讲 座 提 纲
1 什么是分子育种
2 历史回顾
3 全基因组策略
4 基因型鉴定
5 表现型鉴定
6 环境型鉴定 (etyping)
7 标记-性状关联分析
8 标记辅助选择
9 决策支撑系统
10 展望

- Four Strategies-
 Linkage analysis using biparental or multi-parental populations
 Association (LD) analysis using natural populations
 Comparative analysis using mutated populations and near-isogenic (introgression) lines
 Selective analysis using sub-populations based on selective sweeps

QTL Mapping Methodologies
Based on linkage phase
Linkage mapping
Linkage disequilibrium (LD) or association mapping
Joint linkage-LD mapping
Based on the number of markers
Single-marker-based mapping
Interval mapping
Multiple-marker-based mapping
Based on statistical methods
Analysis of variance (ANOVA)
Multiple regression
Maximum likelihood estimation
Bayesian mapping

Log of Likelihood (LOD) = log
Pr QTL
Pr non-QTL
Xu 2010 Molecular Plant Breeding, CABI

Models for QTL Distribution
Xu 1997 Plant Breed Rev 15:85-139

Relationship between phenotype, genes and environments
Xu 1997 Plant Breed Rev 15:85-139

Genetic Populations
Xu 2010 Molecular Plant Breeding, CABI

Linkage mapping
CV1 x CV2
Segregating populations
(F2, BC1, F3, RIL, DH, …)
6
7
8
4
5
9
10
11
12
13
14
Plant
1
2
3
Marker allele Phenotype
A 100
A
B
102
78
B
A
B
B
A
B
A
A
A
B
B
97
103
77
83
79
101
80
98
81
82
99
A-allele group 100
B-allele group 80
Linkage disequilibrium mapping
CV1, CV2, CV3, CV4, CV5, …
CV5
CV6
CV7
CV8
CV9
Variety
CV1
CV2
CV3
CV4
CV10
CV11
CV12
CV13
CV14
Marker allele Phenotype
A
B
100
78
C
D
120
59
A
D
A
B
C
101
60
99
80
119
D
B
A
B
C
82
61
100
80
121
A-allele group 100
B-allele group 80
C-allele group 120
D-allele group 60

Sequencing-based Genetic Mapping a) 直接深度测序，鉴定突变位点。(Plant Physiol, 2010,
153: 652-654) b) 将极端表型材料进行DNA池，进行深度测序，然后统
计分析两组极端表型材料的深度测序结果，寻找基因。
此种策略一般只能定位主效基因。(Nat Methods,
2009, 6:550-551) c) 对构建的分离群体的每个单株进行测序，确定群体中
每个单株基因型。(Genome Res, 2009, 19: 1068-
1076；PNAS, 2010, 107: 10578-10583)

Joint linkage-Association (LD) Mapping
Why Both linkage and LD-based mapping have advantages and disadvantages; Genetic mapping power can be improved through joint mapping
What Use of materials derived from bi- or multi-parental segregating populations (linkage) and inbred lines (linkage disequilibrium)
How Parallel linkage and LD mapping; Integrated linkage-LD mapping
Lu et al 2010. PNAS 107:19585 –19590

522 lines Distribution of minor allele frequencies
305 lines
XB RIL population
Lu et al 2010. PNAS
107:19585 –19590

NAM (A set of RIL populations with a shared parent)
(Tian et al 2011, Kump et al 2011)
NAM + A panel of germplasm (500-2000)
Ongoing projects in China???
A panel of germplasm + several biparental populations
Lu et al 2010. PNAS 107:19585 –19590
Famoso et al 2011. PLoS Genet. 7(8):e1002221

Nov 29,, 2006, CIMMYT, Mexico
“All-in-one plate”

“All-In-One Plate” Project in CIMMYT
Materials collected
1. 8 RIL populations, each with 60 to 150 lines
2. 5 BIL populations
3. 3 F2 populations
4. 800 Inbreds selected from over 2000 of various sources
Representing 2200 extreme entries or over 6000 entries of entire populations
Traits covered:
1. Drought tolerance (multiple sources)
2. Disease resistance (5)
3. Insect resistance (4)
4. Nitrogen response
5. Grain quality and nutrition (10)
6. Lodging resistance
7. Physiological traits (5)
8. Agronomical traits (5+)

eQTL Mapping
Xu 2010 Molecular Plant Breeding, CABI

Xu 2010 Molecular Plant Breeding, CABI

LD Varies Considering by Locus and Species
Species Mating system LD range a Reference
Human
Nigerian
European
Cattle
Drosophila
Maize
Outcrossing
Outcrossing b
Outcrossing
Outcrossing
5kb
80kb
10cM
<1kb
Diverse maize
Diverse inbreds
Elite lines
Arabidopsis
Sugarcane
1kb
1.5kb
Selfing
>100kb
250kb
Outcrossing/vegetative 10cM
Rice xa5 region sd1 region population
Selfing
100kb
220kb
Reich et al 2001
Reich et al 2001
Farnir et al 2000
Long et al 1998
Tenaillon et al 2001
Remington et al 2001
Rafalski 2002
Nordborg et al 2002
Janno et al 1999
Garris et al 2003
Hong et al. person. comm.
a The LD value provided is estimated where r 2 =0.10
b There is an extreme sex bias in terms of number of breeding males versus breeding females

Factors Affecting Mapping: Population Sizes
Xu 2010 Molecular Plant Breeding, CABI

Subspecies-Specific Alleles
Marker RZ87
/HindIII
Chromosome 2
Indica DGWG
IR20
IR24
IR36
IR64
IR8
Teqing
Wen-Xuan-Qing
Zao-Er-Lu 14
Zhai-Ye-Qing 8
Japonica Ai-Jiao-Jing
Asominori
Gihobyeo
Jing-Xi 17
Nipponbare
P127
Shinriki
Taipei 309
Wase Aikoku 3
Xui-Shui 11
RZ166
/ScaI
2
RZ329
/DraI
3
RZ403
/DraI
3
RZ886
/XbaI
7
RG181
/DraI
12