Crop domestication, green revolution, and...
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Transcript of Crop domestication, green revolution, and...
Crop domestication, green revolution, and breeding
Steve Strauss
Source for many slides: www.plantcell.org/cgi/doi/10.1105/tpc.111.tt0511
Strauss the ~human
• Father of two (31, 34) that are grown and gone• Sporty for old fart
– Varsity and club soccer referee (>20 years)– Regular runner and occasionally mtn biker
• Avid hiker, non-technical mtn climber• Craft beer snob
Strauss research
• Web site: http://people.forestry.oregonstate.edu/steve-strauss/
• Current research– Genetic engineering (GE) – poplars and eucalyptus
• Engineer sterile trees to minimize or avoid gene flow• Industrial consortium (22 years)
– Genomic basis of hybrid vigor in trees• Focus on poplar interspecies hybrids• Non-GMO genetics and breeding
The Distant PastCrop plant domestication
The Recent PastHybrid seedThe (First) Green Revolution
Now and Into The FutureBreeding, recent advances in breeding technologies Genetic engineering (next lecture)
Lecture overview
The Distant Past (>10,000 years ago to 1900)
• Homo sapiens originated 250,000 - ~1 million years ago
• Major crops were domesticated ~ ~ 5,000- 15,000 years ago
• The development of human civilizations is correlated with the development of agriculture
Karol Schauer
Pulitzer Prize winner
Agriculture enabled cities, culture, and thus advanced technologies
And then the spread of humans with their ag- and urban animal-associated diseases (to aid in conquest) moved around the globe
X
X
How did people begin to cultivate plants?
It is thought to have been a gradual change from seeking and following food sources to semi-settled migration and finally permanent settlements X
What is domestication?
• Wikipedia
• Domestication (from the Latin domesticus: "of the home") is the cultivating or taming[1] of a population of organisms in order to accentuate traits that are desirable to the cultivator or tamer.
• The desired traits may include a particular physical appearance, behavioral characteristic, individual size, litter size, hair/fur quality or color, growth rate, fecundity, lifespan, ability to use marginal grazing resources, production of certain by-products, and many others.[2]
• Domesticated organisms may become dependent on humans or human activities, since they sometimes lose their ability to survive in the wild.[3]
Plants were domesticated in parallel in several regions of the globe – “centers of origin”
Reprinted by permission from Macmillan Publishers Ltd.: [Nature] Diamond, J. (2002). Evolution, consequences and future of plant and animal domestication. Nature 418: 700-707, copyright 2002.
Wheat, barley, pea, lentil~ 13,000 years ago
Rice, soybean ~ 9000 years ago
Rice, bean ~ 8500 years ago
Corn, squash, bean, potato ~ 10,000 years ago
Genetic modification, in traditional sense, arose as a consequence of cultivation
Natural variation within population
Image courtesy of University of California Museum of Paleontology, Understanding Evolution - www.evolution.berkeley.edu
Planting seeds from “good” plants increased their representation in subsequent generations
The hard casings around many grains were eliminated
Photo by Hugh Iltis; Reprinted from Doebley, J.F., Gaut, B.S., and Smith, B.D. (2006). The Molecular Genetics of Crop Domestication. Cell 127: 1309-1321, with permission from Elsevier.
Teosinte, the wild relative of maize, has hard coverings over each grain. Humans selected against these during maize domestication.
During maize domestication cob size increased
Photo © Robert S. Peabody Museum of Archaeology, Phillips Academy, Andover, Massachusetts. All Rights Reserved.
Cobs from archeological
sites in the Valley of Tehuacan,
Mexico
7000 years ago
500 years ago
Decrease in branching and increase in seed size were also selected for
Image credit Nicolle Rager Fuller, National Science Foundation
Why single-stem vs. bushy maize plants during early domestication?
A. A rare mutation was fixed at the same time a, by chance, when kernel casings were selected against
B. They could better support increasingly large and more numerous cobs
C. They could be packed more tightly into a small area to increase yield
D. Farmers could more easily cultivate (remove weeds) between the rows
E. All of the above
Seeds that don’t break off were selected
WildShattering grain“Brittle rachis”Advantage –maximizes seed dispersal
DomesticatedNon-shattering grain
“Tough rachis”Advantage –
facilitates harvesting
From Konishi, S., Izawa, T., Lin, S.Y., Ebana, K., Fukuta, Y., Sasaki, T., and Yano, M. (2006). An SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396. Reprinted with permission from AAAS.
