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Genotyping by sequencing in almond: SNP discovery, linkage mapping, and marker design
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond. ; The authors gratefully acknowledge financial support from the following: Hort Innovation (the grower-owned, not-for-profit research and development corporation for Australian horticulture), which supported this research using the almond industry and development levy and contributions from the Australian Government; the Commonwealth Scientific and Industrial Research Organization; the South Australian River Murray Sustainability Program (IRSPR2-004) administered by Primary Industries and Regions South Australia; and the Spanish Ministry of Economy and Competitiveness [project AGL2015-68329-R, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 (SEV-2015-0533), CERCA Program of the Generalitat de Catalunya]. S.N.G. was the recipient of an Australian Postgraduate Award administered by the University of Adelaide. ; Peer reviewed
Genotyping by sequencing in almond: SNP discovery, linkage mapping, and marker design
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond. ; The authors gratefully acknowledge financial support from the following: Hort Innovation (the grower-owned, not-for-profit research and development corporation for Australian horticulture), which supported this research using the almond industry and development levy and contributions from the Australian Government; the Commonwealth Scientific and Industrial Research Organization; the South Australian River Murray Sustainability Program (IRSPR2-004) administered by Primary Industries and Regions South Australia; and the Spanish Ministry of Economy and Competitiveness [project AGL2015-68329-R, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 (SEV-2015-0533), CERCA Program of the Generalitat de Catalunya]. S.N.G. was the recipient of an Australian Postgraduate Award administered by the University of Adelaide. ; Peer reviewed
Genotyping by sequencing in almond: SNP discovery, linkage mapping, and marker design
Goonetilleke, Shashi N. (author) / March, Timothy J. (author) / Wirthensohn, Michelle G. (author) / Arús, Pere (author) / Walker, Amanda R. (author) / Mather, Diane E. (author) / Australian Society of Plant Scientists / Commonwealth Scientific and Industrial Research Organisation (Australia) / Australian Government / Department of Environment and Primary Industries (Australia)
2018-01-01
Article (Journal)
Electronic Resource
English
DDC:
690
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