Presentation Sanwen Huang KLV Main Conference klv 10 nov 2011


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The presentation for KLV jubilee Main Conference, by Sanwen Huang from Caas.

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Presentation Sanwen Huang KLV Main Conference klv 10 nov 2011

  1. 1. To redefine plant breeding with genomics Sanwen Huang KLV125, November 10, 2011 Chinese Academy of Agricultural Sciences Beijing, 100081, China
  2. 2. Two solutions to feed China 1) Better seeds 2) Farm cooperative
  3. 3. Plant breeding contributed >50% of growth in agricultural production.
  4. 4. First generation plant breeding Rice SoybeanWheat BarleySunflower Maize Potato Sorghum ~10,000 years ago
  5. 5. Darwin 1859 Mendel 1865 Morgan 1911 Second generation plant breeding
  6. 6. Borlaug 1950s Yuan Longping 1960s P E R S P E C T I V E S Hybrid maize. Within ten years of Jones’ proclamation,the first breeders were produc- ing successful hybrids.Beginning in the early 1930s, interest in, and demand for, hybrid maize rose steadily among farmers in the United States16 (FIG. 2a). Maize breeders have continually turned out higher-yielding hybrids,year after year17–19 (FIG.2b),and farm- ers have adopted them after cautious trials on their own farms.In 1997,United States maize yields averaged 8 tons hectare–1 , compared with 1 ton hectare–1 in 1930 (REF.20). Hybrids were not entirely responsible for advances in maize yields, however. Starting around the 1950s,the increasingly widespread use of synthetic nitrogen fertilizers, chemical weed killers, and more efficient planting and harvesting machinery also contributed to higher yields17–19,21 . Surprisingly, improvements in heterosis have not contributed to higher yields. Experiments have shown that heterosis (calculated as the difference in yield between a single cross hybrid and the mean of its two inbred parents) is unchanged over the years. The yields of the inbred lines have risen at almost the same rate as hybrid yields22 . It seems that yield gains have come primarily from genetic improvements in tolerance to stresses of all kinds (such as tolerance to disease and insects, dense planting, drought or low soil fertility). The newer hybrids are tougher than their predecessors and shrug off droughts (for example) that would have damaged the older hybrids and devastated their open- pollinated parents. but, to this day, there is no completely satis- factory explanation for the phenomenon of heterosis in maize or in any other species14 . Fortunately, a lack of understanding has never hindered the use of the phenomenon. But in the 1920s, these problems were all in the future. The‘hybrid maize’ enthusiasts were occupied primarily with finding inbreds that made outstanding hybrids. As Without the contributions from the public sector, the commercial maize breed- ers probably could not have succeeded in the early years, for individually they simply did not have enough inbred lines or enough knowledge about how best to make and test hybrids15 . Figure 1 | Detasselling maize plants Detasselling — pulling tassels — is vital for the production of hybrid maize. The detasselled plants are called ‘females’; they will bear the hybrid seed. In the early years, men on foot did the detasselling, as in this photo from the 1930s. In later years, high school boys and girls were recruited to do the job, also on foot. Today, youths are still the chief labour source, but they usually ride in special motorized carriers, thereby increasing the speed and precision of their work. (Image courtesy of Pioneer Hi-Bred International, Inc.) a Figure 2 | Maize hybrids: area planted and Pioneer 1930s 72 | JANUARY 2001 | VOLUME 2 P E R S P E C T I V E S tus as independent seed savers, and even though hybrids as such were looked on as strange new creations of science. Having traced the development of hybrid maize,these and related questions can be addressed. Farmers gave up their status as indepen- dent seed savers because they found by expe- rience that they would profit more by doing so.They were already giving up their status as independent power suppliers on their farms, for example,as they moved from horse power to tractor power and from hand harvest to mechanical maize pickers. Although farmers viewed hybrids as new and strange creations of science, they saw no adverse effects on either their crops or their livestock. It is true that, in the early days, some farmers feared that the abnormally high yields from hybrids would drain the soil of needed fertilizer elements.And there were complaints about some of the first hybrids, to the effect that the kernels were too flinty and hard for cows to chew. Seed companies bred new hybrids to satisfy the second com- plaint, and the first concern turned out to be without foundation if normal soil fertility practices were used. The farmers’primary fear was not that sci- ence