Wayne Parrott Department of Crop & Soil Sciences

Institute for Plant Breeding, Genetics & Genomics

The science of crop development: conventional & biotechnology methods

P Simon, USDA-ARS

Mary of Guise Scotland, Stirling Castle, 1540

Modern strawberries never existed in nature

Corbis Fragaria ananassa

Europe, 1740's

http://www.ncwildflower.org

Fragaria virginiana Eastern North America

X

Marina Gambardella, Santiago, Chile

Fragaria chiloensis Chile

Some crops never existed in nature

www.mpiz-koeln.mpg.de/pr/garten/schau/Triticumaestivum/wheat.html

Einkorn x spelt = Emmer x goat grass

= Bread wheat

The starting misconception The Myth of Natural Food

Wild tomato

Cultivated (modified) tomato

Photos: USDA & Frary et al., 2002. Science 289: 85-88

Also has genes from wild species

According to Darwin, our current crops and animals are the result of

"... a kind of Selection, .... which results from every one trying to possess and breed from the best individuals…”

• "...in a vast number of cases, we cannot recognize ... the wild parent-stocks of the plants which have been longest cultivated in our flower and kitchen-gardens."

Origin of Species, 1859

Top: Peggy Lem

aux, John Meade, R

aúl Coronado

Bottom

: Corbis

Wild cabbage

Kale, 500 BC

Kohlrabi Germany, 100 AD

Cabbage, 100 AD

Cauliflower 1400's

Broccoli Italy, 1500's

Brussel sprouts Belgium, 1700's

"... breeders could never have expected or even have wished to have produced the result which ensued."

The Natural History Museum, London

Many crop varieties

Varieties differ by Yield Maturity Composition Disease

resistance

10 University of Kentucky wheat variety trials http://www.uky.edu/Ag/GrainCrops/ID125Section3.html

Agricultural pests

Powdery mildew

Aphids Asian rust

Sooty mold

Control with chemicals or with genetic resistance

Photo by Zachary King

Conventional Plant Breeding Stacks genes for desirable traits

SC: Stem canker SCN: Cyst nematdoe RKN: Root-knot nematode MOR: Frogeye leaf spot PHY: Phytophthora races1, 3 and 4

Nidera Seeds

R. Boerma

Resistant

12

Susceptible

Frogeye leafspot

Variety

Gene Donor Very different from cultivated type

Var iety

Disease

E.g., IR64 stacks traits from 20 different rice landraces

PA CHIAMSERAUP

FORTUNA BESAR 15 MARONG UNKNOWNPAROC

BLUE ROSEBPI 76 REXORO SUPREME

KITCHILI SAMBA

SINAWPAGH

UNKNOWNCINA LATISAIL TEXAS RSBR GEB24

PATNA BLUE BONNETPETA

DGWG CP231 SLO 17 BENONG

IR86 CP SLO 17 SIGADIS

IR95IR127

IR8 CHOW SUNG IR262

IR1103 TADUKAN VELLAIKARIR400 TSAI YUAN CHUNG

IR1006 MUDGOTETEP

IR1163 IR238 TN1IR1416 IR1641

IR1402IR22 TKM6 IR746A

IR1704O. nivara

IR1870 IR1614

IR2006 IR579 IR747 IR24/ IR661 IR1721

IR773 A BPI 121 GAM PAI

IR1915 B IR1833 GAM PAI 15 IR1561 IR1737

IR1916 IR833 IR2040

IR2146 IR 2055IR2061

IR5236 IR5338

IR5657

IR18348

IR64

CO 18

NAHNG MON S4

NMS 4

IR 64 13

Conventional breeding

Modified from: http://www.generationcp.org/plantbreeding/index.php?id=052

Soybean variety trial http://www.plantpath.wisc.edu/soyhealth/bsr/bsrvar.htm

2,000,000 F2 - Disease & habit 50,000 F3 4,000 F4 - Quality 1,000 F5 500 F6 - Yield 50 F7 8 F8 – Regional trials

Elimination of • Undesired types • Unintended types

1,000 Make cross, get F1

1 Variety

Other “conventional” approaches

When necessary trait is not available

Popular Mechanics 1961

Mutation breeding

2543 known varieties developed from mutation breeding FAO/IAEA database

(http://www-infocris.iaea.org/MVD/)

DNA changes 4 bp to 8 kb deletions Inversions of up to 1.5 kb Insertions ~200 bp Frame-shift mutations Premature stop codons

Institute of Radiation Breeding Ibaraki-ken, JAPAN www.irb.affrc.go.jp/

Specialtyproduce.com Corbis.com

Gene transfer, 1950’s style Ln-9 gene for leaf rust resistance from Aegilops to wheat

Sears, E.R. 1956. The transfer of leaf-rust resistance form Aegilops umbellulata to wheat. Genetics in Plant Breeding Brookhaven Symposium #9.

Grass with trait

Problem: Grass will not cross with wheat

Wheat

Need to move gene from grass to wheat

x

So cross with wheat relative

x

Cross hybrid repeatedly to wheat

•Break grass chromosome with X-Rays •Let pieces integrate into wheat •Get wanted gene + many unknown }

Wheat chromosomes

Grass chromosome with desired gene

Final product

Things to notice Move many genes No one knows what genes got moved No safety issues; no regulations

But If would move the wanted gene by itself

Have many regulations Many safety studies

$34 million to show safety

Summary of traits transferred from other species

111 genes introduced into 19 crops over 20 years Tomato = 55 Rice & potato = 12 each

Hajjar & Hodkin, 2007

Wheat Dozens of genes from 6

genera Jones et al., 1995

• Hajjar & Hodgkin (2007) The use of wild relatives in crop improvement: A survey of developments over the last 20 years. EUPHYTICA 156: 1-13 • Jones et al. (1995) Use of alien genes for the development of disease resistance in wheat. ANN. REV PHYTOPATHOL 33:429-443.

