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Soybean Genomics: Developments through the Use of Cultivar “Forrest”

By David A. Lightfoot


Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) ∼200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses

Topics: Review Article
Publisher: Hindawi Publishing Corporation
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  1. (2004). A BAC- and BIBAC-based physical map of the soybean genome,”
  2. (1999). A bacterial artificial chromosome library for soybean PI 437654 and identification of clones associated with cyst nematode resistance,”
  3. (2006). A catalog of duplicated regions from markerampliconhomologsandBACDNAsequenceanalysis in soybean, a paleopolyploid genome,”
  4. (2002). A compilation of soybean ESTs: generation and analysis,”
  5. (2004). A decade of QTL mapping for cyst nematode resistance in soybean,”
  6. (2007). A f z a l ,S .F a s i ,R .M u n g u r ,D .B .G o o d e n o w e ,a n dD
  7. (2000). A method for breeding and genetically manipulating phytoestrogen content in soybeans,”
  8. (2007). A microsatellite map developed from late maturity germplasm ‘Essex’ by ‘Forrest’ detects four QTL for soybean seed yield expected from early maturing germplasm,”
  9. (2002). A pyramid of loci for partial resistance to Fusarium solani f. sp. glycines maintains myo-inositol-1-phoshate synthase expression in soybean roots,”
  10. (2002). A revised classification scheme for genetically diverse populations of Heterodera glycines
  11. A sequence based synteny map between soybean and
  12. (2008). a z i ,J .L .S h u l t z ,R .B a s h i r ,A .J .A f z a l ,V .N .N j i t i ,a n d
  13. (2007). a z i ,V .N .N j i t i ,T .W .D o u b l e r ,e ta l . ,“ R e g i s t r a t i o n of the flyer x hartwig recombinant inbred line mapping population,”
  14. (2001). An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion,”
  15. (2006). An updated ‘Essex’ by ‘Forrest’ inkage map and first composite interval map of QTL underlying six soybean traits,”
  16. Analysis of the activity of the soybean laccase encoded within the Rfs2/Rhg1 locus,” Theoretical and Applied Genetics.
  17. (2004). and K.Wang,“AssessmentofconditionsaffectingAgrobacteriummediated soybean transformation using the cotyledonary node explant,”
  18. (2006). Application of comparative genomics in developing molecular markers tightly linked to the virus resistance gene
  19. (2004). Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis ,”
  20. (2004). Application of DNA markers: soybean improvement,”
  21. (1997). Association of loci underlying field resistance to soybean sudden death syndrome (SDS) and cyst nematode (SCN) race 3,”
  22. (2006). AtCAT6, a sink-tissue-localized transporter for essential amino acids in Arabidopsis ,”
  23. (1998). B e l l - J o h n s o n ,G .R .G a r v e y ,J .E .J o h n s o
  24. (2003). C a r b o n e ,L .O .M e a r n s ,T .M a v r o m a t i s
  25. (2001). c h u s t e r ,R .V .A b d e l n o o r
  26. C.R.Yesudas,J.L.Shultz,andD.A.Lightfoot,“Identification of loci underlying resistance to Japanese beetle herbivory, in soybean,” Theoretical and Applied Genetics.
  27. (2004). Characterization of soybean genomic features by analysis of its expressed sequence tags,”
  28. (2006). Cloning and comparative analysis of the gene encoding diacylglycerol acyltransferase from wild type and cultivated soybean,”
  29. (2002). Common loci underlie field resistance to soybean sudden death syndrome
  30. (2004). Comparative physical mapping reveals features of microsynteny between
  31. (2001). Construct design for efficient, effective and high-throughput gene silencing in plants,”
  32. (2004). Construction and characterization of a soybean bacterial artificial chromosomelibraryand useofmultiple complementary librariesfor genome physical mapping,”
  33. (2004). Definition of soybean genomic regions that control seed phytoestrogen amounts,”
  34. (2004). Deletion of a disease resistance nucleotide-binding-site leucine-rich-repeat-like sequence is associated with the loss of the Phytophthora resistance gene
  35. (2007). Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with F. graminearum genomic
  36. (2006). Development of a pooled probe method for locating small gene families in a physical map of soybean using stress related paralogues and a BAC minimum tile path,”
  37. (2007). Development of microsatellite markers from the soybean sequence ready physical map,”
  38. (1999). Dietary soy protein and soy isoflavones: histological examination of reproductive tissues in rats,”
  39. (2003). Differentially abundant mRNAs in rat liver
  40. (2002). Dissection of gene clusters underlying resistance to Fusarium solani F. sp. glycines (Rfs loci) and Heterodera glycines (Rhg loci) in soybean,”
  41. Duplication of a chromosomal region from linkage group A2 involved in soybean cyst nematode resistance in soybean,” Molecular Breeding.
