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CN 11-5892/Q

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Front Biol    0, Vol. Issue () : 337-348    https://doi.org/10.1007/s11515-011-1116-8
REVIEW
Current development and application of soybean genomics
Lingli HE1,2, Jing ZHAO1,2, Man ZHAO1,2, Chaoying HE1(email.png)
1. 1. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; 2. 2. Graduate University, Chinese Academy of Sciences, Beijing 100049, China
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Abstract

Soybean (BoldItalic), an important domesticated species originated in China, constitutes a major source of edible oils and high-quality plant proteins worldwide. In spite of its complex genome as a consequence of an ancient tetraploidilization, platforms for map-based genomics, sequence-based genomics, comparative genomics and functional genomics have been well developed in the last decade, thus rich repertoires of genomic tools and resources are available, which have been influencing the soybean genetic improvement. Here we mainly review the progresses of soybean (including its wild relative BoldItalic) genomics and its impetus for soybean breeding, and raise the major biological questions needing to be addressed. Genetic maps, physical maps, QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine. Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes, which are instrumental to comparative genomics and functional genomics. Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process. Microarrays resources, mutagenesis and efficient transformation systems become essential components of soybean functional genomics. Furthermore, phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development, in response to abiotic stresses, functioning in plant-pathogenic microbe interactions, and controlling the oil and protein content of seed. These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.
Keywords genetic map      Glycine max      Glycine soja      soybean genomics      transgenic crop     
Corresponding Author(s): HE Chaoying,Email:chaoying@ibcas.ac.cn   
Issue Date: 01 August 2011
 Cite this article:   
Lingli HE,Jing ZHAO,Man ZHAO, et al. Current development and application of soybean genomics[J]. Front Biol, 0, (): 337-348.
 URL:  
https://academic.hep.com.cn/fib/EN/10.1007/s11515-011-1116-8
https://academic.hep.com.cn/fib/EN/Y0/V/I/337
1 Alkharouf N W, Matthews B F (2004). SGMD: the soybean genomics and microarray database. Nucleic Acids Res , 32(90001 Database issue): D398–D400
doi: 10.1093/nar/gkh126 pmid:14681442
2 Arumuganathan K, Earle E D (1991). Nuclear DNA content of some important plant species. Plant Mol Biol Rep , 9(3): 208–219
doi: 10.1007/BF02672069
3 Buhr T, Sato S, Ebrahim F, Xing A, Zhou Y, Mathiesen M, Schweiger B, Kinney A J, Staswick P, Clemente T (2002). Ribozyme termination of RNA transcripts down-regulate seed fatty acid genes in transgenic soybean. Plant J , 30(2): 155–163
doi: 10.1046/j.1365-313X.2002.01283.x pmid:12000452
4 Chen Q S, Zhang Z C, Liu C Y, Xin D W, Qiu H M, Shan D P, Shan C Y, Hu G H (2007). QTL analysis of major agronomic traits in soybean. Agric Sci China , 6(4): 399–405
doi: 10.1016/S1671-2927(07)60062-5
5 Chen R, Hu Z, Zhang H (2009). Identification of microRNAs in wild soybean (Glycine soja). J Integr Plant Biol , 51(12): 1071–1079
doi: 10.1111/j.1744-7909.2009.00887.x pmid:20021554
6 Cheng K C, Str?mvik M V (2008). SoyXpress: a database for exploring the soybean transcriptome. BMC Genomics , 9(1): 368
doi: 10.1186/1471-2164-9-368 pmid:18671881
7 Choi I Y, Hyten D L, Matukumalli L K, Song Q, Chaky J M, Quigley C V, Chase K, Lark K G, Reiter R S, Yoon M S, Hwang E Y, Yi S I, Young N D, Shoemaker R C, van Tassell C P, Specht J E, Cregan P B (2007). A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics , 176(1): 685–696
doi: 10.1534/genetics.107.070821 pmid:17339218
8 Clemente T, LaValle B J, Howe A R, Ward D C, Rozman R J, Hunter P E, Broyles D L, Kasten D S, Hinchee M A (2000). Progeny analysis of glyphosate selected transgenic soybeans derived from Agrobacterium-mediated transformation. Crop Sci , 40(3): 797–803
doi: 10.2135/cropsci2000.403797x
