Abstract
Crop domestication is a good example of plant–human co-evolution. Seed gathering and human cultivation of crops were observed since the Neolithic period, as shown by archeological evidence. Numerous studies have been conducted to identify genes related to domestication. With the development of molecular techniques (molecular markers and next-generation sequencing) and bioinformatics, a greater understanding of crop domestication and improvement has been established, including the origins of crops, the numbers of independent domestication events, the molecular diversity of domestication-related traits (DRTs), and the selection pressures. A comparison of the genome sequences between wild species and cultivated crops may provide key information regarding the genetic elements involved in speciation and domestication. Therefore, sequencing projects of currently important crops and their wild relatives are in progress. Accordingly, whole genome sequencing of soybean could provide new knowledge about domestication of this important crop. In this review, we introduce the archaeological evidence of soybean domestication and summarize the DRTs in soybean populations of crosses between cultivated (Glycine max) and wild soybean (G. soja). Soybean domestication is discussed at the sequence level. The current hypothesis of soybean domestication considers that G. max was domesticated from G. soja. However, our previous work suggested that soybean was domesticated from the G. soja/G. max complex that diverged from a common ancestor of these two species of Glycine. This review explores soybean domestication history by focusing on nucleotide diversity using resequencing. Analysis of genes around DRTs at the population level may clarify the domestication history of soybean.
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References
Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trend Plant Sci 8:554–560
Bailey MA, Mian MAR, Carter TE et al (1997) Pod dehiscence of soybean: identification of quantitative trait loci. J Hered 88:152–154
Barabaschi D, Guerra D, Lacrima K et al (2012) Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 50:250–266
Bennett ST, Barnes C, Cox A et al (2005) Toward the 1,000 dollars human genome. Pharmacogenomics 6:373–382
Boerma HR, Specht JE (2004) Soybeans: improvement, production and uses. Am Soc of Agro, Madison
Buckler ES, Thornsberry JM, Kresovich S (2001) Molecular diversity, structure and domestication of grasses. Genet Res 77:213–218
Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161:1257–1267
Cai HW, Morishima H (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100:840–846
Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228
Carter TE Jr, Nelson R, Sneller CH, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production and uses. Am Soc of Agro, Madison, pp 303–416
Choi I-Y, Hyten DL, Matukumalli LK et al (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696
Clarke J, Wu H-C, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnol 4:265–270
Concibido VC, La Vallee B, Mclaird P et al (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106:575–582
Crawford G (2005) East Asian plant domestication. In: Stark MT (ed) Archaeology of asia. Blackwell Publishing, Oxford, pp 77–95
Crawford G, Lee G-A (2003) Agricultural origins in the Korean Peninsula. Antiquity 77:87–95
Crawford GW, Underhill AP, Zhao J et al (2005) Late neolithic plant remains from northern China: preliminary results from Liangchengzhen, Shandong. Curr Anthropol 46:309–317
Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418:700–707
Doebley JF (1989) Isozymic evidence and the evolution of crop plants. In: Soltis D, Soltis P (eds) Isozymes in plant biology. Dioscorides Press, Portland, pp 165–191
Doebley J, Stec A (1993) Inheritance of the morphological differences between maize and Teosinte—comparison of results for two F2 populations. Genetics 134:559–570
Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize Teosinte F2 population—implications for the origin of maize. Proc Natl Acad Sci USA 87:9888–9892
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Doganlar S, Frary A, Daunay MC et al (2002) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161:1713–1726
Dong YS, Zhao LM, Liu B et al (2004) The genetic diversity of cultivated soybean grown in China. Theor Appl Genet 108:931–936
Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138
Feuillet C, Leach JE, Rogers J et al (2011) Crop genome sequencing: lessons and rationales. Trend Plant Sci 16:77–88
Frary A, Nesbitt TC, Frary A et al (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88
Fuller DQ (2002) Fifty years of archaeobotanical studies in India: laying a solid foundation. In: Settar S, Korisettar R (eds) Indian archaeology in retrospect: archaeology and interactive disciplines, vol III. Manohar, Delhi, pp 247–263
Fuller DQ (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann Bot 100:903–924
Funatsuki H, Ishimoto M, Tsuji H et al (2006) Simple sequence repeat markers linked to a major QTL controlling pod shattering in soybean. Plant Breed 125:195–197
Grandillo S, Tanksley SD (1996) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951
Gross BL, Olsen KM (2010) Genetic perspectives on crop domestication. Trend Plant Sci 15:529–537
Gunter C (2008) Plant genetics rice stands up. Nat Rev Genet 9:816–816
Guo J, Wang Y, Song C et al (2010) A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences. Ann Bot 106:505–514
Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1–13
Harris DR (1998) The origins of agriculture in southwest Asia. Rev Archaeol 19:5–11
Harris TD, Buzby PR, Babcock H et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109
Henry RJ (2012) Next-generation sequencing for understanding and accelerating crop domestication. Brief Func Genom 11:51–56
Hymowitz T (1970) On the domestication of the soybean. Eco Bot 24:408–421
Hyten DL, Song Q, Zhu Y et al (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671
Iqbal SM, Bashir R (2011) Nanopores: sensing and fundamental biological interactions. Springer, New York
Jackson SA, Iwata A, Lee SH et al (2011) Sequencing crop genomes: approaches and applications. New Phytol 191:915–925
Jin J, Huang W, Gao JP et al (2008) Genetic control of rice plant architecture under domestication. Nature Genet 40:1365–1369