Wheat & barley show three key traits….
• Shattering resistance• Loss of dormancy• Synchronous flowering/maturity
Over time, domestication customized crops for specific uses
Food wheat and barley vs. barley for beer
• Non-adhering hull (naked): wheat/barley for food • Adhering hull: barley for beer
Domestication
Radical changes in form: Diversity of crucifer crops derived from wild cabbage
Wildcabbage
Kale, 500 BC
Ornamental kaleLate 1900's
Cauliflower1400's
BroccoliItaly, 1500's
Cabbage, 100 AD
KohlrabiGermany, 100 AD
Brussel sproutsBelgium, 1700's
Many of our crops are products of extensive genomic rearrangements
From Dubcovsky, J. and Dvorak, J. (2007). Genome Plasticity a Key Factor in the Success of Polyploid Wheat Under Domestication. Science. 316: 1862-1866. Reprinted with permission from AAAS. Brassica figure from Adenosine
Common wheat is the result of interspecific hybridization between
three ancestorsPolyploid (multi-
genome) plants are often bigger and so
selected for propagation
The brassicas share three genomes recombined in various ways
Va Va VaVaVbVb VaVaVbVbVdVd
Barley, Einkorn vs. Emmer, Durum, and Bread Wheat
2n = 2x = 1430,000 genesBarley, Einkorn
2n = 4x = 2860,000 genesEmmer, Durum
2n = 6x = 4290,000 genesSpelt, Bread Wheat
Natural selection and domestication polyploidy
Many plant varieties derived from induced mutations
Calrose 76 semi-dwarf rice
High oleic sunflower
Over 2,000 crop varieties derived from mutagenesis have been commercialized
Rio Red grapefruit
Genetic basis of domesticationhas been well-studied
ALL types of mutations selected
• Single nucleotide polymorphisms• Insertions/deletions within genes• Complete gene deletion• Gene duplication/multiplication• Altered regulation (expression)
~ 30 of 30,000 genes altered in a major way during domestication of major crops
Genetic basis of domestication
• Bottlenecks and selective sweeps: Loss of genetic diversity due to selection for domestication traits
• Critical to maintain wild populations and seed banks of diversity
Domestication has reduced genetic diversity compared to wild plants
Numerous genes changed during further breeding over millennia – soy example
• The best genes have been stacked together through selecting based on phenotypes.
4,000 years ago
From Brian Diers, University of Illinois
4,000 years ago 500 years ago Present day
Numerous genes changed – and moving faster with new breeding methods
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 Ultimate LandracesGAM PAI TSAI YUAN CHUNG
IR5657 DEE GEO WOO GEN BENONGCINA Unknow n
IR18348 LATISAIL CHOW SUNGTADUKAN MUDGO
IR64 KITCHILI SAMBA TETEPPA CHIAM SINAWPAGHSERAUPBESAR 15 UNKNOWN (JAPANESE)NAHNG MON S 4 O. nivara (IRGC 101508)VELLAIKAR MARONG PAROC
NAHNG MON S4
NMS 4
IR 64
original rice genome
Mutations
Recombinations Translocations
Deletions
Inversions
One of the most widely grown crops, indica rice IR64 is the product of a complex breeding program that has caused extensive genomic modification, mutation, deletion and rearrangement
Slide courtesy of Ingo Potrykus
Mutations of all kinds common during post-domestication breeding
The recent past – scientific plant breeding
Improvements in plant propagation and breeding were needed to keep up with population growth
Photo credits: Gartons Plant Breeders
The development of hybrid corn led to a big increase in yields
A BB x A A x B The progeny of two genetically different parents often show enhanced growth – this effect is termed “hybrid vigor” or “heterosis”
Occurs in within-species and between species crosses to variable degrees
Inbreeding often precedes hybridization
Shull, G.H. (1909) A pure line method in corn breeding. Am. Breed. Assoc. Rep. 5, 51–59 by permission of Oxford University Press.
Hybrid corn was rapidly adopted because of its increased yields
A BB x A A x B
Percentage of total corn acreage
Even though farmers had to purchase seed every year,
increased yields more than offset increased costs
Shull, G.H. (1909) A pure line method in corn breeding. Am. Breed. Assoc. Rep. 5, 51–59 by permission of Oxford University Press; Economic Research Service / USDA
Norman Borlaug was a plant breeder, and “father of the green revolution”
Distinguished plant breeder and Nobel LaureateNorman Borlaug 1914-2009
One of the most significant accomplishments of 20th
century science was the development of high-yielding, semi-dwarf grain varieties
Why semi-dwarfism?