9 Clemente T E, Cahoon E B (2009). Soybean oil: genetic approaches for modification of functionality and total content. Plant Physiol , 151(3): 1030–1040
doi: 10.1104/pp.109.146282 pmid:19783644
10 Cooper J L, Till B J, Laport R G, Darlow M C, Kleffner J M, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, Bilyeu K D, Meksem K, Comai L, Henikoff S (2008). TILLING to detect induced mutations in soybean. BMC Plant Biol , 8(1): 9
doi: 10.1186/1471-2229-8-9 pmid:18218134
11 Coryell V H, Jessen H, Schupp J M, Webb D, Keim P (1999). Allele-specific hybridization markers for soybean. Theor Appl Genet , 98(5): 690–696
doi: 10.1007/s001220051122
12 Cregan P B, Jarvik T, Bush A, Shoemaker R C, Lark K G, Kahler A L, Kaya N, VanToai T T, Lohnes D G, Chung J, Specht J E (1999a). An integrated genetic linkage map of the soybean genome. Crop Sci , 39(5): 1464–1490
doi: 10.2135/cropsci1999.3951464x
13 Cregan P B, Mudge J, Fickus E W, Danesh D, Denny R, Young N D (1999b). Two simple sequence repeat markers to select for soybean cyst nematode resistance coditioned by the rhg1 locus. Theor Appl Genet , 99(5): 811–817
doi: 10.1007/s001220051300
14 Danesh D, Penuela S, Mudge J, Denny R, Nordstrom H, Martinez J, Young N D (1998). A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor Appl Genet , 96(2): 196–202
doi: 10.1007/s001220050727
15 de Ronde J A, Laurie R N, Caetano T, Greyling M M, Kerepesi I (2004). Comparative study between transgenic and non-transgenic soybean lines proved transgenic lines to be more drought tolerant. Euphytica , 138(2): 123–132
doi: 10.1023/B:EUPH.0000046806.68554.5b
16 Droste A, Pasquali G, Bodanese-Zanettini M H (2000). Integrated bombardment and Agrobacterium transformation system: an alternative method for soybean transformation. Plant Mol Biol Rep , 18(1): 51–59
doi: 10.1007/BF02825294
17 Du W J, Wang M, Fu S X, Yu D Y (2009). Mapping QTLs for seed yield and drought susceptibility index in soybean (Glycine max L.) across different environments. J Genet Genomics , 36(12): 721–731
doi: 10.1016/S1673-8527(08)60165-4 pmid:20129399
18 El-Shemy H A, Khalafalla M M, Fujita K, Ishimoto M (2006). Molecular control of gene co-suppression in transgenic soybean via particle bombardment. J Biochem Mol Biol , 39(1): 61–67
pmid:16466639
19 Falco SC, Mcgonigle B and Maxwell CA. (2005). Transgenic soybean seeds having reduced activity of lipoxygenases. Pub. No. WO/2005/089198.
20 Flor H H (1971). The current status of gene for gene concept. Annu Rev Phytopathol , 9(1): 275–296
doi: 10.1146/annurev.py.09.090171.001423
21 Furutani N, Hidaka S, Kosaka Y, Shizukawa Y, Kanematsu S (2006). Coat protein gene-mediated resistance to soybean mosaic virus in transgenic soybean. Breed Sci , 56(2): 119–124
doi: 10.1270/jsbbs.56.119
22 Ge Y, Li Y, Zhu Y M, Bai X, Lv D K, Guo D, Ji W, Cai H (2010). Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC Plant Biol , 10(1): 153
doi: 10.1186/1471-2229-10-153 pmid:20653984
23 Grant D, Nelson R T, Cannon S B, Shoemaker R C (2010). SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res , 38(Database Database issue): D843–D846
doi: 10.1093/nar/gkp798 pmid:20008513
24 Guzman PS, Diers BW, Neece DJ, Martin SKSt, LeRoy AR, Grau CR, Hughes T J and Nelson RL. (2007). QTL associated with yield in three backcross-derived populations of soybean. Crop Sci , 47: 111–122
doi: 10.2135/cropsci2006.01.0003
25 Haerizadeh F, Wong C E, Singh M B, Bhalla P L (2009). Genome-wide analysis of gene expression in soybean shoot apical meristem. Plant Mol Biol , 69(6): 711–727
doi: 10.1007/s11103-008-9450-1 pmid:19115044
26 He C Y, Tian A G, Zhang J S, Zhang Z Y, Gai J Y, Chen S Y (2003). Isolation and characterization of a full-length resistance gene homolog from soybean. Theor Appl Genet , 106(5): 786–793
pmid:12647051
27 He C Y, Zhang J S, Chen S Y (2002). A soybean gene encoding a proline-rich protein is regulated by salicylic acid, an endogenous circadian rhythm and by various stresses. Theor Appl Genet , 104(6-7): 1125–1131 12582622
doi: 10.1007/s00122-001-0853-5
28 Hinchee MAW, Connor-Ward DV, Newell CA, McDonnell RE, Sato SJ, Gasser CS, Fischhoff DA, Re DB, Fraley RT and Horsch RB. (1988). Production of transgenic soybean plants using Agrobacterium-mediated DNA transfer. Bio/Technol 6: 915–922 .
