http://www.fao.org/asiapacific/events/detail-events/en/c/1440/

1. A case study from crop
genetic resources in China
Xinhai Li
Institute of Crop Science,
Chinese Academy of Agricultural Sciences

2. 1. Crop germplasm resources collection,
conservation, and innovation
2. CGR genomic characterization
3. Crop molecular breeding
4. Challenges and strategies
Content

3. 1. Crop germplasm resources collection,
conservation and innovation in China

4. Crop Germplasm Resources(CGR)
collecting actions in China
• Two nation-wide massive collecting actions
in history: 1950s-1960s and 1970s-1980s
• Complementary collections in 1980s-1990s
• The 3rd national germplasm collecting
action is in progress

5. CGR Conservation System
Center for CGR (ICS, CAAS)Center for CGR (ICS, CAAS)
in situin situ
169 sites169 sites
ex situex situ
Info CenterInfo Center
Medium-
term
Medium-
term
Long-
term
Long-
term
Field
GB
Field
GB
NGB
Beijing
NGB
Beijing
NDGB
Qinghai
NDGB
Qinghai
17 Prov.17 Prov.10 National10 National
43 field GBs43 field GBs

6. CGR conservation
• Low temperature
– long term: -10 ~ -20℃ ， moisture content
5-6% ， 30-50 years
– Mid-term: 0-5℃ ， MC 8-9% ， 10-30 years
• Ultra-low temperature (N)
– DNA, meristem tissues, etc
• Test-tube plantlet
• In situ conservation

7. CGR Information
CGRIS - China Crop Germplasm Resources
Information System
• Databases
— First developed in 1980s
• Stand-alone Management system
— Started in 1995
• Web system
— Online in 1997

8. CGR innovation and utilization
• Over 2,000 elite germplasm materials are
developed per year
• Every year more than 150,000 germplasm
materials are distributed to over 4,000
public users
Pubing wheat materials Landrace introgression lines

9. 2. CGR genomic characterization in China

10. Rice genome (indica rice 93-11 and a wild rice)
① Genome Sequencing Research
The large proportion of rice genes with
no recognizable homologs is due to a
gradient in the GC content of rice
coding sequences (Yu et al., 2002,
Science)
Low activity of long-terminal repeat
retrotransposons and massive internal
deletions of ancient long-terminal repeat
elements lead to the compact genome of
Oryza brachyantha (Chen et al., 2013,
Nature Communications)

11. Wheat A&D genome
Nature, 2013
Comparative analysis
of Ae. tauschii
ordered scaffolds
versus barley and
Brachypodium.
Ae. tauschii gene families and
transcription factors.
An integrated genetic map of Ae. tauschii
chromosome 2D.

12. Core: 48.6% of gene families and 80.1% of genome
sequence
Dispensable: 51.4% of gene families and 19.9% of
genome sequence
59,080 gene families
Genome size: 986.3 Mbp
G. soja pan-genome
6 samples shared
(49.2%)
4 samples shared (5.2%)
3 samples shared (3.5%)
2 samples shared (3.6%)
Sample-specific (9.7%)
5 samples shared
(28.9%)
Core
(80.1%)
Dispensable
(19.9%)
Pan-genome of G. soja Dispensable genome Sample-specific
genome
GsojaA
GsojaB
GsojaC
GsojaD
GsojaE
GsojaF
GsojaG
Nature Biotechnology, 2014

13. Millet Genome
Foxtail millet was split from
sorghum and maize ~27 Myr
ago
Most of the duplications
were generated in the
whole genome
duplication (WGD)
event shared by all
grasses
A close evolutionary
relationship among foxtail
millet, Brachypodium, rice,
sorghum and maize
Nature biotechnology, 2012

14. Cotton Genome
68.5% of the genome is
occupied by repetitive DNA
sequences
A divergence time for G.
arboreum and G. raimondii of
2–13 million years ago, with
their common ancestor
having diverged from T.
cacao 18–58 million years ago
Nature genetics, 2014

15. Cucumber and sweet potato genome
Nature Genetics, 2009
The LOX family is divided into two
groups, type I and type II

16. Haplotype map of millet and cucuber
Nature, 2013

17. ② Crop gene discovery
 High yield: GIF1, IPA1, Ghd7, GS3, GS5, GL7, PROG1,
GW2, GLW7, GL2/GS2, GW5, DEP1 … …
 High quality: Chalk5, OsSPL16 … …
 Resistance to abiotic stress: COLD1, ZmVPP1,
ZmNAC111, SKC1, OsTT1, GmSALT3 … …
 Resistance to biotic stress: ZmWAK, BSR-D1, Pigm,
Stv11, Bph3, Bph9, Bph14 … …
 Efficient utilization of resources: NRT1.1B … …
 Dominate dwarf: D53
 Hybrid sterility: S5
 Dominant male-sterile: Ms2