A. It was the first GMO crop
B. Easier to pick the seeds
C. Plant were prevented from lodging during rain/wind, especially when planted densely and fertilized/irrigated
D. Plants produced higher yields by wasting less energy on stems for height growth
E. C and D
Genetics:• Semi-dwarf genes (qualitative)• Straw strength (quantitative)• Plant architecture (quantitative)• Disease resistance (qualitative/quantitative)• Yield (quantitative)• Quality (qualitative/quantitative)• Nutrition (qualitative/quantitative)
Agronomy:• Fertilizers• Pesticides
• Qualitative traits are distinctive, and controlled by one or a few genes• Quantitative traits are usually controlled by many genes, and give continuous
phenotypes www.achievement.org
A wide variety of genetics, traits, and environment gave rise to the green revolution in wheat
Improved green-revolution plants led to dramatically increased crop yields
The introduction of disease-resistant, semi-dwarf
varieties turning countries from grain importers to grain
exporters
Source: FAO via Brian0918
Dwarf wheat was developed at CIMMYT – the International Maize and Wheat Improvement Center
Rice breeding at IRRI also brought huge yield increases
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
1961 20001980World rice yield (ton/ha) (FAO)
Photo courtesy IRRI
IR8, released in 1966, “…was to tropical rices what the Model T Ford was to automobiles.” It was
known as “miracle rice” because of its high yields.
Crop productivity has kept pace with population because of increased yields
Burney, J.A., Davis, S.J., and Lobell, D.B. (2010). Greenhouse gas mitigation by agricultural intensification. Proc. Natl. Acad. Sci. 107: 12052-12057.
Population (billions) Crop area (hectare)Crop production (gigaton)
Crop area has not increased as rapidly as crop production, because yields (food per hectare) have increased
Growing more food without using more land helps mitigate climate change and slow the loss of biodiversity
100% increase
>100% increase
~20% increase
Modern plant breeders use conventional and molecular methods for plant improvement
Photo credits Scott Bauer USDA; CIMMYT; IRRI; RCMI; Duke Institute for Genome Sciences and Policy
Example: Soybean breeding
Make crosses
Develop experimental lines
Select the best lines
• Soybean is a self pollinated/inbred crop. Bred similar to wheat, barley, dry beans, peanuts. – Self pollinated crops will produce
seed through crossing with itself.
Soybean Breeding – Start with diversity
1. Manually cross diverse types of plants to generate diversity, new combinations of genes
2. Hybrid = F1, highly heterozygous
F11 Aa
X
Not uniform and therefore undesirable unless one can clone (i.e., vegetative propagation, like grape, apple, banana, cassava, potato, eucalypts, poplars)
Soybean breeding – Transform heterozygosity into variation between inbred lines
1. Manually cross plants2. Inbreed plants several generations to
remove heterozygosity, make uniform3. Test thousands of inbred lines in field tests4. Further test in many environments to
develop potential varieties
F11 Aa
F2½ Aa
F3¼ Aa
F41/8 Aa
XXX X
Uniform Potential Variety
Plant Breeding is a Long Term Effort - Soybean
Season Activity Season Activity
1 Make cross 6 Grow new experiment lines in small plots
2 Grow F1 7 Grow yield tests in two environments
3 Grow F2population
8 Grow yield tests in 5 environments
4 Grow F3population
9 Grow yield tests in 20 environments
5 Grow F4population
10 Repeat yield tests and increase seed
Example: Maize (Corn) Breeding
• Cross pollinated/hybrid crop. Bred similar to sunflowers, sorghum, canola
• Takes advantage of hybrid vigor (heterosis)
Maize (Corn) Breeding – heterosis testing
1. Make crosses among lines in program2. Develop inbred lines3. Test performance of inbred lines in hybrid
combinations4. Identify hybrid combinations with the greatest
performance5. Produce seed of hybrid combinations6. Companies sell hybrid seed not inbred
lines to growers (intellectual property protection)
Breeding is a Numbers Game
• Buy more lottery tickets, greater chance of winning
• Test more lines, better chance of selecting a winner as each potential lines has a unique combination of genes. • Use science to improve odds.
