The accurate mapping of quantitative trait loci (QTL) depends notably on the number of recombination events occurring in the segregating population. The cost of phenotyping often limits the sample size used in QTL map...The accurate mapping of quantitative trait loci (QTL) depends notably on the number of recombination events occurring in the segregating population. The cost of phenotyping often limits the sample size used in QTL mapping. To get round this problem, we assessed a selective phenotyping method, called qtlRec sampling. In order to improve the accuracy of QTL mapping, a subset of individuals was selected to maximize the number of recombination events at putative QTL positions;the usefulness of this subset was compared to a selected sample built to maximize the recombination rate over the whole genome. We assessed this method on the quantitative oil content trait in Brassica napus. We showed that the qtlRec strategy could allow increasing accuracy (both support interval and position) of QTL location while it maintained a similar power of detection. We then applied this approach to the B. napus—Leptosphaeria maculans pathosystem for which resistance QTL with minor effect were previously identified. This allowed the validation of the QTL in six genomic regions. The qtlRec method is an attractive strategy for validating QTL in multiple year and/or location trials for a trait which requires costly and time-consuming phenotyping.展开更多
Leptosphaeria maculans is a serious concern for canola production worldwide.For effective disease management,knowledge of the pathogen’s genetic variability and population structure is a prerequisite.In this study,wh...Leptosphaeria maculans is a serious concern for canola production worldwide.For effective disease management,knowledge of the pathogen’s genetic variability and population structure is a prerequisite.In this study,whole-genome sequencing was performed for 162 of 1590 L.maculans isolates collected in the years 2007e2008 and 2012e2014 in Western Canada.DNA variants in genome-wide and specific regions including avirulence(Avr)genes were characterized.A total of 31,870 high-quality polymorphic DNA variants were used to study L.maculans genetic diversity and population structure.Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants.The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations.Principal component analysis with genome-wide variants showed that the isolates collected in 2012e2014 were more genetically diverse than those collected in 2007e2008.Population structure analysis discovered three distinct sub-populations.Although isolates from Saskatchewan and Alberta were of similar genetic composition,Manitoba isolates were highly diverse.Genome-wide association study detected DNA variants in genes AvrLm4-7,Lema_T86300,and Lema_T86310 associated with the years of collection.展开更多
文摘The accurate mapping of quantitative trait loci (QTL) depends notably on the number of recombination events occurring in the segregating population. The cost of phenotyping often limits the sample size used in QTL mapping. To get round this problem, we assessed a selective phenotyping method, called qtlRec sampling. In order to improve the accuracy of QTL mapping, a subset of individuals was selected to maximize the number of recombination events at putative QTL positions;the usefulness of this subset was compared to a selected sample built to maximize the recombination rate over the whole genome. We assessed this method on the quantitative oil content trait in Brassica napus. We showed that the qtlRec strategy could allow increasing accuracy (both support interval and position) of QTL location while it maintained a similar power of detection. We then applied this approach to the B. napus—Leptosphaeria maculans pathosystem for which resistance QTL with minor effect were previously identified. This allowed the validation of the QTL in six genomic regions. The qtlRec method is an attractive strategy for validating QTL in multiple year and/or location trials for a trait which requires costly and time-consuming phenotyping.
文摘Leptosphaeria maculans is a serious concern for canola production worldwide.For effective disease management,knowledge of the pathogen’s genetic variability and population structure is a prerequisite.In this study,whole-genome sequencing was performed for 162 of 1590 L.maculans isolates collected in the years 2007e2008 and 2012e2014 in Western Canada.DNA variants in genome-wide and specific regions including avirulence(Avr)genes were characterized.A total of 31,870 high-quality polymorphic DNA variants were used to study L.maculans genetic diversity and population structure.Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants.The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations.Principal component analysis with genome-wide variants showed that the isolates collected in 2012e2014 were more genetically diverse than those collected in 2007e2008.Population structure analysis discovered three distinct sub-populations.Although isolates from Saskatchewan and Alberta were of similar genetic composition,Manitoba isolates were highly diverse.Genome-wide association study detected DNA variants in genes AvrLm4-7,Lema_T86300,and Lema_T86310 associated with the years of collection.