18. High yield (plant architecture): IPA1
The IPA1 (Ideal Plant Architecture 1) quantitative trait locus encodes
OsSPL14 and is regulated by OsmiR156, with a reduced tiller number,
increased lodging resistance and enhanced grain yield
Nature Genetics, 2010

19. High yield (panicle architecture): DEP1
The effect of dep1 is to enhance meristematic activity, resulting in a
reduced length of the inflorescence internode, an increased number
of grains per panicle and a consequent increase in grain yield
Nature Genetics, 2009

20. High yield (grain filling): GIF1
Nature Genetics, 2008
Control of rice grain-filling and yield by GIF1

21. High quality (chalkiness)
Chalk5
Nature Genetics, 2014, 2015
OsSPL16

22. COLD1 regulates G-protein signaling to confer chilling
tolerance in rice, and a SNP in COLD1 underlies the
adaptation to cold environment in japonica rice
Cell, 2015
Resistance to abiotic stress: COLD1

23. Resistance to abiotic stress: SKC1
Nature Genetics, 2005
SKC1 is involved in regulating K+
/Na+
homeostasis
under salt stress, providing a potential tool for
improving salt tolerance

24. Resistance to abiotic stress: ZmVPP1
Nature Genetics, 2016
The ZmVPP1 improves drought tolerance in maize seedlings

25. Resistance to biotic stress: BSR-D1
bsr-d1 confers broad-spectrum
blast resistance in rice
Cell, 2017

26. Resistance to biotic stress: Stv11
STV11-R confers the resistance to the rice stripe virus in rice
Nature Commutation, 2014

27. Resistance to biotic stress: ZmWAK
ZmWAK was highly expressed in the mesocotyl of
seedlings where it arrested biotrophic growth of the
endophytic S. reilianum in maize
Nature Genetics, 2015

28. Efficient utilization of resources: NRT1.1B
Nature Genetics, 2015
NRT1.1B-indica variation was associated with enhanced
nitrate uptake and root-to-shoot transport

29. 3. Crop molecular breeding in China

30. Molecular pyramiding breeding of resistance to
rice bacterial leaf blight
Shuhui527(xa4xa4xa21xa21) × IRBB60(Xa4Xa4Xa21Xa21)
Shuhui527 × F1(Xa4xa4Xa21xa21)
Shuhui527 × B1F1(Xa4xa4Xa21xa21)
┇
⊗
Resistant 527
Resistant Shuhui527
(Xa4Xa4Xa21Xa21)
Shuhui527
Resistant 527
Target genes (Xa4Xa21)
and agronomic traits selection
Backcrossing and agronomic
traits selection
Target genes (Xa4Xa21)
and genetic background
selection
Restorer line Shuhui527 with resistance to rice bacterial leaf
blight was developed and widely used in hybrid breeding
① Marker-assisted breeding

31. Molecular markers of glutenin subunits (GS) have been
successfully used in wheat quality improvement
HMW
LMW
Bread
5 ＋ 10
A3b
A3d
LMW-GS HMW-GS

32. Molecular breeding of resistance to
maize head smut
Ji-V088 ： improved from the cross between Huangzaosi
and Ji1037, with the resistance to head smut
Jidan 558 ： Ji-V203 X JiV088
Ji-V088 Huangzaosi Jidan 558

33. Molecular breeding for high quality
soybean
Yudou 8 ×L81-4950
Lx1
Lx2
Lx3
SDS-PAGE gel
ti15176 × Century (lox2.3)
F2
.
.
F5
.
.
.
F9
2/134
Zhonghuang28
Loss of Lox-3 and kunitz

34. Haploid inducer 、 automatic
identification 、 double method
Inbred line development in maize
② DH breeding technology

35. ③ Transgenic breeding
2008-2016 ， Bt cotton varieties 159 with a
cumulative extending area of 28.7 million ha

36. 4. Perspectives

37. ① Basic studies on germplasm improvement
Excellent germplasm
Germplasm
evaluation
Germplasm
improvement
Elite gene
Gene mining
Molecular basis

38. Novel techniques in germplasm
improvement
 Double haploid breeding
 Transgenic breeding
 Marker-assisted selection
 Genome-wide selection
 Gene editing

39. Novel germplasm improvement
— Stress resistance and wide adaptation
— Good quality and special use
— Efficient utilization of resources
— Early maturity and lodging resistance

40. Thanks for your attention!