Download Understanding Domestication and Breeding by

Understanding Domestication and Breeding
by Sequencing
Shancen Zhao
BGI-Shenzhen
The Chinese University of Hong Kong
OUTLINE
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Sequencing trends
Footprints of domestication
Modern breeding platforms
A case of rice project
The Genomic Revolution
Haemophilus influenzae was the first organism with its genome decoded
in 1995.
Within less than 20 years, tens of thousands of genomes were decoded
or will be decoded in coming years
http://seedmagazine.com/interactive/genome/
1998 2000
2001
2002
2004
2006
2007
2008
2009
2010
2011
2012
Difficulties for de novo assembly
 High level of heterozygosity
 Abundance of repetitive sequences
 Large genome size
 Polyploidy
Features by K-mer analysis
Features
Common
genomes
Complex
genomes
Genome size
≤3Gb
>3Gb
Chromosome
ploidy
Haploid or
Polyploidy
homozygous
diploid
Heterozygosity <0.5%
>0.5%
Repetitive
contents
<50%
>50%
GC contents
35%-65%
<35% or >65%
Satisfy all
Satisfy either
Modern Trans-Omics
Genomics & Transcriptomics & Proteomics combinational analysis
Generally speaking, the path of sequencing to practice is like
this:
 Genome scale-At this stage we focus on the quality of the
genomes, from draft to high quality to complete;
 Population scale-we mine the variations in the populations,
elucidate their features;
 Panel scale-we prepare enough data, detect the relationsh
ip between genotype and phenotype, the interaction of gen
otype and environment, from which, we redesign the marke
r assistant selection or genome selection, to make the bree
ding easier and better.
Current plant and animal studies (part)
MAS/GS
Bovine
Potato
Pigs
Rice
GxPxE
Maize
Soybean
Variations
Sorghum
Wheat
Sequences
Scales
>1
>100
>1000
>10000
>>10000
OUTLINE
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Sequencing trends
Footprints of domestication
Modern breeding platforms
A case of rice project
What is domestication
 Domestication is a complex evolutionary process in
which human use of plant and animal species leads
to morphological and physiological changes that
distinguish domesticated taxa from their wild
ancestors.
 For example
Maize, Rice, Wheat, Tomato, and so forth.
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 Darwin’s evidence
 Homo special?
Some fungal species have been domesticated by ants
and beetles.
 Plant-animal co-evolution
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The Domestication Syndrome
 Larger fruits or grains, more robust plants
 More determinate growth or increased apical dominance
 Loss of natural seed dispersal so that seeds remain attache
d to the plant for easy harvest
 Crops often have fewer (although larger) fruits or grains.
 A variety of physiological changes are also involved. These
include a loss of seed dormancy, a decrease in bitter
substances in edible structures, changes in photoperiod
sensitivity, and synchronized flowering.
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Domestication syndrome
Multiple vs. single
stalk
tb1
Enclosed vs. naked
grain
sh4
Shattering vs. solid
panicle of grain
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Doebley et al 2006
Effect of population bottleneck
LD increased
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Hamblin et al 2011
Selective sweep: inheritance of regions around
adaptive alleles
Andersson and Georges, Nature
Reviews of Genetic 5: 202-212
(2004)
Extent of selective sweep for domestication in MAIZE: tb1 locus (60 to
90-kb) (Clark et al. 2004), Y1 locus (about 600-kb) (Palaisa et al. 2004)
The case of soybean
Elite
Landrace
G. max
Elite
+
Wild
G. soja =
Landrace
Subgenus Soja
Wild
The yield, height, growth habit greatly changed during domes
tication and following improvement.
Regional/genic diversity reduced due to artificial selection
Wild
Yield related
100-seed weight,
prostrate habit
Quality related
protein、lipid content
Yamasaki et al. The Plant Cell, 2005 17: 2859–2872
Diversity and domestication
Li. et al. BMC Genomics (2013).
