APPLICATION OF SNP CHIP TO

COMMERCIAL BREEDING FOR GREEN

SUPER-RICE CULTIVARS IN CHINA

Junhua Peng
Life Science and Technology Center
China National Seed Group Co., Ltd.
Wuhan, Hubei 430206, China

Asian Seed Congress 2015

Goa, India
November 19, 2015
1
Importance of rice

Ø  Globally, rice is planted in 1/3 of the land for cereal crops
Ø  Rice is staple food for over 40% of the global population
Ø  Provides human beings with 40% of calories
Ø  In China, 1/4 of the cropping land is for rice, and the yield is
of the 50% of the total grain production

The top 10 rice producers in the world in 2013

China

India
Role of the key genes

　 Era
1950-60 1970-80 1980-90 2000-
i-j
Semi- Male
Trait Tall heterosis +
dwarf sterility
ideotype
Variety type Landrace Dwarf Hybrid Super rice
CMS,
Gene Sd1 sd1 S5n, etc.
EGMS
Yield (t/ha) 1.5-2.5 4.5 6.0-7.5 12.0
Breeding for green super rice varieties

Ø Why need the green super rice?

1.  Balance between yield and quality
2.  Food safety
3.  Environment-safety
Ø How define the green super rice?
1.  High yield, good quality, suitable for mechanization
2.  Disease resistance
3.  Pest insect resistance
4.  Tolerance to abiotic stresses,
5.  High-efficiency of fertilizer utilization
6.  Low absorption of heavy metals
Challenges for breeding the green
super rice varieties

Ø  Conventional approaches nearly impossible or very hard to

1.  Maintain the genetic background of the recurrent parents
2.  Integrate many genes into a adapted variety
3.  Develop near-isogenic lines
Genomics tools are necessary and helpful

Ø  The availability of genome sequences of multiple varieties

Ø  Many genes characterized by functional genomics
Ø  Enable us to develop SNP microarrays in rice

Rice genomics data SNP techs Rice SNP chip

 Cutting-edge platform for genomics-
assisted breeding
Number of
markers

Number of samples
7
Principles of genomics-assisted breeding

Genomics data

Directed improvement Designed breeding

Marker platform

Fingerprinting

Novel varieties

8
Principle of the directed improvement

Recurrent parent Donor parent

MAS

Target
gene

Improved variety

Three advantages: fast, accurate, and reliable

9
Available rice SNP chips (6K-60K-90K）
in CNS
In 2012, we developed the 1st rice SNP chip in the world.
There are currently three versions of rice SNP chips available
for research and breeding activities, 6K, 60K and 90K in
CNS.

Number of rice Number of Number of Number of

Bead
Array type
varieties for SNP designed synthesized high-quality
development markers markers markers

RICE6K 6,000 520 5,636 5,102 4,473

RICE60K 60,000 801 58,290 51,599 43,386

RICE90K 90,000 16,000 86,071 77,418 65,065

Markers on Rice60K

(A) Distribution of SNP markers along the entire rice genome. (B) Distances
between the SNPs included on the Rice60K Bead chip; (C) Genomic localization
of the selected SNPs; (D) MAFs of the selected SNPs.
 Polymorphisms among the randomly-
selected rice varieties detected by Rice6K

X axis shows the number of polymorphic markers between two varieties and Y
axis shows the number of pairs.
Polymorphisms among the randomly-selected
rice varieties detected by Rice60K

(A) Polymorphisms among varieties based on re-sequencing data of the whole

genome. (B) Polymorphisms among varieties based on genotyping data using the
RiceSNP60 array.
Phylogenetic analysis of rice lines based on
Rice60K genotyping

The tree of 195 rice inbred lines was constructed from a simple matching
distance of 43,386 SNPs using the neighbor-joining algorithm. The three
divergent groups, indica, japonica, and the intermediate, are colored in red, blue,
and pink, respectively. The scale bar indicates the simple matching distance
 Genotyping of artificial populations

(A) RILs of ZS97/MH63. (B) ZS97/IRGC-105491 introgression lines (IL). (C)

