The presentation for KLV jubilee Main Conference, by Sanwen Huang from Caas.

1. To redefine plant breeding
with genomics
Sanwen Huang
huangsanwen@caas.net.cn
KLV125, November 10, 2011
Chinese Academy of Agricultural Sciences
Beijing, 100081, China

2. Two solutions to feed China
1) Better seeds
2) Farm cooperative

4. Plant breeding contributed
>50% of growth
in agricultural production.

5. First generation plant breeding
Rice
SoybeanWheat BarleySunflower
Maize
Potato
Sorghum
~10,000 years ago

6. Darwin 1859 Mendel 1865 Morgan 1911
Second generation plant breeding

7. Borlaug 1950s Yuan Longping 1960s
P E R S P E C T I V E S
Hybrid maize. Within ten years of Jones’
proclamation,the first breeders were produc-
ing successful hybrids.Beginning in the early
1930s, interest in, and demand for, hybrid
maize rose steadily among farmers in the
United States16
(FIG. 2a). Maize breeders have
continually turned out higher-yielding
hybrids,year after year17–19
(FIG.2b),and farm-
ers have adopted them after cautious trials on
their own farms.In 1997,United States maize
yields averaged 8 tons hectare–1
, compared
with 1 ton hectare–1
in 1930 (REF.20).
Hybrids were not entirely responsible for
advances in maize yields, however. Starting
around the 1950s,the increasingly widespread
use of synthetic nitrogen fertilizers, chemical
weed killers, and more efficient planting and
harvesting machinery also contributed to
higher yields17–19,21
.
Surprisingly, improvements in heterosis
have not contributed to higher yields.
Experiments have shown that heterosis
(calculated as the difference in yield
between a single cross hybrid and the mean
of its two inbred parents) is unchanged
over the years. The yields of the inbred lines
have risen at almost the same rate as hybrid
yields22
. It seems that yield gains have come
primarily from genetic improvements in
tolerance to stresses of all kinds (such as
tolerance to disease and insects, dense
planting, drought or low soil fertility). The
newer hybrids are tougher than their
predecessors and shrug off droughts (for
example) that would have damaged the
older hybrids and devastated their open-
pollinated parents.
but, to this day, there is no completely satis-
factory explanation for the phenomenon of
heterosis in maize or in any other species14
.
Fortunately, a lack of understanding has
never hindered the use of the phenomenon.
But in the 1920s, these problems were all
in the future. The‘hybrid maize’ enthusiasts
were occupied primarily with finding
inbreds that made outstanding hybrids. As
Without the contributions from the
public sector, the commercial maize breed-
ers probably could not have succeeded in
the early years, for individually they simply
did not have enough inbred lines or
enough knowledge about how best to make
and test hybrids15
.
Figure 1 | Detasselling maize plants Detasselling — pulling tassels — is vital for the production of
hybrid maize. The detasselled plants are called ‘females’; they will bear the hybrid seed. In the early
years, men on foot did the detasselling, as in this photo from the 1930s. In later years, high school
boys and girls were recruited to do the job, also on foot. Today, youths are still the chief labour
source, but they usually ride in special motorized carriers, thereby increasing the speed and
precision of their work. (Image courtesy of Pioneer Hi-Bred International, Inc.)
a Figure 2 | Maize hybrids: area planted and
Pioneer 1930s
72 | JANUARY 2001 | VOLUME 2 www.nature.com/reviews/genetics
P E R S P E C T I V E S
tus as independent seed savers, and even
though hybrids as such were looked on as
strange new creations of science. Having
traced the development of hybrid maize,these
and related questions can be addressed.
Farmers gave up their status as indepen-
dent seed savers because they found by expe-
rience that they would profit more by doing
so.They were already giving up their status as
independent power suppliers on their farms,
for example,as they moved from horse power
to tractor power and from hand harvest to
mechanical maize pickers.
Although farmers viewed hybrids as new
and strange creations of science, they saw no
adverse effects on either their crops or their
livestock. It is true that, in the early days,
some farmers feared that the abnormally
high yields from hybrids would drain the soil
of needed fertilizer elements.And there were
complaints about some of the first hybrids,
to the effect that the kernels were too flinty
and hard for cows to chew. Seed companies
bred new hybrids to satisfy the second com-
plaint, and the first concern turned out to be
without foundation if normal soil fertility
practices were used.
The farmers’primary fear was not that sci-
ence might create unmanageable‘monsters’