might create unmanageable‘monsters’ (today’s widespread point of view), but that scientists claimed more power to help agricul- ture than they really possessed. Public and private breeders.In the early years of the hybrid era, people were undecided about how to deliver hybrids to the farmer. Farmers had the option to produce them on their own farm using single cross parent seed purchased from the agricultural colleges,or to purchase ‘ready to plant’ hybrid seed from farmer cooperatives or from commercial seed companies (FIG.3).All methods were tried,but in the end the seed companies turned out to be the farmers’choice. Once the advantages of hybrids (and the factthatfarmerswouldbuythem)wereshown, seed companies sprang up across the country, especially in the Corn Belt states15 (FIG. 4). Starting with four pioneering companies,the numbers grew exponentially in the 1930s.By 1995, 305 independent companies were involvedwiththeproductionandsaleof hybrid maize seed. As with most industries, a small number of large companies dominated the business,accounting for perhaps 70% of the sales.Despitetheirsmallmarketshare,thesmall companieshaveanimportantroleintheindus- try.Theyprovidean alternativetofarmerswho donotwanttobuyfromthelargercompanies. The exchange of information and breed- ing materials among private- and public-sec- tor breeders changed as the seed industry matured. Almost from the beginning, seed companies kept the pedigrees of their hybrids secret and they soon stopped trading their inbred lines. By about the mid-1930s, all exchange of inbreds and other advanced breeding materials was one-way, from the public to the private sector. The roles of the public- and private-sector breeders also changed. The large companies with strong breeding programmes had increasingly less need for inbreds developed by the public sector,although the smaller compa- nies still depended on them.Over time,‘foun- dation seed companies’were formed expressly to breed inbred lines for lease to the small seed companies,thereby filling the role of the pub- lic-sector breeders.The public-sector breeders in turn shifted their primary emphasis from the development of inbreds and hybrids to studying the theoretical basis for producing improved inbreds and hybrids,as well as other needed aspects of maize-breeding research. The relationship between public and pri- vate sector breeders still remains close; they have mutually supportive roles in the nation’s maize breeding programme. Consequences of hybrid maize Acceptance.In the opening paragraphs of this article I asked why the maize hybrids were accepted without public outcry in the 1930s, even though farmers had to give up their sta- An important change in hybrid seed production and performance was, in a sense, a byproduct of the increases in inbred yield. By the 1960s, the newest inbreds were so high-yielding that it became practical to use them as seed par- ents, and so to produce single cross hybrids for sale. The best single crosses always yielded more than the best double crosses but, as noted earlier, commercial produc- tion of single cross hybrids was not feasible in the first decades of hybrid maize breed- ing because of the low yield potential of inbreds from that era. Figure 3 | The introduction of hybrid maize seeds. The ‘seed corn companies’ effectively and energetically introduced hybrid maize to cautious farmers. They recruited well-known and respected farmers as part-time salesmen, working on commission. They gave small amounts of free seed of new hybrids to farmers and encouraged the prospective customers to compare them with their present varieties on their own farms and using their own farming methods. The salesman and/or his supervisor often would help the farmer harvest the comparison. In the process, the sales people learned about the farmers’ needs and desires in maize hybrids, which they passed on to the breeders. So, the relationship between farmers and seed companies from the beginning was almost on a neighbour to neighbour basis. The relationship remains much the same today, with modifications because of the changing nature of farming and farmers (much larger scale, more advanced technologically and more business-like). Image courtesy of Pioneer Hi-Bred International, Inc. Figure 4 | Maize quality control in the early years. The fledgling seed companies devised a ‘sorting belt’, allowing inspectors to examine every ear before shelling. They wanted to be sure the seed ears were free of damage from disease or insects, and of the right type. Women replaced men in many of the seed production operations during the Second World War, when young men were in the armed services. Image courtesy of Pioneer Hi-Bred International, Inc. © 2001 Macmillan Magazines Ltd Second generation plant breeding
  7. 7. Plant Breeding the art and science of changing the genetics of plants for the benefit of humankind.