  42. (2001). e k s e m ,E .R u b e n ,D .H y t e n ,K .T r i w i t a y a k o r n ,a n dD .A .
  43. (2001). e k s e m ,E .R u b e n ,D .L .H y t e n ,M .E .S c h m i d t ,a n dD
  44. (2001). e k s e m ,P .P a n t a z o p o u l o s ,V .N .N j i t i ,L .D .H y t e n
  45. (1999). e k s e m ,T .W .D o u b l e r ,K .C h a n c h a r o e n c h a i ,e ta l . , “Clustering among loci underlying soybean resistance to Fusarium solani,
  46. (2001). e k s e m ,V .N .N j i t i ,W .J .B a n z ,e ta l . ,“ M o l e c u l a rm a r k e r s ofphytoestrogencontentinsoybeans,”JournalofBiomedicine and Biotechnology,
  47. (1999). Effect of diseases on soybean yields in the United States and Ontario
  48. Enhancement of the Forrest physical map with four color fluorescent fingerprints of a minimum tile path,”
  49. (1991). Estimation of nuclear DNA content of plants by flow cytometry,”
  50. (2003). Evaluating physical maps by clone location comparisons,”
  51. (1992). Evaluation of soybean RFLP marker diversity in adapted germplasm,”
  52. (2005). Ex vitro composite plants: an inexpensive, rapid method for root biology,”
  53. (2007). for seed isoflavones, protein, oil and Japanese beetle (Popillia japonica, Newman) resistance in soybean [Glycine max (L.) Merr.],”
  54. (2004). G.Stacey,A.Dorrance,H.Nguyen,etal.,“SoyCAP:roadmap for soybean translational genomics,” white paper.
  55. (2006). Genetic analysis infers Dt loci underlie resistance to Fusarium solani f. sp. glycines in indeterminate soybeans,”
  56. (2007). Genetic analysis of soybean plant height, hypocotyl and internode lengths,”
  57. (2003). Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of
  58. (1996). Genetic diversity patterns in North American public soybean cultivars based on coefficient of parentage,”
  59. (1996). Genetic mapping of loci underlying field resistance to soybean sudden death syndrome
  60. (1995). Genetic mapping of soybean cyst nematode
  61. (1999). Genetics of soybean agronomic traits—I: comparison of three related recombinant inbred populations,”
  62. (1996). Genome duplication in soybean (Glycine subgenus soja),”
  63. (2000). Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis
  64. (2005). Genomic analysis of a region encompassing QRfs1 and QRfs2: genes that underlie soybean resistancetosuddendeathsyndrome,”Genome,v ol.48,no .1,
  65. (2006). Genomic analysis of the Rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode,”
  66. (2005). Gijzen,andI.Rajcan,“MappingQTLforindividualandtotal isoflavone content in soybean seeds,”
  67. (2001). Gresshoff,J .S ti ll e r ,T .L .D .M c G u i r e ,eta l . ,“ I n t egra ti n g functional genomics to define the plants function in symbiotic nodulation,” in Nitrogen Fixation: Global Perspectives,T
  68. GXE interactions and development influence loci underlying seed quality traits in soybean,” Theoretical and Applied Genetics.
  69. (2005). Highly syntenic regions in the genomes of soybean,
  70. (2001). I q b a l ,K .M e k s e m ,V .N .N j i t i ,M .A .K a s s e m ,a n dD .A . Lightfoot, “Microsatellite markers identify three additional quantitative trait loci for resistance to soybean sudden-death syndrome (SDS)
  71. Identification of loci underlying seed yield and resistance to soybean cyst nematode race 2 in ‘Hartwig’,” Theoretical and Applied Genetics.
  72. (1991). Inheritance of resistance and genetic relationships among soybean plant introductions
  73. Inoculum rate influences selection for field resistance to soybean sudden death syndrome in the greenhouse,”
  74. (1994). Isoflavone composition of American and Japanese soybeans in Iowa: effects of variety, crop year, and location,”
  75. (2007). Isolated polynucleotides and polypeptides relating to loci underlying seed protein and oil content and methods of use thereof,”
  76. (2006). LegumeDB1 bioinformatics resource: comparative genomic analysis and novelcross-generamarkeridentificationinlupinandpasture legume species,”
  77. (2004). Loci underlying resistance to manganese toxicity mapped in a soybean recombinant inbred line population of
  78. (2007). Mapping and confirmation of a new sudden death
  79. (2003). Marker assisted selection for soybean,” in Agricultural Biotechnology
  80. (2007). Method of determining soybean sudden death syndrome resistant in a soybean plant,”
  81. (2007). Minimum tile derived microsatellite markers improve the physical map of the soybean genome and the Essex by Forrest genetic map,” M.S. thesis,
  82. (2004). Mining EST databases to resolve evolutionary events in major crop species,”
  83. (2007). Molecular and functional analysis of the Rhg4 locus conferring resistance to the soybean cyst nematode,”
  84. (2000). Molecular markers of phytoestrogen content in soybeans,”
  85. (2001). Novel polynucleotides and polypeptides relating to loci underlying resistance to soybean cyst nematode and methods of use thereof,”