(today’s widespread point of view), but that
scientists claimed more power to help agricul-
ture than they really possessed.
Public and private breeders.In the early years
of the hybrid era, people were undecided
about how to deliver hybrids to the farmer.
Farmers had the option to produce them on
their own farm using single cross parent seed
purchased from the agricultural colleges,or to
purchase ‘ready to plant’ hybrid seed from
farmer cooperatives or from commercial seed
companies (FIG.3).All methods were tried,but
in the end the seed companies turned out to
be the farmers’choice.
Once the advantages of hybrids (and the
factthatfarmerswouldbuythem)wereshown,
seed companies sprang up across the country,
especially in the Corn Belt states15
(FIG. 4).
Starting with four pioneering companies,the
numbers grew exponentially in the 1930s.By
1995, 305 independent companies were
involvedwiththeproductionandsaleof hybrid
maize seed. As with most industries, a small
number of large companies dominated the
business,accounting for perhaps 70% of the
sales.Despitetheirsmallmarketshare,thesmall
companieshaveanimportantroleintheindus-
try.Theyprovidean alternativetofarmerswho
donotwanttobuyfromthelargercompanies.
The exchange of information and breed-
ing materials among private- and public-sec-
tor breeders changed as the seed industry
matured. Almost from the beginning, seed
companies kept the pedigrees of their hybrids
secret and they soon stopped trading their
inbred lines. By about the mid-1930s, all
exchange of inbreds and other advanced
breeding materials was one-way, from the
public to the private sector.
The roles of the public- and private-sector
breeders also changed. The large companies
with strong breeding programmes had
increasingly less need for inbreds developed by
the public sector,although the smaller compa-
nies still depended on them.Over time,‘foun-
dation seed companies’were formed expressly
to breed inbred lines for lease to the small seed
companies,thereby filling the role of the pub-
lic-sector breeders.The public-sector breeders
in turn shifted their primary emphasis from
the development of inbreds and hybrids to
studying the theoretical basis for producing
improved inbreds and hybrids,as well as other
needed aspects of maize-breeding research.
The relationship between public and pri-
vate sector breeders still remains close; they
have mutually supportive roles in the nation’s
maize breeding programme.
Consequences of hybrid maize
Acceptance.In the opening paragraphs of this
article I asked why the maize hybrids were
accepted without public outcry in the 1930s,
even though farmers had to give up their sta-
An important change in hybrid seed
production and performance was, in a
sense, a byproduct of the increases in
inbred yield. By the 1960s, the newest
inbreds were so high-yielding that it
became practical to use them as seed par-
ents, and so to produce single cross hybrids
for sale. The best single crosses always
yielded more than the best double crosses
but, as noted earlier, commercial produc-
tion of single cross hybrids was not feasible
in the first decades of hybrid maize breed-
ing because of the low yield potential of
inbreds from that era.
Figure 3 | The introduction of hybrid maize
seeds. The ‘seed corn companies’ effectively and
energetically introduced hybrid maize to cautious
farmers. They recruited well-known and
respected farmers as part-time salesmen,
working on commission. They gave small
amounts of free seed of new hybrids to farmers
and encouraged the prospective customers to
compare them with their present varieties on their
own farms and using their own farming methods.
The salesman and/or his supervisor often would
help the farmer harvest the comparison. In the
process, the sales people learned about the
farmers’ needs and desires in maize hybrids,
which they passed on to the breeders. So, the
relationship between farmers and seed
companies from the beginning was almost on a
neighbour to neighbour basis. The relationship
remains much the same today, with modifications
because of the changing nature of farming and
farmers (much larger scale, more advanced
technologically and more business-like).
Image courtesy of Pioneer Hi-Bred International, Inc.
Figure 4 | Maize quality control in the early
years. The fledgling seed companies devised a
‘sorting belt’, allowing inspectors to examine
every ear before shelling. They wanted to be sure
the seed ears were free of damage from disease
or insects, and of the right type. Women replaced
men in many of the seed production operations
during the Second World War, when young men
were in the armed services.
Image courtesy of Pioneer Hi-Bred International, Inc.
© 2001 Macmillan Magazines Ltd
Second generation plant breeding