29 Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S (2007). Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res , 14(6): 271–281
doi: 10.1093/dnares/dsm025 pmid:18192281
30 Hwang T Y, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S, Kono I, Hoshi M, Hanawa M, Yano C, Xia Z, Harada K, Kitamura K, Ishimoto M (2009). High-density integrated linkage map based on SSR markers in soybean. DNA Res , 16(4): 213–225
doi: 10.1093/dnares/dsp010 pmid:19531560
31 Hyten D L, Cannon S B, Song Q, Weeks N, Fickus E W, Shoemaker R C, Specht J E, Farmer A D, May G D, Cregan P B (2010). High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics , 11(1): 38
doi: 10.1186/1471-2164-11-38 pmid:20078886
32 Hyten D L, Song Q, Choi I Y, Yoon M S, Specht J E, Matukumalli L K, Nelson R L, Shoemaker R C, Young N D, Cregan P B (2008). High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet , 116(7): 945–952
doi: 10.1007/s00122-008-0726-2 pmid:18278477
33 James C (2009). Global status of commercialized biotech/GM crops: The first fourteen years, 1996 to 2009. SAAA Brief No. 41 . ISAAA: Ithaca, NY.
34 Keim P, Diers B W, Olson T C, Shoemaker R C (1990). RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics , 126(3): 735–742
pmid:1979039
35 Kerr P S, Sebastian S A (2003). Soybean products with improved carbohydrate composition and soybean plants. US Patent 6653451 .
36 Kim K D, Shin J H, Van K, Kim D H, Lee S H (2009). Dynamic rearrangements determine genome organization and useful traits in soybean. Plant Physiol , 151(3): 1066–1076
doi: 10.1104/pp.109.141739 pmid:19684227
37 Kinney A J, Jung R, Herman E M (2001). Cosuppression of the α subunits of β-conglycinin in transgenic soybean seeds induces the formation of endoplasmic reticulum-derived protein bodies. Plant Cell , 13(5): 1165–1178
pmid:11340189
38 Klink V P, Hosseini P, Matsye P D, Alkharouf N W, Matthews B F (2010). Syncytium gene expression in Glycine max([PI 88788]) roots undergoing a resistant reaction to the parasitic nematode Heterodera glycines. Plant Physiol Biochem , 48(2-3): 176–193
doi: 10.1016/j.plaphy.2009.12.003 pmid:20138530
39 Komatsu S, Ahsan N (2009). Soybean proteomics and its application to functional analysis. J Proteomics , 72(3): 325–336
doi: 10.1016/j.jprot.2008.10.001 pmid:19022415
40 Krishnan H B (2005). Engineering soybean for enhanced sulfer amino acid content. Crop Sci , 45(2): 454–461
doi: 10.2135/cropsci2005.0454
41 Lee S H (2010). The genome sequencing of Glycine soja: molecular insignts into the soybean domestication. http://www.docin.com/p-46662095.html#.