Jun T-H, Van K, Kim MY et al (2011) Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance. Genes Genom 33:391–397
Kang S-T, Kwak M, Kim H-K et al (2009) Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.]. Euphytica 166:15–24
Keim P, Diers BW, Olson TC, Shoemaker RC (1990a) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735–742
Keim P, Diers BW, Shoemaker RC (1990b) Genetic analysis of soybean hard seededness with molecular markers. Theor Appl Genet 79:465–469
Kim MY, Lee S, Van K et al (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107:22032–22037
Kim MY, Van K, Kang YJ et al (2012) Tracing soybean domestication history: from nucleotide to genome. Breed Sci 61:445–452
Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36:1037–1045
Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trend Genet 23:578–587
Lam H-M, Xu X, Liu X et al (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genet 42:1053–1059
Lauter N, Doebley J (2002) Genetic variation for phenotypically invariant traits detected in teosinte: implications for the evolution of novel forms. Genetics 160:333–342
Lee G-A (2011) The transition from foraging to farming in prehistoric Korea. Curr Anthropol 52:S307–S329
Lee Y-H, Park T-S (2006) Origin of legumes cultivation in Korean Peninsula by viewpoint of excavated grain remains and genetic diversity of legumes. Kor Agri Hist Assoc 5:1–31 (in Korean)
Lee G-A, Crawford GW, Liu L, Chen X (2007) Plants and people from the early neolithic to shang periods in North China. Proc Natl Acad Sci USA 104:1087–1092
Lee JD, Yu JK, Hwang YH et al (2008) Genetic diversity of wild soybean (Glycine soja Sieb. and Zucc.) accessions from South Korea and other countries. Crop Sci 48:606–616
Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939
Li DD, Pfeiffer TW, Cornelius PL (2008) Soybean QTL for yield and yield components associated with Glycine soja alleles. Crop Sci 48:571–581
Li YH, Guan RX, Liu ZX et al (2008) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 117:857–871
Li YH, Li W, Zhang C et al (2010) Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. New Phytol 188:242–253
Liu B, Fujita T, Yan Z-H et al (2007) QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot 100:1027–1038
Liu B, Watanabe S, Uchiyama T et al (2010) The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol 153:198–210
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
Nagai YS, Sobrizal, Sanchez PL et al (2002) Sh3, a gene for seed shattering, commonly found in wild rices. Rice Genet Newsl 19:74–75
Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39:197–218
Parameswaran P, Jalili R, Tao L et al (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35:e130
Peng JH, Ronin Y, Fahima T et al (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494
Poncet V, Martel E, Allouis S et al (2002) Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet (Pennisetum glaucum L., Poaceae) crosses. Theor Appl Genet 104:965–975
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:843–848
Ross-Ibarra J (2005) Quantitative trait loci and the study of plant domestication. Genetica 123:197–204
Rusk N (2009) Cheap third-generation sequencing. Nat Methods 6:244–245
Sang T, Ge S (2007) The puzzle of rice domestication. J Integr Plant Biol 49:760–768
Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178–183
Schulman AH (2007) Molecular markers to assess genetic diversity. Euphytica 158:313–321
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18
Sobrizal, Ikeda K, Sanchez PL, Yoshimura A (1999) RFLP mapping of a seed shattering gene on chromosome 4 in rice. Rice Genet Newslett 16:74–75
Stupar RM (2010) Into the wild: the soybean genome meets its undomesticated relative. Proc Natl Acad Sci USA 107:21947–21948
Tang H, Sezen U, Paterson AH (2010) Domestication and plant genomes. Curr Opin Plant Biol 13:160–166
Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21:1214–1225
Tian Z, Wang X, Lee R et al (2010) Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107:8563–8568
Van K, Hwang E-Y, Kim MY et al (2004) Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica 139:147–157
Van K, Hwang E-Y, Kim MY et al (2005) Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J Hered 96:529–535
Van K, Kim D, Cai CM et al (2008) Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome. DNA Res 15:93–102
Van K, Kim DH, Shin JH, Lee S-H (2011) Genomics of plant genetic resources: past, present and future. Plant Genet Resour 9:155–158
Van K, Rastogi K, Kim K-H, Lee S-H (2013) Next-generation sequencing technology for crop improvement. SABRAO J Breed Genet 45:84–99
Vaughan DA, Balazs E, Heslop-Harrison JS (2007) From crop domestication to super-domestication. Ann Bot 100:893–901
Vielle-Calzada JP, Martinez delaVO, Hernandez-Guzman G et al (2009) The Palomero genome suggests metal effects on domestication. Science 326:1078
Wilson RF (2008) Soybean: market driven research needs. In: Stacey G (ed) Genetics and genomics of soybean. Plant genetics and genomics, vol 2. Springer, pp 3–15
Xiong LX, Liu KD, Dai XK et al (1999) Identification of genetic factors controlling domestication-related traits of rice using an F-2 population of a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 98:243–251
Xu DH, Gai JY (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breed 122:503–506
Xu DH, Abe J, Gai JY, Shimamoto Y (2002) Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean. Theor Appl Genet 105:645–653
Yuan C, Zhou G, Li Y, Wang K, Wang Z, Li X, Chang R, Qiu L (2008) Cloning and sequence diversity analysis of GmHs1 pro-1 in Chinese domesticated and wild soybeans. Mol Breed 22:593–602
Zhu YL, Song QJ, Hyten DL et al (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134
Acknowledgments
This research was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008117) of the Rural Development Administration, Republic of Korea.
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Van, K., Kim, M., Shin, J., Kim, K., Lee, YH., Lee, SH. (2014). Molecular Evidence for Soybean Domestication. In: Tuberosa, R., Graner, A., Frison, E. (eds) Genomics of Plant Genetic Resources. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7572-5_19
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