8. Plant Breeding
the art and science of changing the
genetics of plants for the benefit of
humankind.

9. Watson and Crick, 1953 Human Genome, 2001 Rice genome, 2002
Third generation plant breeding

10. New tech
600Gb per run

11. 0"
10"
20"
30"
40"
50"
60"
70"
80"
1999" 2000" 2001" 2002" 2003" 2004" 2005" 2006"
Gb"Produc4on"by"year"
0"
200"
400"
600"
800"
1,000"
1,200"
1,400"
1,600"
1,800"
1999" 2000" 2001" 2002" 2003" 2004" 2005" 2006" 2007" 2008"
Gb"
Gb"Produc5on"by"year"
0"
2,000"
4,000"
6,000"
8,000"
10,000"
12,000"
14,000"
16,000"
18,000"
20,000"
1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"2009"
Gb"
Gb"Produc5on"by"year"
to 100,000
in 2010
100,000 Gb
2010Sequence in
database

12. ~100,000X!
$0.1
$0.20/Mb!
$20,000/Mb!
Cost of Sequencing ($ per million bases) !
Moore’s Law!
Sequencing!
Sequencing goes faster than
the Moore’s law

13. What does this mean to
plant breeding?
We can transform plant breeding
from craftsmanship to informatics. It is
like to turn on light in a dark room.

14. The Cucumber Genome
EDITORIAL
NATURE GENETICS | VOLUME 41 | NUMBER 12 | DECEMBER 2009 1259
Cool as a cucumber
The genome of the seventh plant to be sequenced, Cucumis sativus L., was assembled using the conventional long-
read Sanger sequencing and higher-throughput short-read technology. This genome is the entry point for exploring
the diversity and function of the Cucurbitaceae family of agriculturally important plants. Its compact genome,
without evidence of recent duplication, will be useful in comparative analysis of plant genome evolution.
A
gain and again Charles Darwin found inspiration in
the cucumber and its fellow cucurbits.
The first trait to strike him was the unplantlike
motility of the vine’s tendrils, organs adapted to the habits of
climbing and running. Use resulted in adaptation, disuse in
diversification and loss.
In the varieties which grow upright or do not run and climb, the
tendrils, though useless, are either present or are represented by
various semi-monstrous organs, or are quite absent.
Then he noted the diversification of marrow, gourd and
melon fruit forms under agricultural selection and pondered
the irreducible essence of species identity. He decided to trust
the biological species concept, namely that different species
cannot produce fertile offspring.
If we were to trust to external differences alone, and give up the
test of sterility, a multitude of species would have to be formed
out of the varieties of these three species of Cucurbita.
Having a biological definition of species identity, Darwin
was then able to unravel the relationship between species and
apparently stable, taxonomically important traits without fear
of arguing in a circle. He contrasted these traits with variable
features found within a species. He was also able to identify
convergent evolution under selection of the fruit morpholo-
gies of distinct species of melons and cucumbers (C.R. Darwin,
The Variation of Animals and Plants under Domestication 1st
edn., 2nd issue, vol. 1, John Murray, London, 1868).
Now, on p 1275, Sanwen Huang et al. report the de novo
assembly and annotation of the 243.5-Mb genome of the
“Chinese long 9930” inbred line of cucumber and the use of
a linkage map in the assembly process to tie the assembled
contigs to the chromosomes. The Illumina GA technology
has proven practical, so now many diverse lines can be rapidly
sequenced to enable marker-assisted breeding of high-yield-
ing, disease-resistant, and fresh green-scented cucumbers,
along with melons, squash and pumpkins.
Cucumber and melon diverged 4–7 million years ago, and
C. sativus carries chromosome fusions that distinguish the
cucumber karyotypes from those of melon (C. melo) and a
more distant relative, the watermelon (Citrullus lanatus).Were
he here today, Darwin could see that these sets of chromosomes
physically reinforce the biological species barrier to fertility,
were the (widely varying) sexual systems of the plants to per-
mit crossing.
What would Charles do next, equipped with genomes? No
doubt he would be most intrigued to compare the genesis of
the woody and non-woody tendrils of grapevine and cucum-
ber, respectively. Then he might scan for signatures of plant-
human coadaptation during the domestication processes of
early agricultural humans. Then he might travel to investi-
gate the adaptations contributing to the success of Cucumis
dipsaceus, the wild spiny cucumber originating in Eastern
Africa that is now invading the Galapagos Islands he once
explored.
©2009NatureAmerica,Inc.Allrightsreserved.

