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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. Whole Genome Strategies: Concept . Whole genome sequence and high dense molecular markers.

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slide1

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

slide2

Whole Genome Strategies: Concept

Whole genome sequence and high dense molecular markers

All internal and external environmental factors

G

E

Whole

Genome

Strategies

A representative or complete set of genetics and breeding

germplasm

P

M

Precision phenotyping at multi-locations

slide3

Whole genome strategies V.1

Conference presentation

Third International Conference on Plant Molecular Breeding, September 5-9, 2010, Beijing, China

Xu et al. 2012. Molecular Breeding 29:833-854

Whole genome strategies for marker-assisted plant breeding.

Whole genome strategies V.2

Conference presentation

4th International Workshop on Next Generation Genomics and Integrated Breeding for Crop Improvement, ICRISAT, Patancheru. India, February 19-21, 2014

slide4

Factors Affecting Whole Genome Strategies

  • Genome coverage (all omics, DNA, RNA, protein, and coverage of each ome
  • Sequences, markers, haplotypes
  • Breeding populations: type, size, and structure
  • Whole profile of phenomics
  • All traits (coverage)
  • Trait components (dissection)
  • Germplasm representativeness : ecotypes, diversity, trait donors, origins
  • Precision of phenotyping
  • Phenotyping protocols
  • GE interaction and etyping
  • E-dependent traits: e.g., abiotic stresses
  • Selection methods
  • GS, MARS, haplotype-assisted selection, index-based selection, computation and simulation, best combinations
  • Decision support system
slide5

Maize Haplotype Maps

Maize HapMap I

27 diverse maize lines

Array-Maize SNP50 developed

56,110SNPs chosen from >840,000 SNPs

Covering 2/3 predicted genes

Gore et al 2009 Science 326: 1115-1117

Maize HapMap II

103 maize lines and relatives

55M SNPs identified

Chia et al 2012 Nature Genetics

slide7

Genomic Gaps Left by First Generation Sequencing

  • Single genomes that have been sequenced up to 80-90% are used as reference genomes
  • In most cases, only one genotype has been sequenced with relatively high resolution, usually representing a domesticated elite variety
  • Resequencing indicates that 20-50% of the original reads from different ecotypes cannot be mapped to the reference genome

50% Hi-seq reads from tropical maize cannot be mapped; while only 20% of the SNPs from landraces can be mapped to the B73 reference (Peter Wenzel, CIMMYT)

Maize

Rice

75% of the rice germplasm are indica, and 15-20% of their sequence reads cannot be mapped to the Japonica reference (Kenneth McNally, IRRI)

slide8

Maize Genetic Variation

Under-represented by the B73 Reference Genome

Teosinte

Maize landrace

Tropical maize

Temperate maize

B73

B73 reference

A diagram showing genetic variation under-represented by the B73 reference genome, compared with different maize germplasm and their wild relative teosinte.

slide9

The Results of Partial Genome Coverage

  • Single-genome based references provide only a partial genome coverage for a crop species
  • Got lost in map-based cloning
  • Missing of 40% or more important QTL/genes
  • Biased estimation (Ascertainment bias)
  • Genetic diversity
  • ‘Population structure
  • LD and IBD
  • Haplotypes
  • MAS
  • Inefficient procedures
  • Unpredictable results

Multiple genome-based references are needed for whole genome strategies

slide10

Three 1000X Genomes to Fix the Bias

1000 genotypes each at 1X

Good Representativeness

Single marker overlapping

100 genotypes each at 10X

Representativeness + Depth

10 genotypes each at 100X

Good Depth

Multiple marker contigs

slide11

Maize HapMaps 3 and Beyond

Multiple-genome based HapMaps

=> multiple/novel alleles at loci covered by the single references

+

multiple alleles at loci not covered by the single references

=> Unbiased chip

HapMaps 3

Ed Buckler, Personal Comm.

825 inbreds with sequence data from different sources

83 deep-resequencedinbreds from CAAS-BGI-CIMMYT)

GBSed NAM and CIMMYT inbreds and populations

NAM = Nested Association Mapping

slide12

Unlocking Tropical Maize Genomes

through Deep Resequencing and Linkage Mapping

P3

P3

P6

P6

P4

P6

P5

P3

P5

P1

P4

P1

P4

P1

P2

P3

Linkage mapping

P2

P6

Tropical maize genome

Deep sequencing

A diagram showing how genetic gaps can be filled in the tropical maize genomes that are not covered by the B73 reference genome

slide13

Key FactorsAffecting of Whole Genome Strategies

Marker Density

Average and maximum distance expected between markers on a linkage map dependingon number of random markers mapped for a genome with 1200 cM, e.g. 12 chromosomes of 100 cMeach(Tanksley et al. 1988).

slide14

Marker Density Determines Mapping Outputs

15cM

1 cM

0.001 cM

Gene mapping

Rough mapping

Fine mapping

Revised from Xu et al (2010) 5th International Crop Science Congress

slide15

Key FactorsAffecting of Whole Genome Strategies

PopulationSize

Maximum detectable and minimum resolvable map distances between markers utilizing backcross (BC) and F2 populations (Tanksley et al. 1988)

slide16

Effect on QTL detection power (proportion of real QTL detected) of increasing population size for QTL contributing 0.5% to 5.0% of the total phenotypic variation of the target trait (Yan et al 2011)