Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean

Abstract

Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.

References

[1] Zhang GW, Xu SC, Mao WH et al. Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers. J Zhejiang Univ Sci B. 2013; 14: 279-88. https://10.1631/jzus.B1200243.

[2] Young G, Mebrahtu T, Johnson J . Acceptability of green soybeans as a vegetable entity. Plant Foods Hum Nutr. 2000; 55: 323-33.

[3] Rao MSS, Bhagsari AS, Mohamed AI . Fresh green seed yield and seed nutritional traits of vegetable soybean genotypes. Crop Sci. 2002; 42: 1950-8. https://10.2135/cropsci2002.1950.

[4] Kao CF, He SS, Wang CS et al. A modified Roger’s distance algorithm for mixed quantitative-qualitative phenotypes to establish a Core collection for Taiwanese vegetable soybeans. Front Plant Sci. 2021; 11: 612106. https://10.3389/fpls.2020.612106.

[5] Xu S, Liu N, Mao W et al. Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.) . Sci Rep. 2016; 6: 26619. https://10.1038/srep26619.

[6] Kumar V, Rani A, Pratap D et al. Evaluation of vegetable-type soybean for sucrose, taste-related amino acids, and Isoflavones contents. Int J Food Prop. 2011; 14: 1142-51. https://10.1080/10942911003592761.

[7] Jiang GL, Rutto LK, Ren S et al. Genetic analysis of edamame seed composition and trait relationships in soybean lines. Euphytica. 2018; 214: 158. https://10.1007/s10681-018-2237-9.

[8] Graham PH, Vance CP . Legumes: importance and constraints to greater use. Plant Physiol. 2003; 131: 872-7. https://10.1104/pp.017004.

[9] Saldivar X, Wang YJ, Chen P et al. Effects of blanching and storage conditions on soluble sugar contents in vegetable soybean. LWT - Food Science and Technology. 2010; 43: 1368-72. https://10.1016/j.lwt.2010.04.017.

[10] Golicz AA, Batley J, Edwards D . Towards plant pangenomics. Plant Biotechnol J. 2016; 14: 1099-105. https://10.1111/pbi.12499.

[11] Varshney RK, Sinha P, Singh VK et al. 5Gs for crop genetic improvement. Curr Opin Plant Biol. 2020; 56: 190-6. https://10.1016/j.pbi.2019.12.004.

[12] Schmutz J, Cannon SB, Schlueter J et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010; 463: 178-83. https://10.1038/nature08670.

[13] Chan C, Qi XP, Li MW et al. Recent developments of genomic research in soybean. J Genet Genomics. 2012; 39: 317-24. https://10.1016/j.jgg.2012.02.002.

[14] Wang Z, Tian ZX . Genomics progress will facilitate molecular breeding in soybean. Sci China Life Sci. 2015; 58: 813-5. https://10.1007/s11427-015-4908-2.

[15] Li YH, Li W, Zhang C et al. Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol. 2010; 188: 242-53. https://10.1111/j.1469-8137.2010.03344.x.

[16] Zhou Z, Ziang J, Wang Z et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol. 2015; 33: 408-14. https://10.1038/nbt.3096.

[17] Hyten DL, Song Q, Zhu Y et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc Nat Acad Sc U S. 2006; 103: 16666-71. https://10.1073/pnas.0604379103.

[18] Lam HM, Xu X, Liu X et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010; 42: 1053-9. https://10.1038/ng.715.

[19] Li YH, Zhou G, Ma J et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol. 2014; 32: 1045. https://10.1038/nbt.2979.

[20] Liu ZX, Li H, Wen Z et al. Comparison of genetic diversity between Chinese and American soybean (Glycine max (L.)) accessions revealed by high-density SNPs . Front Plant Sci. 2017; 8: 2014. https://10.3389/fpls.2017.02014.

[21] Olsen KM, Wendel JF . A Bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol. 2013; 64: 47-70. https://10.1146/annurev-arplant-050312-120048.

[22] Doebley JF, Gaut BS, Smith BD . The molecular genetics of crop domestication. Cell. 2006; 127: 1309-21. https://10.1016/j.cell.2006.12.006.

[23] Sedivy EJ, Wu FQ, Hanzawa Y . Soybean domestication: the origin, genetic architecture and molecular bases. New Phytol. 2017; 214: 539-53. https://10.1111/nph.14418.

[24] Dong Y, Yang X, Han BH et al. Pod shattering resistance associated with domestication is mediated by a NAC gene in soybean. Nat Commun. 2014; 5: 3552. https://10.1038/ncomms4352.

[25] Sun LJ, Miao Z, Cai C et al. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat Genet. 2015; 47: 939-+. https://10.1038/ng.3339.

[26] Wang M, Li W, Fang C et al. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet. 2018; 50: 1435. https://10.1038/s41588-018-0229-2.

[27] Lu SJ, Dong L, Fang C et al. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet. 2020; 52: 428. https://10.1038/s41588-020-0604-7.