15. CuGI-an international effort to unlock
the genetic potential of an important vegetable
using novel genomic technology
Consortium building

16. Northern China
Cuke 100-to reveal general pattern
of genetic diversity, recombination,
and selection in cucumber
C. s.
xishuangbanna
C. s. hardwickii American Slices Southern China US processing Japan Fresh
EU greenhouse
Xin Liu

17. 86
G8
91
98
27
97
95
201
107
94
101
G6
G17
G3
G2
G16
G4
G15
G14
108
103
93
89
120
102
99
96
100
90
30
28
31
3
29
104
4
105
G13
106
1
115
43
116
112
37
111
8
110
109
11
10
7
44
G5
G12
5
40
113
45
G7
G10
G9
36
13
114
35
32
9
6
19
2
22
87
82
81
85
80
79
G11
84
66
74
83
77
71
69
75
72
78
70
68
65
76
51
50
21
92
20
23
18
17
118
117
16
15
14
12
49
88
0.02
0.27
Indian Xishuangbanna Eurasian East Asian
Indian
Indian
Xishuangbanna
Eurasian
East Asian
a.
b.
c. d.
120 cucumbers sequenced, 4M SNPs
discovered
wild semi-wild cultivated cultivated

18. The genomics of plant breeding
-Variation
intraspecific variation
interpecific variation, pan genome
protein coding/non coding RNA
epigenetic variation/miRNA
EMS mutation library-reseq
- Selection
Allele frequency
Ka/Ks
- Recombination
LD
HapMap
Recombination hotspots
Historical crossover in cucumber breeding
- Genetic drift

19. Green Genetics round table, 2008

20. 中国农业科学院蔬菜花卉研究所
Institute of Vegetables and Flowers
Chinese Academy of Agricultural Sciences
Bernard de Geus

