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THEME – 4 Genomic diversity of domestication in soybean
This document summarizes research on the genomic diversity of soybeans during domestication. It finds: 1) Wild soybeans (G. soja) show more genetic diversity than cultivated soybeans (G. max) due to bottlenecks during domestication and breeding. 2) Analysis of 7 G. soja genomes reveals a pan-genome structure with a large dispensable/variable gene set involved in environmental responses. 3) Comparison of G. soja and G. max genomes identified several million SNPs, indels, and presence/absence variants affecting genes related to domestication traits.
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THEME – 4 Genomic diversity of domestication in soybean
- 1. Genomic diversity ofdomestication in soybean Institute of Crop Science Chinese Academy of Agricultural Sciences Li-juan Qiu International Workshop on “Applied Mathematics and Omics Technologies for Discovering Biodiversity and Genetic Resources for Climate Change Mitigation and Adaptation to Sustain Agriculture in Drylands” IAV Hassan II – Rabat - Morocco, 24-27 June 2014
- 2. 1. Background 2. Geneticdiversity of G. soja and G. max 3. Pan-genome of G. soja 4. Genomic variation between G. sojas and GmaxW82 5. Selection genes during domestication Outline
- 3. Glycine Soja Glycine 26 perenialwild species (mainly in Australia) Annual wild soybean (G.soja) (East Asia) Cultivated soybean (G. max) (Worldwide) Leguminosea, Papilollateae, Glycine 1. Background
- 4. G. soja G. max Landrace G.max Modern Cultivars Domestication Improvement Glycine soja - the wild relative of cultivated soybean G. max S econdary G ene Pool GP-2 unknown Tertiary Gene Pool GP-3 Wild perennial species Tertiary Gene Pool GP-3 Wild perennial species From: Harlan and deWet (1971) Two bottlenecks: domestication and breeding
- 5. G. soja G. maxvs G. soja Plant — Plant height — Growth habit Seed — Size — Color — Pod dehiscence Physiological trait — Protein content — Oil content Modern cultivar
- 6. Genetic variation controlledthe difference The variation of soybean genome during domestication Genetic variation, e.g. SNP, InDel, PAV, CNV Domestication trait related gene The genetic variation between wild and cultivated soybean ？ Domestication related traits The genetic variation between wild and cultivated soybean ？ Domestication related traits
- 7. The historyof soybean cultivation are more than 4500 years since agricultural ancestor Houji, who planted five crops including soybean. According to word record, the earlist name of soybean was “shu” in “The Book of Odes”. The other languages of soybean in the world are was translated from the “shu”. Cultivated soybean is native to China
- 8. China owns themost of soybean germplasms More than 170,000 soybean accessions are in germplasm collections. Among them, 45,000 accessions are unique (Carter et al. 2004) More than 23,000 cultivated and 7,000 soybean accessions are conserved in Chinese National Gene bank (CNGB).
- 9. Constructing different levelof core collections Qiu et al 2003，Scientia Agricultura Sinics; Qiu et al 2009, PMB 2013 Core collection: represent the genetic diversity of a crop species and its relatives with a minimum of repetitiveness Primary core collection Basic collection Core collection AAAABBBB CCCCDDDDEEEE FFFGGGHHH AABB CCDDEE FFGGHHH ABCEFGH Primary core collection (2794) Basic collection (23587) Location Phenotype Phenotype Genotype Core collection in the different level (248; 433…) Methods Methods Primary core collection Basic collection Core collection AAAABBBB CCCCDDDDEEEE FFFGGGHHH AABB CCDDEE FFGGHHH ABCEFGH AAAABBBB CCCCDDDDEEEE FFFGGGHHH AABB CCDDEE FFGGHHH ABCEFGH Primary core collection (2794) Basic collection (23587) Location Phenotype Phenotype Genotype Core collection in the different level (248; 433…) Methods Methods Primary core collection (2794) Basic collection (23587) Location Phenotype Phenotype Genotype Core collection in the different level (248; 433…) Methods Methods
- 10. The primarydivision of genetic diversity was between the wild and domesticated accessions. G. soja and G. max represent distinct germplasm pools. B A G.max G.soja G.max G.soja G.max G.soja K=2 K=3 K=4 K=5 K=6 K=2 K=3 K=4 K=5 K=6 B A G.max G.soja G.max G.soja G.max G.soja K=2 K=3 K=4 K=5 K=6 K=2 K=3 K=4 K=5 K=6 A G.max G.soja G.max G.soja G.max G.soja K=2 K=3 K=4 K=5 K=6 K=2 K=3 K=4 K=5 K=6 2. Differentiation between G.soja and G. max S HH N NE Russia Korea Japa n 99 SSR 554 SNP SSR+SNP S HH N NE Russia Korea Japa n S HH N NE Russia Korea Japa n 99 SSR 554 SNP SSR+SNP Li et al. New Phytologist, 2010; Li et al. Theor Appl Genet, 2008 1863 landraces; 59 SSR 112 wild soybean; 99 SSR, 554 SNP Population structure within species is accordance with geographic origin in cultivated and wild soybeans respectively
- 11. Genetic diversity wasremarkable decreased after domestication Li et al. (2010) New Phytologist Cultivated Wild Hyten et al. (2006) PNAS Accessions: 26 G. soja 94 G. max Molecular data: 111 fragments from 102 genes Accessions: 92 G. soja 279 G. max Molecular data: 554 SNP markers 99 SSR markers 1807 Wild 0.871 1473 Cultivated 0.68778.3% 81.5%
- 12. From Schmutz etal., Nature 2010; 463:178-183 The development of sequencing technique Cultivated soybean reference genome Gmax W82 As an important source of genetic diversity, gene repertoire in G. soja remains largely unexplored
- 13. Pan-genome: Theset of all genes present in the genomes of a group of organisms 3. Pan-genome of G. soja From: Morgante et al. Current Opinion in Plant Biology 10, 149-155 (2007) Core genome: shared among individuals. Dispensable genome: an individual-specific or partially-shared among individuals.
