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

Marker-Trait Association

- 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

Three Combinations

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