21. The Potato Genome
OUTLOOK
Alzheimer’s
disease
NATURE.COM/NATURE
14 July 2011 £10
Vol. 475, No. 7355
HISTORY
PURE
JOY
Arcane mathematics that
changed the world
PAGE166
EVOLUTION
GIANT
DINOSAURS
Seeds of greatness in small
sauropod ancestors
PAGE159
NEUROSCIENCE
SPINAL CORD
REGENERATION
Restoring breath control
after neck injury
PAGES178 &196
THEPOTATO
GENOME
sauropod ancestors
PAGE159
The DNA sequence of
the South American
tuber eaten around
the world PAGE189
THE INTERNATIONAL WEEKLY JOURNAL OF SCIENCE
Cover 14 July.indd 1 08/07/2011 17:39
ARTICLE doi:10.1038/nature10158
Genome sequence and analysis of the
tuber crop potato
The Potato Genome Sequencing Consortium*
Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It
is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a
homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict
39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a
palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to
this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence
variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression.
Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the
evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this
vital crop.
Potato (Solanum tuberosum L.) is a member of the Solanaceae, an
economically important familythatincludes tomato, pepper, aubergine
(eggplant), petunia and tobacco. Potato belongs to the asterid clade of
eudicot plants that represents ,25% of flowering plant species and
fromwhich a complete genomesequence has not yet,toour knowledge,
been published. Potato occupies a wide eco-geographical range1
and is
uniqueamongthemajorworldfoodcropsinproducingstolons(under-
ground stems) that under suitable environmental conditions swell to
formtubers.Itsworldwideimportance,especiallywithinthedeveloping
world, isgrowing rapidly, with production in 2009 reaching 330 million
tons (http://www.fao.org). The tubers are a globally important dietary
source of starch, protein, antioxidants and vitamins2
, serving the plant
asbotha storageorgan andavegetativepropagationsystem.Despitethe
importance of tubers, the evolutionary and developmental mechanisms
of their initiation and growth remain elusive.
Outside of its natural range in South America, the cultivated potato
is considered to have a narrow genetic base resulting originally from
limited germplasm introductions to Europe. Most potato cultivars are
autotetraploid (2n 5 4x 5 48), highly heterozygous, suffer acute
inbreeding depression, and are susceptible to many devastating pests
and pathogens, as exemplified by the Irish potato famine in the mid-
nineteenth century. Together, these attributes present a significant
barrier to potato improvement using classical breeding approaches.
A challenge to the scientific community is to obtain a genome
sequence that will ultimately facilitate advances in breeding.
To overcome the key issue of heterozygosity and allow us to gen-
erate a high-quality draft potato genome sequence, we used a unique
homozygous form of potato called a doubled monoploid, derived
using classical tissue culture techniques3
. The draft genome sequence
from this genotype, S. tuberosum group Phureja DM1-3 516 R44
(hereafter referred to as DM), was used to integrate sequence data
from a heterozygous diploid breeding line, S. tuberosum group
Tuberosum RH89-039-16 (hereafter referred to as RH). These two
genotypes represent a sample of potato genomic diversity; DM with
its fingerling (elongated) tubers was derived from a primitive South
American cultivar whereas RH more closely resembles commercially
cultivated tetraploid potato. The combined data resources, allied to
deep transcriptome sequence from both genotypes, allowed us to
explore potato genome structure and organization, as well as key
aspects of the biology and evolution of this important crop.
Genome assembly and annotation
We sequenced the nuclear and organellar genomes of DM using a
whole-genome shotgun sequencing (WGS) approach. We generated
96.6 Gb of raw sequence from two next-generation sequencing (NGS)
platforms, Illumina Genome Analyser and Roche Pyrosequencing, as
well as conventional Sanger sequencing technologies. The genome
was assembled using SOAPdenovo4
, resulting in a final assembly of
727 Mb, of which 93.9% is non-gapped sequence. Ninety per cent of
the assembly falls into 443 superscaffolds larger than 349 kb. The 17-
nucleotide depth distribution (Supplementary Fig. 1) suggests a gen-
ome size of 844 Mb, consistent with estimates from flow cytometry5
.
Our assembly of 727 Mb is 117 Mb less than the estimated genome
size. Analysis of the DM scaffolds indicates 62.2% repetitive content in
the assembled section of the DM genome, less than the 74.8% esti-
mated from bacterial artificial chromosome (BAC) and fosmid end
sequences (Supplementary Table 1), indicating that much of the unas-
sembled genome is composed of repetitive sequences.
We assessed the quality of the WGS assembly through alignment to
Sanger-derived phase 2 BAC sequences. In an alignment length of
,1 Mb (99.4% coverage), no gross assembly errors were detected
(Supplementary Table 2 and Supplementary Fig. 2). Alignment of
fosmid and BAC paired-end sequences to the WGS scaffolds revealed
limited (#0.12%) potential misassemblies (Supplementary Table 3).
Extensive coverage of the potato genome in this assembly was con-
firmed using available expressed sequence tag (EST) data; 97.1% of
181,558 available Sanger-sequenced S. tuberosum ESTs (.200 bp)
were detected. Repetitive sequences account for at least 62.2% of the
assembled genome (452.5 Mb) (Supplementary Table 1) with long
terminal repeat retrotransposons comprising the majority of the
transposable element classes, representing 29.4% of the genome. In
addition, subtelomeric repeats were identified at or near chromo-
somal ends (Fig. 1). Using a newly constructed genetic map based
on 2,603 polymorphic markers in conjunction with other available
*Lists of authors and their affiliations appear at the end of the paper.
0 0 M O N T H 2 0 1 1 | V O L 0 0 0 | N A T U R E | 1