  86. QTL underlying seedling root traits mapped in the ‘Essex’ by ‘Forrest’ soybean RIL population,” Annals of Botany.
  87. (1987). Quantitative genetics: results relevant to soybean breeding,” in Soybeans: Improvement, Production, and Uses,
  88. (2002). Quantitative trait loci associated with foliar trigonelline accumulation in Glycine max
  89. (2002). Quantitative trait loci in two soybean recombinant inbred line populations segregating for yield and disease resistance,”
  90. (1997). Rate-reducing resistance to Fusarium solani f. sp. phaseoli underlies field resistance to soybean sudden death syndrome,”
  91. (2007). Reannotation of the physical map of Glycine max for ploidy by BAC end sequence driven whole genome shotgun read assembly,”
  92. (2004). Refined glufosinate selection in Agrobacterium-mediated transformation of soybean [Glycine max (L.)
  93. (2005). Registration of Essex x Forrest recombinant inbred line mapping population,”
  94. (1999). Registration of LSG96 soybean germplasm resistant to soybean sudden death syndrome (SDS) and soybean cyst nematode race 3,”
  95. (2005). Report of yield QTL—coordination topic,”
  96. (2002). Resistance locus pyramids alter transcript abundance in soybean roots inoculated with Fusarium solani f.
  97. (1998). Resistance to soybean sudden death syndrome and root colonization by Fusarium solani f. sp. glycine in near-isogenic lines,”
  98. (1999). Root colonization of soybean cultivars in the field by Fusarium solani f.
  99. (2005). Root response to Fusarium solani f. sp. glycines: temporal accumulation of transcripts in partially resistant and susceptible soybean,”
  100. (1999). Selecting soybean cultivars for dual resistance to soybean cyst nematode and sudden death syndrome using two
  101. (2007). Sequencing of BAC ends associated with an updated
  102. (2003). Somers,“Efficientsoybeantransformationusinghygromycin B selection in the cotyledonary-node method,”
  103. (2007). Soybean disease resistance protein RHG1-LRR domain expressed, purified and refolded from Escherichia coli inclusion bodies: preparation for a functional analysis,”
  104. Soybean Genetics Committee Report,
  105. (2001). Soybean sudden death syndrome resistant soybeans, soybean cyst nematode resistant soybeans and methods of breeding and identifying resistant plants,”
  106. (2007). Soybean tilling project,”
  107. (1999). Soybean yield potential—a genetic and physiological perspective,”
  108. (2003). Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex: F. virguliforme
  109. (1999). Survey of trigonelline concentrations in salt-stressed leaves of cultivated
  110. (1999). The effects of soy protein and soy phytoestrogens on symptoms associated with cardiovascular disease in rats,”22
  111. (2004). The genetic diversity of cultivated soybean grown
  112. (1988). The genomic relationship between Glycine max (L.) Merr. and G. soja Sieb. and Zucc. as revealed by pachytene chromosome analysis,”
  113. (2007). The identification of QTL underlying resistance to aluminum toxicity in a soybean recombinant inbred line population of Essex x Forrest,” M.S. thesis,
  114. (2005). The legume information system (LIS): an integrated information resource for comparative legume biology,”
  115. (2006). The soybean genome database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max ,”
  116. (2006). Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. ‘Forrest’): tools for structural and functional genomics,”
  117. (2006). Toward a reference sequence of the soybean genome: a multiagency effort,”
  118. (2005). Transcriptional profile of the Arabidopsis root quiescent center,”
  119. (1996). Two additional loci underlying durable field resistance to soybean sudden death syndrome
  120. (2000). Two largeinsert soybean genomic libraries constructed in a binary vector: applications in chromosome walking and genome wide physical mapping,”
  121. (2003). V.C.Concibido,B.LaVallee,P.Mclaird,etal.,“Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars,”
  122. (2004). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicategenes,”ThePlantCell,vol.16,no.7,pp.1667–1678,
  123. (2003). Wood,“Trigonellineconcentrationinfield-grownsoybeanin response to irrigation,” Biologia Plantarum,v o l .4 6 ,n o .3 ,p p .