42 Li H, Liu H, Han Y, Wu X, Teng W, Liu G, Li W (2010a). Identification of QTL underlying vitamin E contents in soybean seed among multiple environments. Theor Appl Genet , 120(7): 1405–1413
doi: 10.1007/s00122-010-1264-2 pmid:20069414
43 Li X P, Gan R, Li P L, Ma Y Y, Zhang L W, Zhang R, Wang Y, Wang N N (2006). Identification and functional characterization of a leucine-rich repeat receptor-like kinase gene that is involved in regulation of soybean leaf senescence. Plant Mol Biol , 61(6): 829–844
doi: 10.1007/s11103-006-0052-5 pmid:16927199
44 Li Y D, Wang Y J, Tong Y P, Gao J G, Zhang J S, Chen S Y (2005). QTL mapping of phosphorus deficiency tolerance in soybean (Glycine max L. Merr.). Euphytica , 142(1-2): 137–142
doi: 10.1007/s10681-005-1192-4
45 Li Y H, Li W, Zhang C, Yang L, Chang R Z, Gaut B S, Qiu L J (2010b). 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(1): 242–253
doi: 10.1111/j.1469-8137.2010.03344.x pmid:20618914
46 Li Y H, Zhang C, Gao Z S, Smulders M J M, Ma Z, Liu Z X, Nan H Y, Chang R Z, Qiu L J (2009). Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean. Mol Breed , 24(1): 63–76
doi: 10.1007/s11032-009-9272-0
47 Liao Y, Zou H F, Wei W, Hao Y J, Tian A G, Huang J, Liu Y F, Zhang J S, Chen S Y (2008). Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis. Planta , 228(2): 225–240
doi: 10.1007/s00425-008-0731-3 pmid:18365246
48 Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley R J, Bilgin D D, Radwan O, Neece D J, Clough S J, May G D, Stacey G (2010a). Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol , 152(2): 541–552
doi: 10.1104/pp.109.148379 pmid:19933387
49 Libault M, Farmer A, Joshi T, Takahashi K, Langley R J, Franklin L D, He J, Xu D, May G, Stacey G (2010b). An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J , 63(1): 86–99
pmid:20408999
50 Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger R E, Taylor C G, Xu D, Nguyen H T, Stacey G (2009). Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiol , 151(3): 1207–1220
doi: 10.1104/pp.109.144030 pmid:19755542
51 Libault M, Zhang X C, Govindarajulu M, Qiu J, Ong Y T, Brechenmacher L, Berg R H, Hurley-Sommer A, Taylor C G, Stacey G (2010c). A member of the highly conserved FWL (tomato FW2.2-like) gene family is essential for soybean nodule organogenesis. Plant J , 62(5): 852–864
doi: 10.1111/j.1365-313X.2010.04201.x pmid:20230508
52 Liu B, Fujita T, Yan Z H, Sakamoto S, Xu D, Abe J (2007). QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot (Lond) , 100(5): 1027–1038
doi: 10.1093/aob/mcm149 pmid:17684023
53 Liu B, Watanabe S, Uchiyama T, Kong F, Kanazawa A, Xia Z, Nagamatsu A, Arai M, Yamada T, Kitamura K, Masuta C, Harada K, Abe J (2010). The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol , 153(1): 198–210
doi: 10.1104/pp.109.150607 pmid:20219831
54 Liu J, Ha D, Xie Z, Wang C, Wang H, Zhang W, Zhang J, Chen S (2008a). Ectopic expression of soybean GmKNT1 in Arabidopsis results in altered leaf morphology and flower identity. J Genet Genomics , 35(7): 441–449
doi: 10.1016/S1673-8527(08)60061-2 pmid:18640623
55 Liu S J, Wei Z M, Huang J Q (2008b). The effect of co-cultivation and selection parameters on Agrobacterium-mediated transformation of Chinese soybean varieties. Plant Cell Rep , 27(3): 489–498
doi: 10.1007/s00299-007-0475-8 pmid:18004571
56 Luo G Z, Wang H W, Huang J, Tian A G, Wang Y J, Zhang J S, Chen S Y (2005). A putative plasma membrane cation/proton antiporter from soybean confers salt tolerance in Arabidopsis. Plant Mol Biol , 59(5): 809–820
doi: 10.1007/s11103-005-1386-0 pmid:16270232
