Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits.
BACKGROUND
Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits.


RESULTS
Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes.


CONCLUSIONS
Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.
Institut National de la Recherche Agronomique, UR 1052 Génétique et Amélioration des Fruits et Légumes, BP94, 84140 Montfavet, France.
Sarah
S
Danan
Jean-Baptiste
JB
Veyrieras
Véronique
V
Lefebvre
D002874:Chromosome Mapping; D017343:Genes, Plant / Q000235:genetics; D056726:Genetic Association Studies; D005819:Genetic Markers; D007113:Immunity, Innate / Q000235:genetics*; D055750:Phytophthora infestans / Q000502:physiology*; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D040641:Quantitative Trait Loci / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D011198:Solanum tuberosum / Q000235:genetics* / Q000382:microbiology*
D005819:Genetic Markers
Phytopathology. 2006 Feb;96(2):120-9
18943914
Mol Plant Microbe Interact. 2010 Sep;23(9):1206-16
20687810
Theor Appl Genet. 1991 Nov;83(1):49-57
24202256
Genetics. 2006 Jun;173(2):1075-87
16582432
Mol Plant Microbe Interact. 2009 Jun;22(6):630-41
19445588
Genetics. 2003 Dec;165(4):2107-16
14704190
Theor Appl Genet. 2005 Aug;111(3):456-66
15942755
Theor Appl Genet. 2005 Aug;111(3):609-17
15931506
Genetics. 2004 Dec;168(4):2169-85
15611184
Genetics. 2007 Aug;176(4):2577-88
17565937
Theor Appl Genet. 2008 Sep;117(5):729-47
18566796
Theor Appl Genet. 2005 Oct;111(6):1201-14
16133311
Plant J. 2011 Mar;65(5):745-56
21251102
Plant Biotechnol J. 2003 Nov;1(6):399-410
17134399
Theor Appl Genet. 2007 Jun;115(1):101-12
17468842
Mol Plant Microbe Interact. 2002 Jun;15(6):587-97
12059107
Theor Appl Genet. 2007 Feb;114(3):501-13
17177064
Bioinformatics. 2008 Feb 1;24(3):422-3
18202028
Trends Plant Sci. 2010 Apr;15(4):219-26
20153971
Mol Plant Microbe Interact. 2004 Oct;17(10):1126-38
15497405
BMC Plant Biol. 2008 Jan 23;8:8
18215301
Mol Plant Microbe Interact. 2008 Jul;21(7):859-68
18533827
Theor Appl Genet. 2010 Nov;121(8):1465-82
20658277
Genetics. 1992 Dec;132(4):1141-60
1360934
Theor Appl Genet. 2009 Aug;119(4):705-19
19533081
Nat Genet. 1996 Dec;14(4):421-9
8944022
BMC Bioinformatics. 2007 Feb 08;8:49
17288608
Cell Mol Biol Lett. 2004;9(4B):855-67
15647802
Theor Appl Genet. 2007 Feb;114(3):569-84
17171391
Bioinformatics. 2004 Sep 22;20(14):2324-6
15059820
Behav Genet. 1997 Mar;27(2):125-32
9145551
Theor Appl Genet. 2006 Sep;113(5):943-51
16845519
Planta. 2008 Jul;228(2):293-306
18431595
Mol Plant Microbe Interact. 2008 Jul;21(7):909-18
18533831
Mol Plant Pathol. 2009 May;10(3):347-60
19400838
Mol Gen Genet. 1998 Aug;259(3):233-45
9749666
Genetics. 1994 May;137(1):67-77
7914505
BMC Genomics. 2005 Sep 14;6:124
16162286
Theor Appl Genet. 2003 Jan;106(2):317-25
12582858
Genetics. 2000 May;155(1):463-73
10790417
Plant Mol Biol. 2002 Mar-Apr;48(5-6):601-13
11999837
Theor Appl Genet. 2009 Aug;119(3):383-95
19430758
Genetics. 1988 Dec;120(4):1095-103
17246486
Genomics. 2008 Nov;92(5):344-52
18755262
Genetics. 2009 Jul;182(3):851-61
19414564
BMC Genomics. 2009 Jun 22;10:276
19545420
Mol Gen Genet. 1998 Aug;259(2):150-60
9747706