  8. 8. Watson and Crick, 1953 Human Genome, 2001 Rice genome, 2002 Third generation plant breeding
  9. 9. New tech 600Gb per run
  10. 10. 0" 10" 20" 30" 40" 50" 60" 70" 80" 1999" 2000" 2001" 2002" 2003" 2004" 2005" 2006" Gb"Produc4on"by"year" 0" 200" 400" 600" 800" 1,000" 1,200" 1,400" 1,600" 1,800" 1999" 2000" 2001" 2002" 2003" 2004" 2005" 2006" 2007" 2008" Gb" Gb"Produc5on"by"year" 0" 2,000" 4,000" 6,000" 8,000" 10,000" 12,000" 14,000" 16,000" 18,000" 20,000" 1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"2009" Gb" Gb"Produc5on"by"year" to 100,000 in 2010 100,000 Gb 2010Sequence in database
  11. 11. ~100,000X! $0.1 $0.20/Mb! $20,000/Mb! Cost of Sequencing ($ per million bases) ! Moore’s Law! Sequencing! Sequencing goes faster than the Moore’s law
  12. 12. What does this mean to plant breeding? We can transform plant breeding from craftsmanship to informatics. It is like to turn on light in a dark room.
  13. 13. The Cucumber Genome EDITORIAL NATURE GENETICS | VOLUME 41 | NUMBER 12 | DECEMBER 2009 1259 Cool as a cucumber The genome of the seventh plant to be sequenced, Cucumis sativus L., was assembled using the conventional long- read Sanger sequencing and higher-throughput short-read technology. This genome is the entry point for exploring the diversity and function of the Cucurbitaceae family of agriculturally important plants. Its compact genome, without evidence of recent duplication, will be useful in comparative analysis of plant genome evolution. A gain and again Charles Darwin found inspiration in the cucumber and its fellow cucurbits. The first trait to strike him was the unplantlike motility of the vine’s tendrils, organs adapted to the habits of climbing and running. Use resulted in adaptation, disuse in diversification and loss. In the varieties which grow upright or do not run and climb, the tendrils, though useless, are either present or are represented by various semi-monstrous organs, or are quite absent. Then he noted the diversification of marrow, gourd and melon fruit forms under agricultural selection and pondered the irreducible essence of species identity. He decided to trust the biological species concept, namely that different species cannot produce fertile offspring. If we were to trust to external differences alone, and give up the test of sterility, a multitude of species would have to be formed out of the varieties of these three species of Cucurbita. Having a biological definition of species identity, Darwin was then able to unravel the relationship between species and apparently stable, taxonomically important traits without fear of arguing in a circle. He contrasted these traits with variable features found within a species. He was also able to identify convergent evolution under selection of the fruit morpholo- gies of distinct species of melons and cucumbers (C.R. Darwin, The Variation of Animals and Plants under Domestication 1st edn., 2nd issue, vol. 1, John Murray, London, 1868). Now, on p 1275, Sanwen Huang et al. report the de novo assembly and annotation of the 243.5-Mb genome of the “Chinese long 9930” inbred line of cucumber and the use of a linkage map in the assembly process to tie the assembled contigs to the chromosomes. The Illumina GA technology has proven practical, so now many diverse lines can be rapidly sequenced to enable marker-assisted breeding of high-yield- ing, disease-resistant, and fresh green-scented cucumbers, along with melons, squash and pumpkins. Cucumber and melon diverged 4–7 million years ago, and C. sativus carries chromosome fusions that distinguish the cucumber karyotypes from those of melon (C. melo) and a more distant relative, the watermelon (Citrullus lanatus).Were he here today, Darwin could see that these sets of chromosomes physically reinforce the biological species barrier to fertility, were the (widely varying) sexual systems of the plants to per- mit crossing. What would Charles do next, equipped with genomes? No doubt he would be most intrigued to compare the genesis of the woody and non-woody tendrils of grapevine and cucum- ber, respectively. Then he might scan for signatures of plant- human coadaptation during the domestication processes of early agricultural humans. Then he might travel to investi- gate the adaptations contributing to the success of Cucumis dipsaceus, the wild spiny cucumber originating in Eastern Africa that is now invading the Galapagos Islands he once explored. ©2009NatureAmerica,Inc.Allrightsreserved.