[28] Dong DK, Fu XJ, Yuan F et al. Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers. Kulturpflanze. 2014; 61: 173-83. https://10.1007/s10722-013-0024-y.

[29] Liu Y, Du H, Li P et al. Pan-genome of wild and cultivated soybeans. Cell. 2020; 182: 162, e113-176.e13. https://10.1016/j.cell.2020.05.023.

[30] Song JF, Liu CQ, Li DJ et al. Evaluation of sugar, free amino acid, and organic acid compositions of different varieties of vegetable soybean (Glycine max [L.] Merr). Ind Crops Prod. 2013; 50: 743-9. https://10.1016/j.indcrop.2013.08.064.

[31] Keatinge JDH, Easdown WJ, Yang RY et al. Overcoming chronic malnutrition in a future warming world: the key importance of mungbean and vegetable soybean. Euphytica. 2011; 180: 129-41. https://10.1007/s10681-011-0401-6.

[32] Luquez VM, Guiamet JJ . Effects of the ’stay green’ genotype GGd1d1d2d2 on leaf gas exchange, dry matter accumulation and seed yield in soybean (Glycine max L. Merr). Ann Bot. 2001; 87: 313-8. https://10.1006/anbo.2000.1324.

[33] Jiang GL, Rutto LK, Ren SX . Evaluation of soybean lines for Edamame yield traits and trait genetic correlation. HortScience. 2018; 53: 1732-6. https://10.21273/Hortsci13448-18.

[34] Magee PJ, McGlynn H, Rowland IR . Differential effects of isoflavones and lignans on invasiveness of MDA-MB-231 breast cancer cells in vitro. Cancer Lett. 2004; 208: 35-41. https://10.1016/j.canlet.2003.11.012.

[35] Messina M. Soy and health update: evaluation of the clinical and epidemiologic literature. Nutrients. 2016; 8: 754. https://10.3390/nu8120754.

[36] Hu QG, Zhang M, Mujumdar AS et al. Performance evaluation of vacuum microwave drying of edamame in deep-bed drying. Dry Technol. 2007; 25: 731-6. https://10.1080/07373930701291199.

[37] Zhang YM, Hu R, Li H et al. Proteomics changes in filling seeds of vegetable soybean. HortScience. 2016; 51: 1397-401. https://10.21273/Hortsci10911-16.

[38] Shen YT, Liu J, Geng H et al. De novo assembly of a Chinese soybean genome. Sci China Life Sci. 2018; 61: 871-84. https://10.1007/s11427-018-9360-0.

[39] Badouin H, Gouzy J, Grassa CJ et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature. 2017; 546: 148-+. https://10.1038/nature22380.

[40] Clavijo BJ, Venturini L, Schudoma C et al. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res. 2017; 27: 885-96. https://10.1101/gr.217117.116.

[41] Raymond O, Gouzy J, Just J et al. The Rosa genome provides new insights into the domestication of modern roses. Nat Genet. 2018; 50: 772-+. https://10.1038/s41588-018-0110-3.

[42] Yang JH, Liu D, Wang X et al. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet. 2016; 48: 1225-32. https://10.1038/ng.3657.

[43] Kreplav J, Madoui MA, Capal P et al. A reference genome for pea provides insight into legume genome evolution. Nat Genet. 2019; 51: 1411. https://10.1038/s41588-019-0480-1.

[44] Zhang LS, Chen F, Zhang X et al. The water lily genome and the early evolution of flowering plants. Nature. 2020; 577: 79. https://10.1038/s41586-019-1852-5.

[45] Yu Y, Fu J, Xu Y et al. Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Nat Commun. 2018; 9: 5404. https://10.1038/s41467-018-07744-3.

[46] Qi JJ, Liu X, Shen D et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet. 2013; 45: 1510-5. https://10.1038/ng.2801.

[47] Kim MS, Lozano R, Kim JH et al. The patterns of deleterious mutations during the domestication of soybean. Nat Commun. 2021; 12: 97. https://10.1038/s41467-020-20337-3.

[48] Hu Y, Colantonio V, Muller BSF et al. Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nat Commun. 2021; 12: 1227. https://10.1038/s41467-021-21380-4.

[49] Fang C, Ma Y, Wu S et al. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biol. 2017; 18: 161. https://10.1186/s13059-017-1289-9.

[50] Gazave E, Tassone EE, Baseggio M et al. Genome-wide association study identifies acyl-lipid metabolism candidate genes involved in the genetic control of natural variation for seed fatty acid traits in Brassica napus L. Ind Crops Prod. 2020; 145: 112080. https://10.1016/j.indcrop.2019.112080.

[51] Studer A, Zhao Q, Ross-Ibarra J et al. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet. 2011; 43: 1160-3. https://10.1038/ng.942.

[52] Lv SW, Wu W, Wang M et al. Genetic control of seed shattering during African rice domestication. Nat Plants. 2018; 4: 331. https://10.1038/s41477-018-0164-3.

