title: Prospects for advancing defense to cereal rusts through genetical genomics.
abstract: Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99), was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are susceptible to this new race. Pgt TTKSK has already spread northward into Iran and will likely spread eastward throughout the Indian subcontinent in the near future. This scenario is not unique to stem rust; new races of leaf rust (Puccinia triticina) and stripe rust (Puccinia striiformis) have also emerged recently. One strategy for countering the persistent adaptability of these pathogens is to stack complete- and partial-resistance genes, which requires significant breeding efforts in order to reduce deleterious effects of linkage drag. These varied resistance combinations are typically more difficult for the pathogen to defeat, since they would be predicted to apply lower selection pressure. Genetical genomics or expression Quantitative Trait Locus (eQTL) analysis enables the identification of regulatory loci that control the expression of many to hundreds of genes. Integrated deployment of these technologies coupled with efficient phenotyping offers significant potential to elucidate the regulatory nodes in genetic networks that orchestrate host defense responses. The focus of this review will be to present advances in genetical genomic experimental designs and analysis, particularly as they apply to the prospects for discovering partial disease resistance alleles in cereals.
authors: Corn Insects and Crop Genetics Research, Department of Plant Pathology and Microbiology, US Department of Agriculture - Agricultural Research Service, Center for Plant Responses to Environmental Stresses, Iowa State University Ames, IA, USA.
authors: Elsa
authors: E
authors: Ballini
authors: Nick
authors: N
authors: Lauter
authors: Roger
authors: R
authors: Wise
keywords: Puccinia; Triticeae; barley; cereal rusts; eQTL; parallel expression; wheat
references: Genetics. 2004 Aug;167(4):1949-59
references: 15342532
references: Trends Genet. 1991 Feb;7(2):55-60
references: 2035192
references: Nat Rev Genet. 2006 Nov;7(11):862-72
references: 17047685
references: Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71
references: 21536894
references: PLoS Genet. 2011 Jul;7(7):e1002208
references: 21829384
references: PLoS One. 2011;6(8):e24230
references: 21909385
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D1194-201
references: 22084198
references: Mol Plant Pathol. 2005 Mar 1;6(2):99-111
references: 20565642
references: Yi Chuan Xue Bao. 2006 Jul;33(7):617-24
references: 16875319
references: Annu Rev Genet. 2001;35:303-39
references: 11700286
references: Mol Plant Pathol. 2008 Jul;9(4):463-78
references: 18705861
references: BMC Proc. 2007;1 Suppl 1:S94
references: 18466598
references: Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15253-8
references: 14645721
references: Funct Integr Genomics. 2008 Aug;8(3):187-98
references: 18196301
references: Mol Plant Pathol. 2008 Sep;9(5):563-75
references: 19018988
references: Plant Physiol. 2004 Mar;134(3):960-8
references: 15020760
references: Mol Biol Rep. 2008 Sep;35(3):337-43
references: 17564813
references: Annu Rev Plant Biol. 2009;60:139-64
references: 19014346
references: Plant Cell. 2002 May;14(5):979-92
references: 12034891
references: Theor Appl Genet. 2009 Jan;118(2):385-97
references: 18956175
references: Mamm Genome. 2006 Jun;17(6):509-17
references: 16783633
references: Mol Plant Microbe Interact. 2011 Jun;24(6):694-705
references: 21323465
references: Genetics. 2007 Mar;175(3):1441-50
references: 17179097
references: Science. 2011 Jul 29;333(6042):596-601
references: 21798943
references: Genetics. 2003 Jun;164(2):655-64
references: 12807786
references: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1708-13
references: 17237218
references: Mol Plant Pathol. 2007 Jul;8(4):451-67
references: 20507513
references: Mycol Res. 2007 Feb;111(Pt 2):163-75
references: 17324755
references: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14970-5
references: 18812501
references: Plant Dis. 2006 Apr;90(4):476-480
references: 30786597
references: BMC Genomics. 2008 May 23;9:242
references: 18498664
references: Nat Immunol. 2006 Dec;7(12):1243-9
references: 17110940
references: Plant Physiol. 2010 Feb;152(2):480-6
references: 19933384
references: Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9328-33
references: 12077318
references: PLoS One. 2012;7(2):e32253
references: 22389690
references: Phytopathology. 2009 Jan;99(1):89-94
references: 19055439
references: Plant J. 2008 Jan;53(1):90-101
references: 17944808
references: Genetics. 2008 Dec;180(4):2237-50
references: 18845849
references: Science. 2007 Mar 30;315(5820):1786-7
references: 17395806
references: Plant Dis. 2004 Jul;88(7):703-708
references: 30812479
references: Genome Res. 2007 Dec;17(12):1707-16