  14. 14. CuGI-an international effort to unlock the genetic potential of an important vegetable using novel genomic technology Consortium building
  15. 15. Northern China Cuke 100-to reveal general pattern of genetic diversity, recombination, and selection in cucumber C. s. xishuangbanna C. s. hardwickii American Slices Southern China US processing Japan Fresh EU greenhouse Xin Liu
  16. 16. 86 G8 91 98 27 97 95 201 107 94 101 G6 G17 G3 G2 G16 G4 G15 G14 108 103 93 89 120 102 99 96 100 90 30 28 31 3 29 104 4 105 G13 106 1 115 43 116 112 37 111 8 110 109 11 10 7 44 G5 G12 5 40 113 45 G7 G10 G9 36 13 114 35 32 9 6 19 2 22 87 82 81 85 80 79 G11 84 66 74 83 77 71 69 75 72 78 70 68 65 76 51 50 21 92 20 23 18 17 118 117 16 15 14 12 49 88 0.02 0.27 Indian Xishuangbanna Eurasian East Asian Indian Indian Xishuangbanna Eurasian East Asian a. b. c. d. 120 cucumbers sequenced, 4M SNPs discovered wild semi-wild cultivated cultivated
  17. 17. The genomics of plant breeding -Variation intraspecific variation interpecific variation, pan genome protein coding/non coding RNA epigenetic variation/miRNA EMS mutation library-reseq - Selection Allele frequency Ka/Ks - Recombination LD HapMap Recombination hotspots Historical crossover in cucumber breeding - Genetic drift
  18. 18. Green Genetics round table, 2008
  19. 19. 中国农业科学院蔬菜花卉研究所 Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Bernard de Geus
  20. 20. The Potato Genome OUTLOOK Alzheimer’s disease NATURE.COM/NATURE 14 July 2011 £10 Vol. 475, No. 7355 HISTORY PURE JOY Arcane mathematics that changed the world PAGE166 EVOLUTION GIANT DINOSAURS Seeds of greatness in small sauropod ancestors PAGE159 NEUROSCIENCE SPINAL CORD REGENERATION Restoring breath control after neck injury PAGES178 &196 THEPOTATO GENOME sauropod ancestors PAGE159 The DNA sequence of the South American tuber eaten around the world PAGE189 THE INTERNATIONAL WEEKLY JOURNAL OF SCIENCE Cover 14 July.indd 1 08/07/2011 17:39 ARTICLE doi:10.1038/nature10158 Genome sequence and analysis of the tuber crop potato The Potato Genome Sequencing Consortium* Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. Potato (Solanum tuberosum L.) is a member of the Solanaceae, an economically important familythatincludes tomato, pepper, aubergine (eggplant), petunia and tobacco. Potato belongs to the asterid clade of eudicot plants that represents ,25% of flowering plant species and fromwhich a complete genomesequence has not yet,toour knowledge, been published. Potato occupies a wide eco-geographical range1 and is uniqueamongthemajorworldfoodcropsinproducingstolons(under- ground stems) that under suitable environmental conditions swell to formtubers.Itsworldwideimportance,especiallywithinthedeveloping world, isgrowing rapidly, with production in 2009 reaching 330 million tons ( The tubers are a globally important dietary source of starch, protein, antioxidants and vitamins2 , serving the plant asbotha storageorgan andavegetativepropagationsystem.Despitethe importance of tubers, the evolutionary and developmental mechanisms of their initiation and growth remain elusive. Outside of its natural range in South America, the cultivated potato is considered to have a narrow genetic base resulting originally from limited germplasm introductions to Europe. Most potato cultivars are autotetraploid (2n 5 4x 5 48), highly heterozygous, suffer acute inbreeding depression, and are susceptible to many devastating pests and pathogens, as exemplified by the Irish