57 Manavalan L P, Guttikonda S K, Tran L S P, Nguyen H T (2009). Physiological and molecular approaches to improve drought resistance in soybean. Plant Cell Physiol , 50(7): 1260–1276
doi: 10.1093/pcp/pcp082 pmid:19546148
58 Marek L F, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow J A, Retzel E, Young N D, Shoemaker R C (2001). Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome , 44(4): 572–581
doi: 10.1139/gen-44-4-572 pmid:11550890
59 Marek L F, Shoemaker R C (1997). BAC contig development by fingerprint analysis in soybean. Genome , 40(4): 420–427
doi: 10.1139/g97-056 pmid:18464837
60 Mathieu M, Winters E K, Kong F, Wan J, Wang S, Eckert H, Luth D, Paz M, Donovan C, Zhang Z, Somers D, Wang K, Nguyen H, Shoemaker R C, Stacey G, Clemente T (2009). Establishment of a soybean (Glycine max Merr. L.) transposon-based mutagenesis repository. Planta , 229(2): 279–289
doi: 10.1007/s00425-008-0827-9 pmid:18855007
61 Matthews B F, Devine T E, Weisemann J M, Beard H S, Lewers K S, MacDonald M H, Park Y B, Maiti R, Lin J J, Kuo J, Pedroni M J, Cregan P B, Saunders J A (2001). Incorporation of sequenced cDNA and genomic markers into the soybean genetic map. Crop Sci , 41(2): 516–521
doi: 10.2135/cropsci2001.412516x
62 McPherson R M, MacRae T C (2009). Evaluation of transgenic soybean exhibiting high expression of a synthetic Bacillus thuringiensis cry1A transgene for suppressing lepidopteran population densities and crop injury. J Econ Entomol , 102(4): 1640–1648
doi: 10.1603/029.102.0431 pmid:19736779
63 Meksem K, Ruben E, Zobrist K, Zhang H B, Lightfoot D (2000). Two large insert libraries for soybean: Application in cyst nematode resistance and genome wide physical mapping. Theor Appl Genet , 101: 747–755
doi: 10.1007/s001220051540
64 Men A E, Laniya T S, Searle I R, Iturbe-Ormaetxe I, Gresshoff I, Jiang Q, Carroll B J, Gresshoff P M (2002). Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion in linkage group H. Genome Lett , 13(3): 147–155
doi: 10.1166/gl.2002.017
65 Moravec T, Schmidt M A, Herman E M, Woodford-Thomas T (2007). Production of Escherichia coli heat labile toxin (LT) B subunit in soybean seed and analysis of its immunogenicity as an oral vaccine. Vaccine , 25(9): 1647–1657
doi: 10.1016/j.vaccine.2006.11.010 pmid:17188785
66 Moschini G, Lapan H, Sobolevsky A (2000). Roundup Ready soybeans and welfare effects in the soybean complex. Agribusiness , 16(1): 33–55
doi: 10.1002/(SICI)1520-6297(200024)16:1<33::AID-AGR4>3.0.CO;2-5
67 Nunes A C, Vianna G R, Cuneo F, Amaya-Farfán J, de Capdeville G, Rech E L, Arag?o F J (2006). RNAi-mediated silencing of the myo-inositol-1-phosphate synthase gene (GmMIPS1) in transgenic soybean inhibited seed development and reduced phytate content. Planta , 224(1): 125–132
doi: 10.1007/s00425-005-0201-0 pmid:16395584
68 Ohkama N, Goto D B, Fujiwara T, Naito S (2002). Differential tissue-specific response to sulfate and methionine of a soybean seed storage protein promoter region in transgenic Arabidopsis. Plant Cell Physiol , 43(11): 1266–1275
doi: 10.1093/pcp/pcf149 pmid:12461126
69 Olhoft P M, Flagel L E, Donovan C M, Somers D A (2003). Efficient soybean transformation using hygromycin B selection in the cotyledonary-node method. Planta , 216(5): 723–735
pmid:12624759
70 PalmerR G, Ortiz-PerezE, Cervantes-Martinez I G, WileyH, Hamlin S J, Healy R A, Horner H T, Davis W H (2003). Hybrid soybean–current status and future outlook. In: Proceedings of the 33rd Soybean Seed Research Conference, Washington, DC: American Seed Trade Association, 267–304
71 Perez P T, Cianzio S R, Palmer R G (2009). Evaluation of soybean [Glycine max (L.) Merr.] F1 hybrids. J Crop Improv , 23(1): 1–18
doi: 10.1080/15427520802417832