Breeders Have Increased Their Capacity to Phenotype
100,000’s of potential varieties will be evaluated annually.
Advances in genetic technologies increasingly contribute to improved plants
• Marker assisted selection (specific genes)
• Genomic selection (whole genomes)
• Recombinant DNA technology and transgenic plants
Photo credit: IRRI
Genetic Markers Are Being Used in Selection
• Phenotyping is expensive and inaccurate.• Identify the gene controlling the trait and directly
select for this.
Rag1 gene
Satt5400.0Satt4353
Rag17
Satt46315
Satt24520
Satt32325Satt22028
Genetic Markers Are Being Used in Selection
Collect leaf tissue Amplify specific genetic regions
Load DNA on a gel
Separate DNA on a gel, score and select
Currrent methodsNow entire process of marker generation and use is
automated and robotized – tens of housands to millions of markers on chromosomes routinely studied
Prior methods
A genome from many short sequences
Next-generation sequencing
From Glenn Howe, Oregon State University
Single nucleotide polymorphism (SNP)
Parent 1 is heterozygous Parents 2 and 3 are homozygous
A C G T G T C G G T C T T A Maternal chrom.A C G T G T C A G T C T T A Paternal chrom.
A C G T G T C G G T C T T A Maternal chrom.A C G T G T C G G T C T T A Paternal chrom.
A C G T G T C A G T C T T A Maternal chrom.A C G T G T C A G T C T T A Paternal chrom.
Parent 1
Parent 2
Parent 3
SNPUsually 2 alleles
Many many loci
Genetic Markers Are Used on an Industrial Level in the Private Sector
Monsanto’s seed chipper
Marker DNA from automated systems.
Marker assisted selection (MAS): Statistically associate traits with specific genes, then select directly for the genes
Phenotype: physical expression of traits
Genotype: Look at a large proportion of DNA segements and/or genes in a genome
Photo credit LemnaTec; Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122.
Introgression of a disease resistance gene that can be identified via MAS
Elite tomato Poor tomato but disease resistant (resistance gene indicated)
We want to add a disease resistance trait to an “elite” tomato plant.
Step 1: Make a hybrid
We cross the two plants. Some of their progeny inherit the disease resistance trait, some don’t – how can we tell the difference?
Photo by Stephen Ausmus USDA
Step 2: Retain only plants with desired gene
We can use markers to look at their DNA and identify those with the resistance gene.It’s faster and easier than infecting them to see the phenotype
The hybrid has the traits but also undesirable traits
Is this an elite, disease-resistant tomato? No, half of its genes are from the poor tomato
Backcross to crop parent multiple times and select for the marker (or the new trait)
We have to repeatedly cross back to the elite tomato, using markers to identify plants with the disease resistance gene
Repeat until genome “cleaned enough” of DNA from donor parent (can be a wild, toxic species)
After several generations, elite, disease resistant tomato
Markers greatly accelerate breeding
programs
F. Nogue – INRA France
10 % of the genome of the cultivated tomato (3,000 genes) come from interspecies crosses
From www.eu-sol.net
Repetitive hybridization and introgression leave large marks on plant genomes
But, Most Economic Traits Controlled by Many Genes
• Locations of female (DS) (36 genes) and male (DA) (39) flowering date genes in maize.
Buckler et al. Science. 2009. 325:714-718.
Advances in genomics technologies facilitate breeding for complex traits – can sequence ~whole genome now and thus look at quantitative traits too
• Genome sequence data are available for hundreds of plant species
• Molecular breeding and mapping tools are developed for many species
• Genomic selection now common
Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122.
Phenomics now more limiting than genomics
Genotype analysis
Genome-wide methods make it possible to identify genes associated with complex traits, like yield or water use efficiency
Association analysis
Gene discovery
Summary• Early, scientific, and molecular phases of plant improvement• Domestication – emphasis on early, major genes that enable
cultivation, consumption• Green revolution – semi-dwarfism genes and other ag
technologies to improve cereal yields• Heterosis – breeding for hybrid vigor, natural intellectual
property protection• Clonal propagation: Sterile or highly outcrossing (fruit and
forest trees)• Marker-aided selection enables genes for major traits to be
tracked and introgressed rapidly – pest resistance, nutrition• Genomic selection enables rapid improvement of complex,
polygenic traits like yield, adaptation