[53] Fader GM, Koller HR . Seed growth-rate and carbohydrate Pool sizes of the soybean fruit. Plant Physiol. 1985; 79: 663-6. https://10.1104/pp.79.3.663.

[54] Ruan YL . Sucrose metabolism: gateway to diverse carbon use and sugar Signaling. Annu Rev Plant Biol. 2014; 65: 33-67. https://10.1146/annurev-arplant-050213-040251.

[55] Jin Y, Ni DA, Ruan YL . Posttranslational elevation of Cell Wall Invertase activity by silencing its inhibitor in tomato delays leaf senescence and increases seed weight and fruit hexose level. Plant Cell. 2009; 21: 2072-89. https://10.1105/tpc.108.063719.

[56] Li B, Liu H, Zhang Y et al. Constitutive expression of cell wall invertase genes increases grain yield and starch content in maize. Plant Biotechnol J. 2013;11:1080-91. https://10.1111/pbi.12102.

[57] Wang L, Ruan YL . New insights into roles of Cell Wall Invertase in early seed development revealed by comprehensive spatial and temporal expression patterns of GhCWIN1 in cotton. Plant Physiol. 2012; 160: 777-87. https://10.1104/pp.112.203893.

[58] Gutierrez L, Van Wuytswinkel O, Castelain M et al. Combined networks regulating seed maturation. Trends Plant Sci. 2007; 12: 294-300. https://10.1016/j.tplants.2007.06.003.

[59] Julius BT, Leach KA, Tran TM et al. Sugar transporters in plants: new insights and discoveries. Plant Cell Physiol. 2017; 58: 1442-60. https://10.1093/pcp/pcx090.

[60] Ma L, Zhang D, Miao Q et al. Essential role of sugar transporter OsSWEET11 during the early stage of Rice grain filling. Plant Cell Physiol. 2017; 58: 863-73. https://10.1093/pcp/pcx040.

[61] Hou J, Jiang Q, Hao C et al. Global selection on sucrose synthase haplotypes during a century of wheat breeding. Plant Physiol. 2014; 164: 1918-29. https://10.1104/pp.113.232454.

[62] Chourey PS, Taliercio EW, Carlson SJ et al. Genetic evidence that the two isozymes of sucrose synthase present in developing maize endosperm are critical, one for cell wall integrity and the other for starch biosynthesis. Mol Gen Genet. 1998; 259: 88-96. https://10.1007/s004380050792.

[63] Yang JL, Luo DP, Yang B et al. SWEET11 and 15 as key players in seed filling in rice. New Phytol. 2018; 218: 604-15. https://10.1111/nph.15004.

[64] Sosso D, Luo D, Li QB et al. Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nat Genet. 2015; 47: 1489. https://10.1038/ng.3422.

[65] Chen LQ, Lin IW, Qu XQ et al. A Cascade of sequentially expressed sucrose transporters in the seed coat and endosperm provides nutrition for the Arabidopsis embryo. Plant Cell. 2015; 27: 607-19. https://10.1105/tpc.114.134585.

[66] Eom JS, Chen LQ, Sosso D et al. SWEETs, transporters for intracellular and intercellular sugar translocation. Curr Opin Plant Biol. 2015; 25: 53-62. https://10.1016/j.pbi.2015.04.005.

[67] Ren Y, Li M, Guo S et al. Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits. Plant Cell. 2021; 33: 1554-73. https://10.1093/plcell/koab055.

[68] Wang SD, Liu S, Wang J et al. Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication. Natl Sci Rev. 2020; 7: 1776-86. https://10.1093/nsr/nwaa110.

[69] Li L, Stoeckert CJ, Roos DS . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13: 2178-89. https://10.1101/gr.1224503.

[70] Guindon S, Dufayard JF, Lefort V et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59: 307-21. https://10.1093/sysbio/syq010.

[71] Hedges SB, Dudley J, Kumar S . TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006; 22: 2971-2. https://10.1093/bioinformatics/btl505.

[72] De Bie T, Cristianini N, Demuth JP et al. CAFE: a computational tool for the study of gene family evolution. Bioinformatics. 2006; 22: 1269-71. https://10.1093/bioinformatics/btl097.

[73] Yang JH, Deng G, Lian J et al. The chromosome-scale genome of melon dissects genetic architecture of important agronomic traits. Iscience. 2020; 23: 101422. https://10.1016/j.isci.2020.101422.

[74] Li H . Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. eprint arXiv. 2013; 00: 1-3.

[75] Li H, Handsaker B, Wysoker A et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25: 2078-9. https://10.1093/bioinformatics/btp352.

[76] Kumar S, Stecher G, Tamura K . MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016; 33: 1870-4.

[77] Zhang C, Dong SS, Xu JY et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics. 2019; 35: 1786-8. https://10.1093/bioinformatics/bty875.

[78] Pickrell JK, Pritchard JK . Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8: e1002967. https://10.1371/journal.pgen.1002967.