Key message
Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding.
Abstract
Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.
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Acknowledgements
The authors thank the staff at SARDI Crop Pathology and SARDI Nematology groups for providing the initial seeds of the RIL populations and support in setting up the nematode experiments, respectively. We would also like to thank SARDI Root Disease Testing Service for their help and constructive interaction throughout this project. The 90K marker work was done with the support of DAV00127, a joint project Agriculture Victoria Research (AVR), CSIRO Agriculture and GRDC. Our appreciation is extended to the Grains Research and Development Corporation for their financial assistance and the University of Adelaide for the postgraduate scholarship to MSR. NCC was supported by the University of Adelaide, the GRDC and the Government of South Australia.
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MSR and KHO designed the research (project conception and development of overall research plan). MSR conducted hands-on experiments and data collection. MSR, KL, NCC and KHO conducted data analysis. MSR, MH and JT performed statistical analysis. MSR, KL, NCC and KHO wrote the paper and have primary responsibility for the final content.
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Details of SNPs from the 90K wheat SNP array that were shown using bulked segregation analysis to be linked to the QRlnt.sk-6D nematode resistance locus. Details of these SNPs were derived from Wang et al. (2014) (XLSX 19 kb)
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Details of SNPs from the 90K wheat SNP array that were shown using bulked segregation analysis to be linked to the QRlnt.sk-2B (XLSX 20 kb)
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Genetic linkage map of chromosome 6D of Sokoll/Krichauff doubled haploid population (65 lines) obtained using the 90K what SNP chip (XLSX 22 kb)
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Genetic linkage map of chromosome 6D of Sokoll/Krichauff doubled haploid population (65 lines) obtained using the 90K what SNP chip assay (XLSX 52 kb)
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Details of KASP markers used for constructing the genetic linkage map of chromosome 6DS. 1: ‘A’ refers to 90K wheat SNP chip array (XLSX 35 kb)
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List of gene models between the markers flanking QRlnt.sk-6D QTL. Gene annotation based in Chinese Spring IWGSC RefSeq version 1.0 (XLSX 22 kb)
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Details of KASP markers used for constructing the genetic linkage map of chromosome 2BS. 1: Source of SNPs, 1 refers to 90K wheat SNP chip array (Wang et al. 2014) and 2 refers to cereal database, University of Bristol (Allen et al. 2011) (XLSX 24 kb)
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List of gene modes located between markers flanking QRlnt.sk-2B QTL. Gene annotation based in Chinese Spring IWGSC RefSeq version 1.0 (XLSX 23 kb)
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Rahman, M.S., Linsell, K.J., Taylor, J.D. et al. Fine mapping of root lesion nematode (Pratylenchus thornei) resistance loci on chromosomes 6D and 2B of wheat. Theor Appl Genet 133, 635–652 (2020). https://doi.org/10.1007/s00122-019-03495-x
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DOI: https://doi.org/10.1007/s00122-019-03495-x