- 14. Why pan-genome ? Liet al. New Phytologist, 2010 The largest component of variation (~75%) was among individuals within population A single genome sequence might not reflect the entire genomic complement of a species AMOVA
- 15. 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1 3 57 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 65 67 69 71 73 75 77 79 81 83 85 87 89 91 GsojaC GsojaB GsojaA GsojaG GsojaE GsojaD Seven representative wild soybean (New Phytologist, 2010) China: Northeast, North, Huanghuai and South regions Other countries: Japan, Korea, Russia Three libraries: 180bp, 500bp, 2kbp Data 817Gb, 111.9 X in average Pan-genome of annual wild soybean
- 16. ID GsojaA GsojaBGsojaC GsojaD GsojaE GsojaF GsojaG Predicated genome size (Mbp) 981.0 1000.8 1053.78 1118.34 956.43 992.66 889.33 Assembled geneome size(Mbp) 813 895 841 985 920 886 878 Contig N50 (Kbp)* 9 22.2 8 11 27 24.3 19.2 Scaffold N50 (Kbp) 18.3 57.2 17 48.7 65.1 52.4 44.9 No. of genes predicated 58,756 56,655 60,377 62,048 58,414 57,573 58,169 No. of genes confirmed 55,061 54,256 56,542 57,631 55,901 54,805 54,797 Number of predicated genes: average 55,570 genes/ genome RNA-Seq validation: 67.3% of predicated genes Summary of data and assembly
- 17. The pan-genome isdynamic and a single genome does not adequately represent the diversity of the species The number of total genes increased as additional genomes were added and the no of core genes decreased The average pan-genome size of any two accessions accounted for 78.2% of that found using all seven accessions
- 18. Pan-genome Core: 48.6%of genes and 80.1% of genome sequence Dispensable: 51.4% of genes and 19.9% of genome sequence 59,080 genes Genome size: 986.3 Mbp Pan-genome of annual wild soybean
- 19. 8.86/kb 19.93/kb The dispensablegene set was more variable than the core gene set, both structurally and functionally. The dispensable genes have experienced weaker purifying selection and evolved more quickly than core genes Core genome vs. dispensable genome
- 20. 58.3% ofthe dispensable could not be assigned any functional annotation versus 33.9% for the core genes set. 95.5% of core genes had homologs in other species based on blast searches to 32 plant genomes (excluding soybean), significantly more than the dispensable gene set (83.5%, chi-square test, p< 0.01). lineage-specific genes evolved faster than genes that were shared between species, either via a higher evolutionary rate or a higher gene loss rate Core genes were more functionally conservative among plant species than dispensable genes
- 21. Evolution of theG. max /G. soja species complex G. soja diverged from G. max more than 0.8 mya Nearly 3 times older than a previous estimate of 0.27 mya based on re-sequencing of a single G. soja genome 670 conserved single-copy gene orthologs
- 22. 4.Genomic variation betweenG. soja and GmaxW82 SNPs: 3.63~4.72 million Indels: 0.50~0.77 million Structure var: CNV, PAV Thousands of genes affected by above variations, some of which may be useful for future crop improvement.
