, NDSU

Discovery of Phyto resistance gene Rps1a Bernard et al. 1957 Phyto. stem and root rot first reported in 1948. F2 generation Obs Res. Susc. Exp (3:1) Res. Susc. Blackhawk (R) X Lincoln (S) 13 7 15 5 Mukden (R) X Lincoln (S) 39 8 35.2 11.8 Illini (R) X Lincoln (S) 50 17 50.2 16.8

Introducing Phyto resistance Backcrossing procedure Harosoy (S) x Mukden (R) F1 x Harosoy (S) Select for res BC1 plants Select for res BC2 plants BC1 x Harosoy (S) BC2 x Harosoy (S) Harosoy 63 Converted varieties Clark 63 Hawkeye 63 Chippewa 64 Lindarin 63 Lee 68 Amsoy 71 Pickett 71

Introgressing Phyto resistance Forward breeding R Parent x S Parent Inbreeding Single-row eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Select for Phyto resistance New resistant candidate varieties carrying Rps1a

2016 UMN Variety Trials

2016 UMN Variety Trials 90 80 70 60 50 40 30 20 10 0 Number of varieties 82 36 18 7 7 4 3 Rps1k Rps1c Rps1a Susc Rps3a Rps1c + 3a Rps3a + 4

Example of oligogenic trait Soybean cyst nematode resistance extension.umn.edu extension.entm.purdue.edu

Concibido et al. (2004) SCN resistance rhg1 120 Normalized female index rhg1 LG G 100 80 60 40 20 0 Susc NIL Res NIL Normalized female index Glover et al. (2004)

Example of oligogenic trait Soybean cyst nematode resistance Major QTL: Genomic region or locus that has large effect on phenotype

Introducing SCN resistance R Parent x S Parent Inbreeding Single-row eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Select for SCN resistance New resistant candidate varieties with PI 88788 ancestry

Introgressing SCN resistance R Parent x S Parent Inbreeding Single-row eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Select for SCN resistance New resistant candidate varieties with PI 88788 ancestry

SCN Variety Trials

Private sector SCN resistance breeding MN Statewide Public and Private Variety Trial 2015 Southern region 3 Central region 3 Northern region 20 28 22 Peking 88788 Peking 88788 Peking 88788

Durable resistance to the soybean aphid Can reduce yield by 50%!

Resistance to Aphis glycines (Rag) genes

Concibido et al. (2004) Breeding more efficiently Using markers for simple and oligogenic traits

Phenotype for genetic value SNP Line 1 Line 2 Goals 1) Perform selection during off G C G C G C G C T season A G C G C G C G C G C T A T A T A G C G C G C 2) Increase selection accuracy 3) Increase selection intensity Causal polymorphism (not observed) Trait value

Breeding more efficiently Using markers for simple and oligogenic traits Genotyping for SCN resistance fatty acid composition aphid resistance

Example of complex trait Seed yield

Plant breeding in the 21 st century Two important trends Genotypic data $ Phenotypic data $

Genomic prediction DNA marker data Model training y = Xb+Zu+e Training Population Calibration Set Phenotypic data No QTL mapping No testing for significant markers Predict and select Selection candidates

Genomic prediction for soybean at UNL Grain yield 2 h ppppppppp =0.69 Observed Predicted

A genome-wide approach typically provides better predictions Genomic r A Lorenzana and Bernardo (2009) Lorenz (2013) MAS r A MAS GS MAS GS

Success in Holsteins Badger-Bluff Fannie Freddie

Genomic prediction for cross performance Parent selection Generation N Season Nursery Cross ~160 0, SN F1 ~160 1, WN Inbreeding generations (F2-F4) 2-4, SN- WN Activity Inbreeding generations, modified SSD F4:5 Plant Rows 12K 17K 5, SN Visual obs, NIR, SCN genotyping GENOMIC SELECTION Locations 1-2 locations F4:6 PYTs ~2100 6, SN Prelim yield trials, GEBVs 2 locs, 2 reps F4:7 NELs ~100 7, SN MN adv yield trials, GEBVs 3 locs, 2 reps F4:8 Prelim Regionals ~45 8, SN Regional trials 5 11 locs, 3 reps F4:9 Uniform Regionals ~10 9, SN Regional trials and seed purification F9 Candidates for release ~1-4 10 5 11 locs, 3 reps

Introgressing a new trait Parent 1 x Parent 2 Inbreeding Single-row eval. Preliminary yield trials Advanced yield trials Regional yield trials (2-3 yrs) Search/access germplasm collection for novel trait

Introgressing a new trait Trait/gene

Roundup Ready Soybeans Agrobacterium tumefaciens CP4 aroa Glyphosate-tolerant EPSP enzyme Construct containing foreign gene plus promoters, etc. Gene gun delivery

Roundup Ready Soybeans

Genome editing Native traits Genome editing Transgenic Dr. Bob Stupar UMN Dept. of Agronomy and Plant Genetics

Genome editing Field of research dedicated to developing site-directed DNA sequence modification methodologies and applications. Curtain et al. (2012)

Genome editing

Kim and Kim (2014)

Targeted gene editing Normal soybean Gene of interest Transgenic transformation CRISPR, TALEN, or ZFN transformed; Gene of interest

Targeted mutagenesis Normal soybean Gene of interest CRISPR, TALEN, or ZFN transformed; Mutates Gene of interest Gene of interest

Targeted mutagenesis Normal soybean Gene of interest CRISPR, TALEN, or ZFN transformed; Mutates Gene of interest Gene of interest Non-transgenic soybean with altered trait

Deletions in polyphenol oxidase gene (1 of 6) Knock out Reduces enzyme activity by 30%

Take home messages Seed technologies have revolutionized farming and will continue to do so. Breeding/genetic engineering/genome editing are crucial to protecting crops. Be assured the seeds you are purchasing carry the traits you need. New, better seeds are coming. Specialty soybeans for new markets

Thank you soybeanbreeding.cfans.umn.edu @UmnSoyBreeding 2016 UMN Variety Trials soybeans.umn.edu

High Throughput phenotyping of soybean IDC Soil EC

Zonal statistics using QGIS Masking plant from soil using unsupervised classification

Supplementing aerial data with ground based data Ground based pictures Crop Circle - NDVI Aerial data Visual Scores

Preliminary results: R^2 = 0.85 R^2 = 0.80 *Preliminary results indicate that we can achieve as good, if not better accuracy from aerial imagery