references: 18063559
references: Theor Appl Genet. 2008 Jul;117(2):261-72
references: 18542913
references: Science. 2009 Mar 6;323(5919):1360-3
references: 19229000
references: Annu Rev Plant Biol. 2009;60:93-114
references: 19012536
references: BMC Bioinformatics. 2008 Jun 17;9:284
references: 18559105
references: Plant Physiol. 2004 Jun;135(2):695-701
references: 15208416
references: Bioinformatics. 2007 Sep 1;23(17):2290-7
references: 17599927
references: Genetics. 2007 May;176(1):645-57
references: 17339203
references: Trends Plant Sci. 2009 Jan;14(1):21-9
references: 19062327
references: Nature. 2012 Nov 29;491(7426):711-6
references: 23075845
references: Annu Rev Phytopathol. 2011;49:391-413
references: 21599495
references: PLoS Genet. 2008 Oct;4(10):e1000232
references: 18949031
references: Trends Plant Sci. 2008 Feb;13(2):72-7
references: 18262820
references: PLoS Genet. 2008 Nov;4(11):e1000260
references: 19008955
references: Mol Plant Microbe Interact. 2013 Apr;26(4):407-18
references: 23216085
references: Mol Plant. 2008 May;1(3):538-51
references: 19825559
references: Plant J. 2008 Oct;56(2):287-296
references: 18643973
references: PLoS One. 2013;8(1):e54603
references: 23372741
references: Mol Plant Pathol. 2008 Mar;9(2):157-69
references: 18705849
references: Annu Rev Phytopathol. 2007;45:399-436
references: 17506648
references: Mol Plant Pathol. 2005 Mar 1;6(2):139-51
references: 20565645
references: Mol Plant Microbe Interact. 2001 Dec;14(12):1376-83
references: 11768532
references: BMC Genomics. 2009 Jun 29;10:285
references: 19558723
references: Science. 2011 Jul 29;333(6042):601-7
references: 21798944
references: Plant Dis. 2006 Jan;90(1):113
references: 30786499
references: Genetics. 2008 Jan;178(1):539-51
references: 18202393
references: Genome Res. 2004 Jun;14(6):997-1001
references: 15173107
references: Plant Cell. 2007 Dec;19(12):4035-45
references: 18156216
references: Poult Sci. 2007 Jul;86(7):1501-9
references: 17575201
references: Gene. 2007 May 15;393(1-2):145-52
references: 17566170
references: Nat Rev Genet. 2002 Jan;3(1):43-52
references: 11823790
references: Trends Genet. 2008 Aug;24(8):408-15
references: 18597885
references: Cell. 1999 Nov 12;99(4):355-66
references: 10571178
references: Physiol Genomics. 2006 Dec 13;28(1):15-23
references: 16985008
references: Cell. 2006 Feb 24;124(4):803-14
references: 16497589
references: Plant Biotechnol J. 2010 Jan;8(1):10-27
references: 20055957
references: Curr Opin Plant Biol. 2008 Apr;11(2):187-92
references: 18343713
references: Curr Opin Biotechnol. 2003 Apr;14(2):177-93
references: 12732319
references: Cell Microbiol. 2012 Jul;14(7):1071-84
references: 22372664
references: Trends Genet. 2008 Oct;24(10):518-24
references: 18774198
references: PLoS One. 2007 Dec 19;2(12):e1322
references: 18094747
references: Plant J. 2002 May;30(4):415-29
references: 12028572
references: Theor Appl Genet. 2008 Aug;117(3):401-11
references: 18470504
references: Annu Rev Phytopathol. 2007;45:329-69
references: 17480183
references: Genetics. 2007 Jun;176(2):789-800
references: 17409081
references: Mol Plant Microbe Interact. 2008 Dec;21(12):1515-27
references: 18986248
references: BMC Genomics. 2010 Nov 11;11:629
references: 21070652
references: PLoS Genet. 2013;9(1):e1003202
references: 23341782
references: Science. 2009 Mar 6;323(5919):1357-60
references: 19228999
references: Plant J. 2003 Nov;36(3):353-65
references: 14617092
references: Nature. 2006 Nov 16;444(7117):323-9
references: 17108957
references: Nature. 2012 Nov 29;491(7426):705-10
references: 23192148
references: Trends Genet. 2001 Jul;17(7):388-91
references: 11418218
references: Nat Genet. 2006 Aug;38(8):855-6; author reply 856-9
references: 16874319
references: Nat Genet. 2010 Dec;42(12):1060-7
references: 21037569
references: Genetics. 2002 Sep;162(1):381-94
references: 12242248
references: Trends Plant Sci. 2004 Oct;9(10):490-8
references: 15465684
references: Proteomics. 2006 Mar;6(6):1897-907
references: 16479535
references: Int J Plant Genomics. 2007;2007:17542
references: 18288238
references: Mol Ecol. 2008 Sep;17(17):3818-26
references: 18673440
references: PLoS One. 2010 Jan 06;5(1):e8598
references: 20066049
references: Theor Appl Genet. 2006 Sep;113(5):847-55
references: 16832646
references: Mol Plant Pathol. 2008 Jul;9(4):479-93
references: 18705862
references: Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):302-7
references: 14694194
references: Phytopathology. 2007 Sep;97(9):1083-93
references: 18944173
references: Semin Cancer Biol. 2007 Apr;17(2):166-87
references: 17218111
references: Plant Cell. 1999 Jul;11(7):1365-76
references: 10402435
references: Cell Cycle. 2009 Apr 1;8(7):977-81
references: 19270526
references: Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945-50
references: 12684538
references: Trends Genet. 2005 Jul;21(7):377-81
references: 15908034