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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. Marker-Trait Association - Four Strategies- . Linkage analysis using biparental or multi-parental populations

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讲 座 提 纲

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  1. 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

  2. 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

  3. 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

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

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

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

  7. Genetic Populations Xu 2010 Molecular Plant Breeding, CABI

  8. Linkage disequilibrium mapping A-allele group 100 B-allele group 80 C-allele group 120 D-allele group 60 Linkage mapping CV1 x CV2 CV1, CV2, CV3, CV4, CV5, … Segregating populations (F2, BC1, F3, RIL, DH, …) A-allele group 100 B-allele group 80

  9. Sequencing-based Genetic Mapping • 直接深度测序，鉴定突变位点。(Plant Physiol, 2010, 153: 652-654) • 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) • 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)

  10. 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

  11. 522 lines Distribution of minor allele frequencies 305 lines XB RIL population Lu et al 2010. PNAS 107:19585–19590

  12. 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

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

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

  15. eQTL Mapping Xu 2010 Molecular Plant Breeding, CABI

  16. Xu 2010 Molecular Plant Breeding, CABI

  17. LD Varies Considering by Locus and Species Species Mating system LD rangea Reference Human Outcrossing Nigerian 5kb Reich et al 2001 European 80kb Reich et al 2001 Cattle Outcrossingb 10cM Farnir et al 2000 Drosophila Outcrossing <1kb Long et al 1998 Maize Outcrossing Diverse maize 1kb Tenaillon et al 2001 Diverse inbreds 1.5kb Remington et al 2001 Elite lines >100kb Rafalski 2002 Arabidopsis Selfing 250kb Nordborg et al 2002 Sugarcane Outcrossing/vegetative 10cM Janno et al 1999 population Rice Selfing xa5 region 100kb Garris et al 2003 sd1 region 220kb Hong et al. person. comm. aThe LD value provided is estimated where r2=0.10 bThere is an extreme sex bias in terms of number of breeding males versus breeding females

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

  19. RZ87 RZ329 RZ403 RG181 RZ166 RZ886 Marker /HindIII /DraI /DraI /DraI /ScaI /XbaI Chromosome 2 2 3 3 7 12 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 Subspecies-Specific Alleles

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