potato famine in the mid- nineteenth century. Together, these attributes present a significant barrier to potato improvement using classical breeding approaches. A challenge to the scientific community is to obtain a genome sequence that will ultimately facilitate advances in breeding. To overcome the key issue of heterozygosity and allow us to gen- erate a high-quality draft potato genome sequence, we used a unique homozygous form of potato called a doubled monoploid, derived using classical tissue culture techniques3 . The draft genome sequence from this genotype, S. tuberosum group Phureja DM1-3 516 R44 (hereafter referred to as DM), was used to integrate sequence data from a heterozygous diploid breeding line, S. tuberosum group Tuberosum RH89-039-16 (hereafter referred to as RH). These two genotypes represent a sample of potato genomic diversity; DM with its fingerling (elongated) tubers was derived from a primitive South American cultivar whereas RH more closely resembles commercially cultivated tetraploid potato. The combined data resources, allied to deep transcriptome sequence from both genotypes, allowed us to explore potato genome structure and organization, as well as key aspects of the biology and evolution of this important crop. Genome assembly and annotation We sequenced the nuclear and organellar genomes of DM using a whole-genome shotgun sequencing (WGS) approach. We generated 96.6 Gb of raw sequence from two next-generation sequencing (NGS) platforms, Illumina Genome Analyser and Roche Pyrosequencing, as well as conventional Sanger sequencing technologies. The genome was assembled using SOAPdenovo4 , resulting in a final assembly of 727 Mb, of which 93.9% is non-gapped sequence. Ninety per cent of the assembly falls into 443 superscaffolds larger than 349 kb. The 17- nucleotide depth distribution (Supplementary Fig. 1) suggests a gen- ome size of 844 Mb, consistent with estimates from flow cytometry5 . Our assembly of 727 Mb is 117 Mb less than the estimated genome size. Analysis of the DM scaffolds indicates 62.2% repetitive content in the assembled section of the DM genome, less than the 74.8% esti- mated from bacterial artificial chromosome (BAC) and fosmid end sequences (Supplementary Table 1), indicating that much of the unas- sembled genome is composed of repetitive sequences. We assessed the quality of the WGS assembly through alignment to Sanger-derived phase 2 BAC sequences. In an alignment length of ,1 Mb (99.4% coverage), no gross assembly errors were detected (Supplementary Table 2 and Supplementary Fig. 2). Alignment of fosmid and BAC paired-end sequences to the WGS scaffolds revealed limited (#0.12%) potential misassemblies (Supplementary Table 3). Extensive coverage of the potato genome in this assembly was con- firmed using available expressed sequence tag (EST) data; 97.1% of 181,558 available Sanger-sequenced S. tuberosum ESTs (.200 bp) were detected. Repetitive sequences account for at least 62.2% of the assembled genome (452.5 Mb) (Supplementary Table 1) with long terminal repeat retrotransposons comprising the majority of the transposable element classes, representing 29.4% of the genome. In addition, subtelomeric repeats were identified at or near chromo- somal ends (Fig. 1). Using a newly constructed genetic map based on 2,603 polymorphic markers in conjunction with other available *Lists of authors and their affiliations appear at the end of the paper. 0 0 M O N T H 2 0 1 1 | V O L 0 0 0 | N A T U R E | 1