72 Qiu B X, Sleper D A, Rao-Arelli A P (1997). Genetic and molecular characterization of resistance to Heterodera glycines race isolates 1, 3 and 5 in Peking. Euphytica , 96(2): 225–231
doi: 10.1023/A:1002996613227
73 Raymer P L, Grey T L (2003). Challenges in comparing transgenic and nontransgenic soybean cultivars. Crop Sci , 43(5): 1584–1589
doi: 10.2135/cropsci2003.1584
74 Rech E L, Vianna G R, Arag?o F J (2008). High-efficiency transformation by biolistics of soybean, common bean and cotton transgenic plants. Nat Protoc , 3(3): 410–418
doi: 10.1038/nprot.2008.9 pmid:18323812
75 Salimath S, Bhattacharyya M K (1999). Generation of a soybean BAC library, and identification of DNA sequences tightly linked to the Rps1-k disease resistance gene. Theor Appl Genet , 98(5): 712–720
doi: 10.1007/s001220051125
76 Santra D K, Sandhu D, Tai T, Bhattacharyya M K (2003). Construction and characterization of a soybean yeast artificial chromosome library and identification of clones for the Rps6 region. Funct Integr Genomics , 3(4): 153–159
doi: 10.1007/s10142-003-0092-8 pmid:14520523
77 Sayama T, Nakazaki T, Ishikawa G, Yagasaki K, Yamada N, Hirota N, Hirata K, Yoshikawa T, Saito H, Teraishi M, Okumoto Y, Tsukiyama T, Tanisaka T (2009). QTL analysis of seed-flooding tolerance in soybean (Glycine max [L.] Merr.). Plant Sci , 176(4): 514–521
doi: 10.1016/j.plantsci.2009.01.007
78 Schmutz J, Cannon S B, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D L, Song Q, Thelen J J, Cheng J, Xu D, Hellsten U, May G D, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M K, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X C, Shinozaki K, Nguyen H T, Wing R A, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker R C, Jackson S A (2010). Genome sequence of the palaeopolyploid soybean. Nature , 463(7278): 178–183
doi: 10.1038/nature08670 pmid:20075913
79 Schupp J M, Dick A B, Zinnamon K N, Keim P (2001). Serial analysis of gene expression applied to soybean. Plant & Animal Genome IX Conference, Town & Country Hotel, San Diego, CA . http://www.intl-pag.org/9/abstracts/P08_14.html.
80 Seo J K, Hwang S H, Kang S H, Choi H S, Lee S H, Sohn S H, Kim K H (2007). Interaction study of soybean mosaic virus proteins with soybean proteins using the yeast-two hybrid system. Plant Pathol J , 23(4): 281–286
doi: 10.5423/PPJ.2007.23.4.281
81 Shi J, Wang H, Schellin K, Li B, Faller M, Stoop J M, Meeley R B, Ertl D S, Ranch J P, Glassman K (2007). Embryo-specific silencing of a transporter reduces phytic acid content of maize and soybean seeds. Nat Biotechnol , 25(8): 930–937
doi: 10.1038/nbt1322 pmid:17676037
82 Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton S W, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop E G, Vielweber C J, Schmatz M, Pape D, Bowers Y, Theising B, Martin J, Dante M, Wylie T, Granger C (2002). A compilation of soybean ESTs: generation and analysis. Genome , 45(2): 329–338
doi: 10.1139/g01-150 pmid:11962630
83 Shoemaker R C, Grant D, Olson T, Warren W C, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton S W, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schmutz J, Stacey G, Jackson S (2008). Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome , 51(4): 294–302
doi: 10.1139/G08-010 pmid:18356965
84 Shoemaker R C, Polzin K, Labate J, Specht J, Brummer E C, Olson T, Young N, Concibido V, Wilcox J, Tamulonis J P, Kochert G, Boerma H R (1996). Genome duplication in soybean (Glycine subgenus soja). Genetics , 144(1): 329–338
pmid:8878696
85 Shoemaker R C, Schlueter J, Doyle J J (2006). Paleopolyploidy and gene duplication in soybean and other legumes. Curr Opin Plant Biol , 9(2): 104–109
