Institute for Ag Professionals

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1 Institute for Ag Professionals Proceedings 2016 Crop Pest Management Short Course & Minnesota Crop Production Retailers Association Trade Show Do not reproduce or redistribute without the written consent of author(s).

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

3 Soybeans in the 21 st Century

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

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

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

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

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

9 Pace of variety development varieties were registered 3 per year varieties were registered 57 per year Specht et al. (2014) Mikel et al. (2010)

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

11 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

12 Genetic gain Rincker et al. 2015

13 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

14 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

15 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,

16 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

17 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

18 Discovery of Phyto resistance gene Rps1a Bernard et al Phyto. stem and root rot first reported in F2 generation Obs Res. Susc. Exp (3:1) Res. Susc. Blackhawk (R) X Lincoln (S) Mukden (R) X Lincoln (S) Illini (R) X Lincoln (S)

19 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

20 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

21 2016 UMN Variety Trials

22 2016 UMN Variety Trials Number of varieties Rps1k Rps1c Rps1a Susc Rps3a Rps1c + 3a Rps3a + 4

23 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

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

25 Concibido et al. (2004) SCN resistance rhg1 120 Normalized female index rhg1 LG G Susc NIL Res NIL Normalized female index Glover et al. (2004)

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

27 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 ancestry

28 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 ancestry

29 SCN Variety Trials

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

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

33 Resistance to Aphis glycines (Rag) genes

34 rag3

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

36 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

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

38 Example of complex trait Seed yield

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

40 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

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

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

43 Success in Holsteins Badger-Bluff Fannie Freddie

44 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 ~ locs, 3 reps

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46 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

47 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

48 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

49 Introgressing a new trait Trait/gene

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

51 Roundup Ready Soybeans

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

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

54 Genome editing

55 Kim and Kim (2014)

56 Kim and Kim (2014)

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

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

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

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

61 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

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

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64 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

65 Thank you 2016 UMN Variety Trials soybeans.umn.edu

66 High Throughput phenotyping of soybean IDC Soil EC

67 Zonal statistics using QGIS Masking plant from soil using unsupervised classification

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

69 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