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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6 环境型鉴定 (etyping)
Whole genome sequence and high dense molecular markers
All internal and external environmental factors
A representative or complete set of genetics and breeding
Precision phenotyping at multi-locations
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
4th International Workshop on Next Generation Genomics and Integrated Breeding for Crop Improvement, ICRISAT, Patancheru. India, February 19-21, 2014
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
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)
75% of the rice germplasm are indica, and 15-20% of their sequence reads cannot be mapped to the Japonica reference (Kenneth McNally, IRRI)
Under-represented by the B73 Reference Genome
A diagram showing genetic variation under-represented by the B73 reference genome, compared with different maize germplasm and their wild relative teosinte.
Multiple genome-based references are needed for whole genome strategies
1000 genotypes each at 1X
Single marker overlapping
100 genotypes each at 10X
Representativeness + Depth
10 genotypes each at 100X
Multiple marker contigs
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
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
through Deep Resequencing and Linkage Mapping
Tropical maize genome
A diagram showing how genetic gaps can be filled in the tropical maize genomes that are not covered by the B73 reference genome
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).
Revised from Xu et al (2010) 5th International Crop Science Congress
Maximum detectable and minimum resolvable map distances between markers utilizing backcross (BC) and F2 populations (Tanksley et al. 1988)
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)