Genotyping of ZS97/MH63 RILs via different marker systems: (a) 220 RFLP/SSR
markers; (b) NGS technology (0.06×); (c) RICE6K array; (d) Rice60K array.
BSA mapping of a fertility restorer gene using
RICE6K array

The map shows different genotypes between the DNA bulk sample from 10
fertile plants and the sample from 20 sterile plants. The blue bands on the
chromosomes represent the SNP sites with different genotypes, at which the
fertility bulk was heterozygous and the sterility bulk was homozygous. The
red dot indicates the positions of the cloned fertility restorer gene Rf1/Rf1a/Rf5..
 Genetic background screening using
RICE6K array

(a) The genetic background of all the 29 plants in BC4F1. (b) Genotyping map of
the plant L28. (c) Genotyping map of the plant L50. The triangles and the dots
indicate the positions of the two target genes. The blue lines indicated the
positions of the SNPs with heterozygous genotypes where genomic fragments
of the donor parent were introgressed and the genotypes of the rest genomic
regions were the same as the recurrent parents.
Genomic distribution of the 6K SNPs
per  250  kb  ≥  1  SNP:  98.6%  cov.  
per  100  kb  ≥  1  SNP:  90.5%  cov.
5,034  SNPs  
i/j:  39.3%    
i/i:  41.0%  
j/j:  4.7%  
n:  15.0%

Addi:onal  68  SNPs/INDELs  

for  cloned  genes  

Total  5,102  markers  

The Genomic distribution of the 60K SNPs

per  100  kb  ≥  1  SNP:  99.6%  cov.

58,149  SNPs  
i/j:  10.9%  
i/i:  49.3%  
j/j:  27.1%  
n:  12.7%

Addi:onal  141  SNPs/INDELs  

for  cloned  genes  

Total  58,290  markers  

70.8%  in  genic  regions  
Polymorphism revealed by RICE60K
and Rice44K SNP arrays

23000 12000 8000

Illumina Infinium RICE60K Genotyping Array

23000 6000 3000

Affymetrix GeneChip Rice 44K SNP Genotyping Array

Chen,  et  al.  Mol  Plant,  2014,  7:  541-­‐553
The procedure of genomics-assisted
commercial breeding

① ② ③ ④ ⑤
Germplasm

Seed prod.
⑥

Sales
LDB

CB

TD
Genomics tools

21
Genomics-assited breeding in the lab

Sowing Nursery

Sampling Testing

22
The lab and greenhouse in CNS
Field evaluation

24
Field evaluation

25
Directed improvement of rice resistance
against blast

Improved Non-improved
Directed improvement of rice
resistance against planthopper

Susc. CK Improved Non-improved

Directed improvement of rice
resistance against brown plant hopper
Yuehui9113-
Bph14 Yuehui9113-
Bph14+15

Yuehui9113 Yuehui9113-
Bph15
Field demo of genomics-improved blast-
resistance lines

Using the SNP chips and MAS, we have

successfully achieved the breeding goals
in a very short period of 2-3 years.

CHINA SEED
Acknowledgments

Dr. Fasong Zhou, Dr. Huihui Yu, Dr. Shuqing Qiu

Life Science and Technology Center, China National Seed
Group Co., Ltd.
Grants from the MOST and Sinochem

References
1.  Yu, H., Xie, W., Li, J., Zhou, F. and Zhang, Q. (2014) A whole-genome SNP
array (RICE6K) for genomic breeding in rice. Plant Biotechnol J 12, 28-37.
2.  Chen, H., Xie, W., He, H., Yu, H., Chen, W., Li, J., Yu, R., Yao, Y., Zhang, W.,
He, Y., Tang, X., Zhou, F., Deng, X.W. and Zhang, Q. (2014) A high-density
SNP genotyping array for rice biology and molecular breeding. Mol Plant 7,
541-553.
SNP array service
Contact: Dr. Junhua Peng
Tel: +86-15927184078
E-mail: pengjunhua@sinochem.com.