讲 座 提 纲

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. 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

3. 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

4. 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

5. 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

6. Distribution of SNP and gene density in HapMap1 and HapMap2.

7. 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)

8. 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.

9. 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

10. 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

11. 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

12. 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

13. 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).

14. 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

15. 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)

16. 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)