Corbis

Unintended effects of breeding Of millions of conventional varieties, only 9

have been reported to have unintended effects Dermatitis and stomach aches One of the safest technologies

All involved elevated levels of known toxins When crops have known toxins, testing of

new varieties has become customary

What about unknown toxins? In all the history of breeding

A toxin that did not exist at the genus level has NEVER appeared unintentionally

Previous report that a novel toxin was found in a potato somatic hybrid

Laurila et al., 1996. Plant Sci 118:145-155 Missed the fact that same toxin was previously

described in some genotypes of potato Jadav et al. 1981. CRC Critical Reviews in Toxicology pp

21-104.

19

The result: Improved yield Genetic modification + agronomic practices

Source: June 2006. USDA NASS

0

660

1320

1980

2640

3300

1925 1935 1945 1955 1965 1975 1985 1995 2005

Yiel

d (k

g pe

r ha)

US soybean yields

Agronomy + Genetics = Yield

Troyer AF 2006. Crop Sci. 46:528-543

The Era of Genetic Engineering

When traditional methods fail

Papaya ringspot virus

Veracruz, México

Genetic engineering A crop that needs a new trait

Tissue culture in a laboratory

DNA is added to give it the new trait

The same crop + 1 new trait

Regeneration of plants from cell culture

What is genetic modification?

Genetic Engineering Biotechnology Transgenic GMO Genetically modified

organism

In the modern meaning

Biotechnology & GMOs

Biotechnology

Genetic modification

Transgenics (GMOs)

Making modern GMOs

10,000’s T1 - Gene expression 1000’s T2 - Phenotype 100’s T3 - T4 - Gene Stability 10’s T5 - Potential lead events T6 – Composition & agronomic T8 – Composition & agronomic 1 Lead event for Regulatory Approval ● Used as a parent in traditional crosses

Elimination of • Undesired types • Unintended types

Selection process means that a transgene should be more stable during breeding and not show unintended effects.

1,000’s T0

Foods produced from genetic engineering must be at least as safe as their conventional counterparts

The criterion

Prior to commercialization Must ensure there are no unintended effects

29

International market

Lead Event

China MOA

Use of GM microbes Many common food ingredients are

from GM microorganisms Not controversial or labeled

www.isaaa.org & http://www.organic-world.net

0

20

40

60

80

100

120

140

160

180

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011

Use of GM crops (millions of ha) 16.7 million farmers in 31 countries

GM crop overview Major traits

Virus resistance Herbicide

tolerance Insect resistance Miscellaneous

Remember when they said “Genetically Engineered potatoes, what can possibly go wrong?”

Transgenic crops

Brazilean bean

Photos: Franciso Aragão, EMBRAPA

Herbicide tolerance

Honduras, 2010

Conventional Transgenic

Insect resistance

Photo: Zamorano, Honduras

Corn Earworm

Photos: Zamorano, Honduras by María Mercedes Roca; NPR

Rootworm-resistant corn

Control

Transgenic

With insecticide

Insect resistance Cotton bollworm

0% 50% 100%

Soybean

High Oleic Soy

OliveStearicLinoleicLinolenicOleic

Oil Quality

Drought 2012

http://www.napsnet.com/articles/68490.html

"We have recently advanced our knowledge of genetics to the point where we can manipulate life in a way never intended by nature. We must proceed with utmost caution in the application of this new found knowledge."

Luther Burbank, 1906

http://www.sciencecontrol.com/luther-burbank-biography-1849%E2%80%931926.html

Is engineering safe?

Regulatory concern over DNA insertions

Evaluate by looking at traditional breeding

Corbis

L Li, USDA-ARS

Corbis

The human genome technology Gives insight into new traits

I. Paran, E. van der Knaap, 2007. J. Exp. Bot. 58, 3841

Many traits appeared in recent history

E.g., the elongated tomato Probably Spain

Photo: Corbis

Elongated fruit in tomato It is impossible to change the appearance of a plant without changing its DNA

Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. 2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.

24.7 kb duplication on Chromosome 10

Movement of duplicated segment onto chromosome 7

Insertions & jumping genes

© Eduardo Forno

Pariti island, Lake Titicaca “Jumping genes” DNA sections that

move naturally move around the genome

Jumping genes are common

Dooner & He. 2009. Plant Cell 20:249-258

Unique jumping gene insertions in soybean Compared to master genome

Tian et al. 2012. Nonreference TE insertions identified in the 31 wild and cultivated soybean genomes. Plant Cell 24:4422-4436

N = 25,628 unique insertions

S Wessler, L Lu, S Robb, J Stajich, unpublished

Comparison of Jumping Genes after 20 generations in rice

20 generations

mPing insertions 435 A119

243 A123

23

Summary

Breeding depends on changes at the DNA level

These modifications have been harmless

Changes brought about by transgenics are very similar to natural changes

Corbis

“The risks that hurt people and the risks that upset people are almost completely unconnected” Peter M. Sandman, risk communications consultant, as quoted in the New York Times article by Henry Fountain as quoted in Tomorrow’s Table