RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.
The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 genes with SNPs were identified between the parents, and then classified based on the results from the sequenced bulks. We calculated the bulk frequency ratio (BFR) of SNPs between resistant and susceptible bulks, selecting those showing sixfold enrichment/depletion in the corresponding bulks (BFR > 6). Using additional filtering criteria, we reduced the number of genes with a putative SNP to 175. The 35 SNPs with the highest BFR values were converted into genome-specific KASP assays using an automated bioinformatics pipeline (PolyMarker) which circumvents the limitations associated with the polyploid wheat genome. Twenty-eight assays were polymorphic of which 22 (63%) mapped in the same linkage group as Yr15. Using these markers, we mapped Yr15 to a 0.77-cM interval. The three most closely linked SNPs were tested across varieties and breeding lines representing UK elite germplasm. Two flanking markers were diagnostic in over 99% of lines tested, thus providing a reliable haplotype for marker-assisted selection in these breeding programmes. Our results demonstrate that the proposed methodology can be applied in polyploid F2 populations to generate high-resolution genetic maps across target intervals.
The Genome Analysis Centre, Norwich, UK.
Ricardo H
RH
Ramirez-Gonzalez
John Innes Centre, Norwich, UK.
Vanesa
V
Segovia
John Innes Centre, Norwich, UK.
Nicholas
N
Bird
Limagrain UK Ltd, Rothwell, UK.
Paul
P
Fenwick
RAGT Seeds, Saffron Walden, UK.
Sarah
S
Holdgate
Limagrain UK Ltd, Rothwell, UK.
Simon
S
Berry
RAGT Seeds, Saffron Walden, UK.
Peter
P
Jack
The Genome Analysis Centre, Norwich, UK.
Mario
M
Caccamo
John Innes Centre, Norwich, UK.|National Institute of Agricultural Botany, Cambridge, UK.
Cristobal
C
Uauy
D001483:Base Sequence; D001487:Basidiomycota / Q000502:physiology*; D001947:Breeding; D002874:Chromosome Mapping; D060467:Disease Resistance; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D010935:Plant Diseases / Q000276:immunology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011123:Polyploidy; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000235:genetics* / Q000276:immunology
D005819:Genetic Markers; D018749:RNA, Plant
PolyMarker; SRA project numbers; Yr15; bulk frequency ratio; haplotype; marker-assisted selection; yellow rust