- 23. G.soja vs G.max:Genomic basis of agronomic traits photosensing and light signaling coordinately controlsling flowering Two 3nt-indel and 9 non-synonymous SNP; two variation hotpots photosensing and light signaling coordinately controlsling flowering Two 3nt-indel and 9 non-synonymous SNP; two variation hotpots
- 24. G. max G. soja Re-sequencing* 1G.soja+1 G.max Re-sequencing # 25 G.soja+30 G.max De novo sequencing 7 G.soja+1 G.max ？712？？？19.6M？250M 33816117972615M85M480M510M ？？？？？70M？510M ？712？？？19.6M？250M 33816117972615M85M480M510M ？？？？？70M？510M #: From Li et al. BMC Genomics, 2013; *: FromKim et al. PNAS, 2010 G.soja- specific G.max- specific CNV-lossCNV-gainLarge InDel (5-100bp) Small InDel (1-5bp) SNP missed in Re-seq SNP G.soja- specific G.max- specific CNV-lossCNV-gainLarge InDel (5-100bp) Small InDel (1-5bp) SNP missed in Re-seq SNP Specific variations identified in this comparison
- 25. 9 SNPsin a 62bp fragment More SNPs were found by assembly-based method 10 million SNPs, two time of SNPs identified by re-sequencing (Li et al. BMC Genomics, 2013) New SNP mostly from divergent regions where assembled sequences could be aligned and short sequencing reads are difficult to be mapped
- 26. Copy numbervariation: 1978 genes 1179 loss 726 gain 73 gain and loss Category: G. soja > G.max Number: G. max > G. soja R genes
- 27. >100 bp and<95% identity PAV sequence: 30.3 Mb G. soja specific: 11.3 Mb G. max specific: 19 Mbp PAV gene：354 G. soja specific: 338 G. max specific:16
- 28. PAV: 24.3％of involved in defense response Gs1-3: biotic and abiotic stress tolerance or plant development 56 resequencing accession: frequency G. soja> G. max Gs1 Gs2 Gs3 8kb
- 29. Wild Culitvated 1 2 3 4 5 1 2 3 4 5 Population bottleneckor artificial selection will result in the fixation of alleles during domestication 5. Selection genes during domestication
- 30. G. Soja Landrace Elite cultivar 25accessions 93.55Gb 98.2%Glyma1.01 31 accessions (Lam et al. 2010) 17 G. soja 14 G. max 25 accessions Total: 5,102,244 SNPs Special: 25.5% specific to our accessionsspecific to our accessions Li et al. BMC Genomics, 2013
- 31. 0 10 20 30 40 50 60 G m 01G m 02G m 03G m 04G m 05G m 06G m 07G m 08G m 09G m 10G m 11G m 12G m 13G m 14G m 15G m 16G m 17G m 18G m 19G m 20 0 20 40 60 80 100 120 140 No. of regionNo. of genes No.ofregions No.ofgenes 394 regions: 1.47% of the whole genome (950M) 928 genes: 2.0% of 46,430 predicted genes θπ(cultivated/wild) , Tajima’s D values, FST 20 Kb sliding window (2Kb step-size). Artificial Selection
- 32. The distributionof selection regions were not random or even uniform throughout the genome Appeared to be apparent clusters in certain genomic regions Gm08 Gm12 Similar to the distribution pattern of QTLs underlying domestication related traits (Ross-Ibarra, Genetics of Adaptation, 2005)
- 33. A homolog ofthe domestication gene Grain Incomplete Filling 1 (GIF1) in rice GIF1 encodes cell-wall invertase that regulates sugar levels to meet with the demands of cell division and growth during the grain development. Increased grain size and weight in transgenic rice From: Wang et al. Nat Genet, 2008 Selection gene: Glyma03g35520.1
- 34. GmTfl1 (Glyma19g37890.1):Tian et al. 2010; Liu et al. 2010 gDNA cDNA θ π θ π GmTfl1 Glyma19g37890.1 Elite cultivars 1.86 0.98 0.98 0.52 Landraces 1.78 1.05 1.78 1.61 G. soja 1.65 1.28 0 0 Glyma03g35250.1 G. max (89) 0 0 0 0 Elite cultivars 0 0 0 0 Landraces 0 0 0 0 G. soja (20) 0.66 0.73 0.85 0.54 The homolog of Glyma03g35250.1 in sunflower experienced selective sweeps during evolution (From Blackman et al. 2011). Selection gene: Glyma03g35250.1
- 35. Confirmed some regionsor genes • 100-seed weight: QTL by Yan et al 2014 Plant Breeding, 2014 Type No. of SNPs No. of haplotype Haplotype diversity Total 72 32 0.762 G.soja 71 28 0.952 Landrace 29 5 0.568 Elite 3 4 0.552 Total Wild Landrace Elite
- 36. Black Diverse color Yellow G. soja Landrace Elite cultivar CHS1, CHS3,CHS4, CHS5, and CHS9 Multiple-allele I locus Soybean seed coat color 0 1 2 3 4 5 6 -40000 10000 60000 110000 160000 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
- 37. The hierarchicalgenetic structure of soybean landraces was reflected with the geographic region. A pan-genome was constructed by de novo sequencing and assembling seven G. soja accessions. Inter-genomic comparisons identified up to 3,000 lineage- specific genes and genes with CNV, PAV or large-effect mutations, some of which may contribute to variation of agronomic traits such as resistance, seed composition, flowering time, biomass etc. A set of candidate genes significantly affected by selection for preferred agricultural traits underlying soybean domestication were identified and some genes were confirmed. These results will facilitate the harnessing of untapped genetic diversity from wild soybean for developing elite cultivars. Summary
- 38. Funding: National Natural ScienceFoundation of China State Key Basic Research and Development Plan of China (973) National Key Technologies R&D Program in the 11th Five-Year Plan (863) Acknowledgments Novogene Prof. Ruiqiang Li Guangyu Zhou Wenkai Jiang Zhouhuao Zhang University of Georgia Prof. Scott A. Jackson Purdue University Dr. Jianxin Ma