Genetic diversity and Core Collection of Chinese Rice Germplasm

1
Genetic diversity and Core Collection of Chinese
Rice Germplasm

• Zichao Li
• College of Agronomy and Biotechnology
• China Agricultural University

2
Chinese rice germplasm resources gt 70,000
Accessions
Core collection
3

• The framework of the core collection
• Sampling strategy
• Evaluation system of the core collection

4
Hierarchical establishment of the rice core
collection
Rice Germplasm
Stratified establishment of the core collection
5
Stepwise framework of the core collection
6
The steps to establish each level of the core
collection

• Data collection and analysis
• Determination of the population scale of the core
  collection
• Grouping the parental population
• Determination of accession number within each
  group
• Sampling individual acc. within each group

7
Establishment of the primary core collection of
Chinese rice germplasm
8
Stratified sampling of the primary core
collection of local rice varieties in China
Grouping Principles
Sampling Proportions of each group
Sampling method within group
Non-grouping
P
Sampling strategy
Randomly sampling
DY(24)
L
PR(31)
S
PR-IJ(51)
Hierarchy
G
Clustered sampling
EZ(6)
P
EZ-IJ(12)
L
ST
S
P
DY Dingyings taxonomic system S Square
root G Growth habits P Certain fixed
percentage
9
Sampling scheme of the primary core collection of
local rice varieties in China

• Final sampling proportion is 7.2, including
• 3008 accessions sampled according to the optimal
  sampling scheme
• 624 accessions sampled practice-oriented
• Optimal sampling scheme
• Grouping according to Ding Yings taxonomy
• Determining the accession number in each group by
  square root (or logarithmic) method

10
Results of the primary core collection of each
kind of reserved rice collections
96.5
97.0
100
94.6
90.4
90
80
70
60
The total genetic diversity
50
Sampling Proportion
40
Retain of phenotype
30
20
15.5
12.7
8.4
7.2
10
0
IRV
CWR
LRV
TOTAL
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Morphological evaluation and molecular analysis
on PCC

• Evaluation and observation on morphology
• Cultivated ricelocal rice varieties (LRV, 3632)
  and improved rice varieties (IRV, 678)
• 61 traits4 taxonomic traits, 21 biological
  traits, 14 yield-related traits, 22 other
  agronomic traits
• Nearly 6000 accessions were planted
• Isozyme analysis
• 4 - 8 types of isozymes
• 17 loci
• SSR analysis
• Primary core collection common wild rice (CWR,
  864) and cultivated rice (ACR, 4310)
• About 200,000 data points of 36 DNA markers

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Selection of SSR loci (Numbers) in estimating
rice genetic diversity

• Landraces (358 accessions)
• Guangxi province in South China 212 accessions
• Four provinces in North China 146 accessions

• Results Optimal number of SSR loci 24-36

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Establishment of the core collection from PCC
14
Establishment of the core collection from PCC

• Acquirement of data of morphological and
  molecular markers
• Type and number of molecular markers
• Determination of the population scale of core
  collection
• Establishment of core collection

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The results of t-tests Representation No
significant differences among different data
typesGenetic diversity the morphological data
are not significantly different from data types.
Only that of SSR, T-test revealed obviously
different.
Significance (2-tailed)
df
t

0.819
18
0.233
SSR vs (SSRMOR)
0.000
18
6.289
SSR vs MOR
0.000
18
5.134
(SSRMOR) vs MOR
16
?????????
Rice resources of China
Morphological
Morphological
PCC of Asian cultivated rice
PCC of Common wild rice
SSR
SSR
DY S
GB P
CC of Asian cultivated rice
CC of Common wild rice
?????????????????????????????? DY Dingyings
taxonomic system S Square root GB Growth
habits P Certain fixed percentage
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SSR genetic diversity of rice germplasm resources
in the primary core collection
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Alleles per SSR locus 9-53,23.6 on average
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The number of alleles in the primary core
collection of rice resources
The genetic diversity in the primary core
collection of rice resources
PCC - the primary core collection of rice CWR -
the common wild rice ACR - the Asian cultivated
rice LR - the landraces IRV - the improved rice
varieties
20
0.9459
1
p
Alleles in different PCC (CWR, LR, IRV)
Total alleles
0.9
Specific alleles
0.8
0.6910
0.7
0.5464
0.6
0.5
0.4
0.2891
0.3
0.2
0.1
0.0212
0.0059
0
CWR
LR
IRV
NA per
Range
Population
NA
NAP()
NSA
locus
of NA
CWR
805
94.6
22.4
9-53
246
LR
588
69.1
16.3
3-32
18
Primary core
ACR
IRV
465
54.6
12.9
2-25
5
collection
Subtotal
605
71.1
16.8
3-32
46
Total
851
-
23.6
9-53
-
21
Hierarchical framework of core collection system
22
Dynamic core collections of ACR
Mor-Retention () the ratio of morphological
variations retained SSR-Retention () the ratio
of SSR alleles retained
23
Representation of mini core collection and core
collections to PCC for CWR
24
Representation of dynamic core collections to
reserved collection for ACR
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• Database of Primary Core Collection, Core
  Collections
• Database of 61 phenotypic traits for ACR
• Database of 8 isozymes (17 loci) for ACR
• Database of 36 SSR loci for ACR and CWR
• The technical system and software for
  establishing core collection

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Acknowledgements

• This project was supported by
• Key technologies RD programme
• The National Natural Science Foundation of China
  (NSFC)
• The National Key Basic Research Program (also
  called 973 Program)

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Research members Wang XK, Qiu ZE, Cao YS,
Tang SX, Yang QW, Wei XH, Jiang YZ , Li
DY, Fan ZL, Zhang HL, Pan DJ, Liu X,
Wang MX, Liao DQ, Yu P, Zhang DL, Sun JL,
Qi YW, Liu Y, Li ZC
Research organizations Chinese Academy of
Agricultural Science China National Rice Research
Institute Guangxi Academy of Agricultural
Science Guangdong Academy of Agricultural
Science China Agricultural University