讲 座 提 纲讲 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

 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 Marker-Trait Association - Four Strategies-

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 QTL Mapping Methodologies

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

Genetic Populations Xu 2010 Molecular Plant Breeding, CABI

Linkage mapping VarietyMarker allelePhenotype CV1A100 CV2B78 CV3C120 CV4D59 CV5A101 CV6D60 CV7A99 CV8B80 CV9C119 CV10D82 CV11B61 CV12A100 CV13B80 CV14C121 PlantMarker allelePhenotype 1A100 2A102 3B78 4B79 5A101 6B80 7A98 8B81 9B82 10A99 11A97 12A103 13B77 14B83 A-allele group 100 B-allele group 80 CV1 x CV2 Segregating populations (F2, BC1, F3, RIL, DH, …) CV1, CV2, CV3, CV4, CV5, … A-allele group 100 B-allele group 80 C-allele group 120 D-allele group 60 Linkage disequilibrium mapping

Sequencing-based Genetic Mapping a) 直接深度测序，鉴定突变位点。 (Plant Physiol, 2010, 153: ) 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: ) 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: ； PNAS, 2010, 107: )

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 PNAS 107:19585–19590

Distribution of minor allele frequencies 522 lines 305 lines XB RIL population Lu et al 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 ( ) Ongoing projects in China??? A panel of germplasm + several biparental populations Lu et al PNAS 107:19585–19590 Famoso et al PLoS Genet. 7(8):e Three Combinations

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

Materials collected 1.8 RIL populations, each with 60 to 150 lines 2.5 BIL populations 3.3 F2 populations Inbreds selected from over 2000 of various sources 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+) Representing 2200 extreme entries or over 6000 entries of entire populations “All-In-One Plate” Project in CIMMYT

eQTL Mapping Xu 2010 Molecular Plant Breeding, CABI

LD Varies Considering by Locus and Species Species Mating systemLD range a Reference HumanOutcrossing Nigerian5kb Reich et al 2001 European80kb Reich et al 2001 Cattle Outcrossing b 10cM Farnir et al 2000 DrosophilaOutcrossing<1kb Long et al 1998 MaizeOutcrossing Diverse maize1kb Tenaillon et al 2001 Diverse inbreds1.5kb Remington et al 2001 Elite lines>100kb Rafalski 2002 Arabidopsis Selfing250kb Nordborg et al 2002 SugarcaneOutcrossing/vegetative10cM Janno et al 1999 population RiceSelfing xa5 region100kb Garris et al 2003 sd1 region220kb 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

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