Key findings
 Early domestication: 928 genes;
 Intensive breeding: 1106 genes;
 In total, 3.01% of the whole soybean genomic regions
and 4.40% of total annotated genes were impacted b
y artificial selection for agricultural traits;
 A multiple-allele I locus, which was an unusual cluster
arrangement of chalcone synthase (CHS) genes,
showed a strong selection signal;
 Most changes happened in regulation regions;
Distribution of selected genes and regions
Accumulation of domestication and improvement genes in
different pathways of KEGG (χ2 test, P<0.05)
OUTLINE
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Sequencing trends
Footprints of domestication
Modern breeding platforms
A case of rice project
Natural and Artificial Crop Populations
DS
Phenotyping Platform
Genotyping Platform
Environments
Genotyping of Core Materials
Water
Chip-based array
Large-Scale Multi-Location Phenotyping
Yield and quality
Light
Genotyping by sequencing
Biotic and abiotic stresses
Temperature
Transcriptome and proteome analysis
Input use efficiency
Fertilizer
DS
Soil DS
DS
DS
Breeding Informatics Platform
Marker Development
Information Collection, Management and D
ata Analysis
and Gene Discovery
DS
Genetic diversity analysis
DS
Decision
Support S
ystem
Gene function analysis
GWAS/GS/MARS/MAS
DS
Generation Advancement + GS/MARS/MAS
DS
Multi-Environmental Trials
DS
Novel Germplasm
Xu et al. 2012 Mol Breed
 Whole genome strategy
 Genotyping
 Phenotyping
 Environment (E-) typing
 Marker-trait association
 Marker assistant selection
Whole genome
All genomic and
sequence and high
environmental
dense molecular
factors
markers
Whole
Genome
Strategies
A representative
or complete set of
genetics and breed
ing germplasm
Precision phenotyping
at multi-locations
Marker density determines mapping outputs
15cM
Rough mapping
1 cM
0.001 cM
Fine mapping
Gene mapping
Revised from Xu et al (2010)
Population size
Yan et al 2011
Effect on QTL detection power (proportion of real QTL detected)
of increasing population size for contributing 0.5% to 5.0% of the
total phenotypic variation of the target trait
Selection Methodology
Genetic gains achieved for oil and protein content in 100
generations of selection (Dudley and Lambert 2004)
Can we achieve the same result in less years with marker-assisted plant breeding?
Systems
From gels to chips and sequencing (GBS)
Throughput
From singles to millions
Resolution
10-30 cM to many markers per gene
Cost (per data point)
Several US dollars to 1/1000 cent
Sequencing Everything !!
De Novo sequencing to generate reference sequence map(s)
Resequencing to discover SNPs, haplotypes and tag SNPs
Tag SNPs can be developed to represent haplotypes. Each tag
SNP represents one haplotype fragment.
A set of tag SNPs can be developed to represent whole genome
diversity.
- 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
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 se
gregating 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
OUTLINE




Sequencing trends
Footprints of domestication
Modern breeding platforms
A case of rice project
Decoding hybrid rice in China
What is super hybrid rice ?
For High yield
Crossing within or between
indica and japonica.
Super rice breeding
program in 1996.
Population Sequencing and Linkage Map Construction
Schematic overview of the parents–RIL system construction and
the map of genome-wide graphic genotypes
Assembly of Parental
Genomes Using RIL
Population
Comparative Analysis of Three Rice Genomes
Detection and Analysis Using the LYP9 RIL Population
Fine-Mapping of QTLs
for Yield-Associated
Traits
Acknowledgements
 BGI-Shenzhen
Chi Zhang, Dong Li, Yong Tao, Junyi Wang, Jianwen Li, Jianbo Jian, et al;
 Institute of Crop Science, CAAS
Prof. Lijuan Qiu, Yinghui Li, et al;
Prof. Yunbi Xu;
 China National Rice Research Institute, CAAS
Prof. Qian Qian, Zhenyu Gao, et al;
 My Supervisor in CUHK
Prof. Hon-Ming Lam;
Thank you!