  21. 21. Potato Genome Sequencing Consortium 14 countries and 28 institution
  22. 22. High-profile visit from Wageningen, 2005
  23. 23. 2005年工作总结 • 艾菲特·雅可布森(Evert Jacobsen)教授 荣获2005年度中国国际科技合作奖,由温家 宝总理在全国科技大会宣布。 中国驻荷兰大使薛捍勤女士向雅可布森夫妇表示祝贺! Prof. Evert Jacobsen got his big award, 2006
  24. 24. 1)Dicot evolution Rosids Asterids 25% flower plants Asterid-specific genes: 2,642 Potato-specific: 3,372
  25. 25. 2) Genomic basis of inbreeding depression Potato suffers acute inbreeding depression that likely involve thousand genes DM: 1X RH: 2X
  26. 26. 3) Tuber biology Supplementary Figure 9. Proposed roles of FT homologues in potato. A, Simplified Arabidopsis pathway, redrawn according to Michaels (ref. 57 in Supplemental Text). B, Proposed potato pathway. SP3D regulates flowering time, SP6A regulates tuber initiation and SP5G represses sprouting. A functional homolog of FD-L exists in potato (S. Prat, personal communication). B. Proposed potato pathway WWW.NATURE.COM/NATURE | 22 Genes for tuber biotic resistance and tuber initiation and sprouting Prat et al., Nature 2011
  27. 27. “The breakthrough holds out the promise of boosting harvests of one of the world's most important staple crops.” “...this is a first big step for scientists as well as political leaders anxiously watching the vagaries in the world's food supply.” Press coverage
  28. 28. Traditional potato breeding 10-12 years 1,000,000 100,000 40,000 4,000 1,000 250 40 20 4 1
  29. 29. Genomics-based breeding 4-6 years 12 trait genes/cross 1,000,000 250 20 1 • sow seeds in vitro • type trait genes • multiply candidadate 0.5 year • field observation • more disease test • more quality analysis 1.5 year • yield stableness test • multiply seed potato2-4 year
  30. 30. “One potato genome unravelled, three to go!” Tetraploid genome sequencing remains a huge challenge
  31. 31. Ally for true potato seeds to create a potato propagated and bred in a tomato way A new paradigm in potato breeding Pim Lindhout EAPR meeting, OULU, Finland July 25th, 2011 EAPR meeting, OULU, Finland novomeinnovative agriculture Mr. GeertVeenhuizen, may you rest in peace!
  32. 32. 100+ plant species: from algae to angiosperm, including 60 major crops, evolutionary continuum of each gene family. 100+ genotypes/species: core collections, major version of genetic variation 100 x 100 Plant Genome Project
  33. 33. Tree of plant kingdom 95% Arable land
  34. 34. Paradigm shift for plant biology
  35. 35. Major ag-biological questions 1. C4 photosynthesis 2. N2 fixation 3. Seed and flower development 4. Heterosis
  36. 36. C4 1. C4 photosynthesis C3
  37. 37. 2. N2 fixation with Prof.Ton Bisseling Understanding symbiosis by evolutionary genomics!
  38. 38. 3. Seed and flower development Out of the past. Tiny Amborella sits at the bottom of the angiosperm family tree. Seed Flower
  39. 39. 4. Heterosis
  40. 40. Now: 7B 2050: 9B To the expanding world’s population requires innovation!
  41. 41. Redefine Plant Breeding NEW: the science and technology of optimizing the genome of plants for the benefit of humankind OLD: the art and science of changing the genetics of plants for the benefit of humankind.
  42. 42. Rice 3.0 High partition in seeds N2 fixation + drought tolerance C4 photo- synthesis Strong heterosis Durable resistance, less pesticide
  43. 43. “The people who are crazy enough to think they can change the world, are the ones who do. ”
  44. 44. The education centre of the third generation of plant breeders