Abstract
BackgroundIntegrating 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.ResultsNineteen 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.ConclusionsMeta-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.
Highlights
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
Bibliographic review of QTL mapping studies The initial map set comprised a total of 37 maps divided into i) 29 QTL maps from 19 publications related to QTL detection of late blight resistance and maturity type, and ii) eight independent reference maps (Table 1)
Resistance tests were based on disease spread on foliage in the field (FF) or in the greenhouse (FG), sporulation or necrosis spots on in vitro detached leaflets or leaf discs (LT), necrosis progression on stems (ST) and disease damage on tuber slices (TS) or whole tubers (T% or WT) in controlled conditions
Summary
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). 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. The general principle of a meta-analysis is to pool the results of several studies that address the same issue to improve the estimate of targeted parameters. QTL meta-analyses have been achieved for traits related to plant development and plant response to environment (nutrients, abiotic and biotic stresses) in maize, wheat, rice, rapeseed, cotton, soybean, cocoa and apricot [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18]
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