22. Potato Genome Sequencing Consortium
14 countries and 28 institution

23. High-profile visit from Wageningen, 2005

24. 2005年工作总结
• 艾菲特·雅可布森（Evert Jacobsen）教授
荣获2005年度中国国际科技合作奖，由温家
宝总理在全国科技大会宣布。
中国驻荷兰大使薛捍勤女士向雅可布森夫妇表示祝贺！
Prof. Evert Jacobsen got his big award, 2006

25. 1）Dicot evolution
Rosids
Asterids
25% flower
plants
Asterid-specific genes: 2,642
Potato-specific: 3,372

26. 2) Genomic basis of inbreeding depression
Potato suffers acute inbreeding depression
that likely involve thousand genes
DM: 1X
RH: 2X

27. 3) Tuber biology
Supplementary Figure 9. Proposed roles of FT homologues in potato. A, Simplified Arabidopsis
pathway, redrawn according to Michaels (ref. 57 in Supplemental Text). B, Proposed potato pathway. SP3D
regulates flowering time, SP6A regulates tuber initiation and SP5G represses sprouting. A functional
homolog of FD-L exists in potato (S. Prat, personal communication).
B. Proposed potato
pathway
WWW.NATURE.COM/NATURE | 22
Genes for tuber biotic
resistance and tuber
initiation and sprouting
Prat et al., Nature 2011

28. “The breakthrough holds out the
promise of boosting harvests of
one of the world's most important
staple crops.”
“...this is a first big step for
scientists as well as political leaders
anxiously watching the vagaries in
the world's food supply.”
Press coverage

29. Traditional
potato breeding
10－12 years
1,000,000
100,000
40,000
4,000
1,000 250
40
20
4
1

30. Genomics-based
breeding
4-6 years
12 trait genes/cross
1,000,000
250
20
1
• sow seeds in vitro
• type trait genes
• multiply candidadate
0.5 year
• field observation
• more disease test
• more quality analysis
1.5 year
• yield stableness test
• multiply seed potato2－4 year

31. “One potato genome
unravelled, three to go!”
Tetraploid genome sequencing
remains a huge challenge

32. Ally for true potato seeds
to create a potato propagated and bred in a tomato way
A new paradigm in potato breeding
Pim Lindhout
EAPR meeting, OULU, Finland
July 25th, 2011
www.solynta.com
EAPR meeting, OULU, Finland
novomeinnovative agriculture
Mr. GeertVeenhuizen, may you rest in peace!

33. 100+ plant species: from algae to
angiosperm, including 60 major
crops, evolutionary continuum of
each gene family.
100+ genotypes/species: core
collections, major version of
genetic variation
100 x 100 Plant Genome Project

34. Tree of plant kingdom
95%
Arable
land

35. Paradigm shift for
plant biology

36. Major ag-biological questions
1. C4 photosynthesis
2. N2 fixation
3. Seed and flower development
4. Heterosis

37. C4
1. C4 photosynthesis
C3

38. 2. N2 fixation
with
Prof.Ton Bisseling
Understanding
symbiosis by
evolutionary
genomics!

39. 3. Seed and
flower
development
Out of the past.
Tiny Amborella sits
at the bottom of the
angiosperm family tree.
Seed
Flower

40. 4. Heterosis

41. Now: 7B
2050: 9B
To the expanding world’s
population requires innovation!

42. Redefine Plant Breeding
NEW: the science and technology of
optimizing the genome of plants for the
benefit of humankind
OLD: the art and science of changing
the genetics of plants for the benefit
of humankind.

43. Rice 3.0
High
partition
in seeds
N2 fixation
+
drought
tolerance
C4
photo-
synthesis
Strong
heterosis
Durable
resistance,
less pesticide

44. “The people who
are crazy enough to
think they can
change the world,
are the ones who
do. ”

45. The education centre of the third
generation of plant breeders