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Understanding Domestication and Breeding by Sequencing Shancen Zhao BGI-Shenzhen The Chinese University of Hong Kong OUTLINE 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 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. 9 Darwin’s evidence Homo special? Some fungal species have been domesticated by ants and beetles. Plant-animal co-evolution 10 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. 11 Domestication syndrome Multiple vs. single stalk tb1 Enclosed vs. naked grain sh4 Shattering vs. solid panicle of grain 12 Doebley et al 2006 Effect of population bottleneck LD increased 13 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 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!