doi: 10.1016/j.pbi.2006.01.007 pmid:16458041
86 Shultz J L, Kazi S, Bashir R, Afzal J A, Lightfoot D A (2007). The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet , 114(6): 1081–1090
doi: 10.1007/s00122-007-0501-9 pmid:17287974
87 Song Q J, Marek L F, Shoemaker R C, Lark K G, Concibido V C, Delannay X, Specht J E, Cregan P B (2004). A new integrated genetic linkage map of the soybean. Theor Appl Genet , 109(1): 122–128
doi: 10.1007/s00122-004-1602-3 pmid:14991109
88 Stacey G, Libault M, Brechenmacher L, Wan J, May G D (2006). Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol , 9(2): 110–121
doi: 10.1016/j.pbi.2006.01.005 pmid:16458572
89 Subramanian S, Graham M Y, Yu O, Graham T L (2005). RNA interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to Phytophthora sojae. Plant Physiol , 137(4): 1345–1353
doi: 10.1104/pp.104.057257 pmid:15778457
90 Sun H, Zhao L M, Huang M (1994). Studies on cytoplasmic-nuclear male sterile soybean. Chin Sci Bull , 39(2): 175
91 Tanksley S D, McCouch S R (1997). Seed banks and molecular maps: unlocking genetic potential from the wild. Science , 277(5329): 1063–1066
doi: 10.1126/science.277.5329.1063 pmid:9262467
92 Tian A G, Wang J, Cui P, Han Y J, Xu H, Cong L J, Huang X G, Wang X L, Jiao Y Z, Wang B J, Wang Y J, Zhang J S, Chen S Y (2004). Characterization of soybean genomic features by analysis of its expressed sequence tags. Theor Appl Genet , 108(5): 903–913
doi: 10.1007/s00122-003-1499-2 pmid:14624337
93 Tian Z, Wang X, Lee R, Li Y, Specht J E, Nelson R L, McClean P E, Qiu L, Ma J (2010). Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA , 107(19): 8563–8568
doi: 10.1073/pnas.1000088107 pmid:20421496
94 Tomkins J P, Mahalingam R, Smith H, Goicoechea J L, Knap H T, Wing R A (1999). A bacterial artificial chromosome library for soybean PI 437654 and identification of clones associated with cyst nematode resistance. Plant Mol Biol , 41(1): 25–32
doi: 10.1023/A:1006277417789 pmid:10561065
95 Wang B J, Wang Y J, Wang Q, Luo G Z, Zhang Z G, He C Y, He S J, Zhang J S, Gai J Y, Chen S Y (2004a). Characterization of an NBS-LRR resistance gene homologue from soybean. J Plant Physiol , 161(7): 815–822
doi: 10.1016/j.jplph.2004.01.007 pmid:15310071
96 Wang C M, Wang H W, Zhang J S, Chen S Y (2008). A seed-specific AP2-domain transcription factor from soybean pays a certain role in regulation of seed germination. Sci in China , 51: 336–345 (Series C)
97 Wang D, Arelli P R, Shoemaker R C, Diers B W (2001). Loci underlying resistance to race 3 of soybean cyst nematode in Glycine soja plant introduction 468916. Theor Appl Genet , 103(4): 561–566
doi: 10.1007/PL00002910
98 Wang H W, Zhang B, Hao Y J, Huang J, Tian A G, Liao Y, Zhang J S, Chen S Y (2007). The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J , 52(4): 716–729
doi: 10.1111/j.1365-313X.2007.03268.x pmid:17877700
99 Wang Y, Suo H, Zheng Y, Liu K, Zhuang C, Kahle K T, Ma H, Yan X (2010). The soybean root-specific protein kinase GmWNK1 regulates stress-responsive ABA signaling on the root system architecture. Plant J , 64(2): 230–242
doi: 10.1111/j.1365-313X.2010.04320.x pmid:20735771
100 Wang Y J, Dongfang Y, Wang X Q, Yang Y L, Yu D Y, Gai J Y, Wu X L, He C Y, Zhang J S, Chen S Y (2004b). Mapping of five genes resistant to SMV strains in soybean. Yi Chuan Xue Bao , 31(1): 87–90
pmid:15468924
101 Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S, Nakamoto Y, Yamanaka N, Takahashi R, Ishimoto M, Anai T, Tabata S, Harada K (2009). Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics , 182(4): 1251–1262
doi: 10.1534/genetics.108.098772 pmid:19474204
102 Wei W, Huang J, Hao Y J, Zou H F, Wang H W, Zhao J Y, Liu X Y, Zhang W K, Ma B, Zhang J S, Chen S Y (2009). Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants. PLoS ONE , 4(9): e7209
doi: 10.1371/journal.pone.0007209 pmid:19789627
103 Wong C E, Singh M B, Bhalla P L (2009). Molecular processes underlying the floral transition in the soybean shoot apical meristem. Plant J , 57(5): 832–845
doi: 10.1111/j.1365-313X.2008.03730.x pmid:18980639
104 Wu C, Sun S, Nimmakayala P, Santos F A, Meksem K, Springman R, Ding K, Lightfoot D A, Zhang H B (2004). A BAC- and BIBAC-based physical map of the soybean genome. Genome Res , 14(2): 319–326
doi: 10.1101/gr.1405004 pmid:14718376
105 Wu X, Blake S, Sleper D A, Shannon J G, Cregan P, Nguyen H T (2009). QTL, additive and epistatic effects for SCN resistance in PI 437654. Theor Appl Genet , 118(6): 1093–1105
doi: 10.1007/s00122-009-0965-x pmid:19184662
106 Wu X L, He C Y, Wang Y J, Zhang Z Y, Dongfang Y, Zhang J S, Chen S Y, Gai J Y (2001a). Construction and analysis of a genetic linkage map of soybean. Yi Chuan Xue Bao , 28(11): 1051–1061
pmid:11725640
107 Wu X L, Wang Y J, He C Y, Chen S Y, Gai J Y, Wang X C (2001b). QTLs mapping of some agronomic traits of soybean. Yi Chuan Xue Bao , 28(10): 947–955
pmid:11695267
108 Xie Z M, Zou H F, Lei G, Wei W, Zhou Q Y, Niu C F, Liao Y, Tian A G, Ma B, Zhang W K, Zhang J S, Chen S Y (2009). Soybean Trihelix transcription factors GmGT-2A and GmGT-2B improve plant tolerance to abiotic stresses in transgenic Arabidopsis. PLoS ONE , 4(9): e6898
doi: 10.1371/journal.pone.0006898 pmid:19730734
109 Yang J Y, Gai J Y (2009). Heterosis, combining ability and their genetic basis of yield among key parental materials of soybean in Huang-Huai Valleys. Acta Agron Sin , 35(4): 620–630
doi: 10.3724/SP.J.1006.2009.00620
110 Yang K, Moon J K, Jeong N, Back K, Kim H M, Jeong S C (2008). Genome structure in soybean revealed by a genomewide genetic map constructed from a single population. Genomics , 92(1): 52–59
doi: 10.1016/j.ygeno.2008.03.008 pmid:18486440
111 Yi J, Derynck M R, Li X, Telmer P, Marsolais F, Dhaubhadel S (2010). A single-repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J , 62(6): 1019–1034
pmid:20345602
112 Zhang W K, Wang Y J, Luo G Z, Zhang J S, He C Y, Wu X L, Gai J Y, Chen S Y (2004). QTL mapping of ten agronomic traits on the soybean ( Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet , 108(6): 1131–1139
doi: 10.1007/s00122-003-1527-2 pmid:15067400
113 Zhou Q Y, Tian A G, Zou H F, Xie Z M, Lei G, Huang J, Wang C M, Wang H W, Zhang J S, Chen S Y (2008). Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol J , 6(5): 486–503
doi: 10.1111/j.1467-7652.2008.00336.x pmid:18384508
114 Zhu S, Saski C A, Boerma H R, Tomkins J P, All J N, Parrott W A (2009). Construction of a BAC library for a defoliating insect-resistant soybean and identification of candidate clones using a novel approach. Plant Mol Biol Rep , 27(2): 229–235
doi: 10.1007/s11105-008-0077-9
115 Zhu T, Shi I, Funke R P, Gresshoff P M, Keim P (1996). Characterization and application of soybean YACs to molecular cytogenetics. Mol Gen Genet , 252(4): 483–488
doi: 10.1007/BF02173014 pmid:8879250
116 Zhu Y L, Song Q J, Hyten D L, Van Tassell C P, Matukumalli L K, Grimm D R, Hyatt S M, Fickus E W, Young N D, Cregan P B (2003). Single-nucleotide polymorphisms in soybean. Genetics , 163(3): 1123–1134
pmid:12663549
[1] TAO Yongsheng, ZHANG Zuxin, CHEN Yonglin, LI Lijia, ZHENG Yonglian. Technological exploration of BAC-FISH on mitotic chromosomes of maize[J]. Front. Biol., 2008, 3(4): 414-418.
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