Theoretical and Applied Genetics

, Volume 130, Issue 6, pp 1135–1154 | Cite as

Physical mapping of DNA markers linked to stem rust resistance gene Sr47 in durum wheat

  • Daryl L. Klindworth
  • Jyoti Saini
  • Yunming Long
  • Matthew N. Rouse
  • Justin D. Faris
  • Yue Jin
  • Steven S. XuEmail author
Original Article


Key message

Markers linked to stem rust resistance gene Sr47 were physically mapped in three small Aegilops speltoides chromosomal bins. Five markers, including two PCR-based SNP markers, were validated for marker-assisted selection.


In durum wheat (Triticum turgidum subsp. durum), the gene Sr47 derived from Aegilops speltoides conditions resistance to race TTKSK (Ug99) of the stem rust pathogen (Puccinia graminis f. sp. tritici). Sr47 is carried on small interstitial translocation chromosomes (Ti2BL-2SL-2BL·2BS) in which the Ae. speltoides chromosome 2S segments are divided into four bins in genetic stocks RWG35, RWG36, and RWG37. Our objective was to physically map molecular markers to bins and to determine if any of the molecular markers would be useful in marker-assisted selection (MAS). Durum cultivar Joppa was used as the recurrent parent to produce three BC2F2 populations. Each BC2F2 plant was genotyped with markers to detect the segment carrying Sr47, and stem rust testing of BC2F3 progeny with race TTKSK confirmed the genotyping. Forty-nine markers from published sources, four new SSR markers, and five new STARP (semi-thermal asymmetric reverse PCR) markers, were evaluated in BC2F2 populations for assignment of markers to bins. Sr47 was mapped to bin 3 along with 13 markers. No markers were assigned to bin 1; however, 7 and 13 markers were assigned to bins 2 and 4, respectively. Markers Xrwgs38a, Xmag1729, Xwmc41, Xtnac3119, Xrwgsnp1, and Xrwgsnp4 were found to be useful for MAS of Sr47. However, STARP markers Xrwgsnp1 and Xrwgsnp4 can be used in gel-free systems, and are the preferred markers for high-throughput MAS. The physical mapping data from this study will also be useful for pyramiding Sr47 with other Sr genes on chromosome 2B.


Durum Wheat Common Wheat Stem Rust BC2F2 Plant Single Sequence Repeat 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank Drs. Shunwen Lu and Guojia Ma for critically reviewing the manuscript. This research was supported in part by funds to S. S. X. provided through a grant from the Bill & Melinda Gates Foundation to Cornell University for the Borlaug Global Rust Initiative (BGRI) Durable Rust Resistance in Wheat (DRRW) Project and the USDA-ARS CRIS Project No. 3060-520-037-00D. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Compliance with ethical standards

Conflict of interest

All authors have no conflict of interest.

Ethical standards

The experiments were performed in compliment with the current laws of United States of America.

Supplementary material

122_2017_2875_MOESM1_ESM.pdf (2.3 mb)
Supplemental Figure S1. Separation of amplicons from primer Xrwgs38 illustrating amplicons designated as Xrwgs38a and Xrwgs38b. Plants 3 thru 7 were derived from the Joppa-RWG35 population and include three heterozygous (#4, 5, and 6) and two homozygous plants (#3 and 7). Supplemental Figure S2. Detection of polymorphisms between Rusty and Joppa observed in RWG35 and RWG37 when amplified with co-dominant markers Xmag1729 and Xrwgs38. A. Marker Xmag1729 separated with 0.5× TBS buffer for 2.0 h at 40 W of current. RWG35 carries the 433 bp amplicon from Rusty and lacks the 444 bp amplicon from DAS15. A-C. Amplicons designated as Xrwgs38b separated in (B) 0.5× TBS buffer for 1.5 h at 70 W of current, (C) 0.5× TBS buffer for 2.0 h at 40 W of current, and (D) 1.0× TBS buffer at 70 W of current. RWG37 carries amplicons from Rusty and lacks the amplicons from DAS15. Figures B-D illustrate that migration of amplicons from Rusty was highly influenced by electrophoretic conditions. Supplemental Figure S3. Effects of number of PCR cycles on amplicon expression of marker Xwmc41. Supplemental Figure S4. Electrophoretograms of 12 dominant repulsion-phase markers tested on the RWG35, RWG36, and RWG37 populations. Only the first 12 plants of each population are shown. When markers produced multiple polymorphic amplicons, only the size of the smallest amplicon is reported. For an explanation of assigning markers to bins, see Fig. 3. X = a plant exhibiting recombination between Joppa and Rusty chromatin. For an explanation of classifying plants for recombination, see Fig. S5. Supplemental Figure S5. Electrophoretograms of co-dominant markers Xgwm120, Xgwm191, and Xgwm388 tested on the RWG36 population. The polymorphisms observed are between Joppa and Rusty. X = a plant exhibiting a recombination between Joppa and Rusty chromatin. Arrows in lane 3 (Plant 1) show the bands that are diagnostic for recombination. The steps to classify plants for recombination are 1) use the check marker (Xrwgs38a) to classify each plant for the presence of Ae. speltoides (S) or Joppa (J) chromatin, and 2) for the marker being tested, classify each plant for the presence of Rusty (R) or Joppa (J) chromatin. For example, for plants 1–5, marker Xrwgs38a indicates genotypes of SJ, SJ, SS, SS, and SJ, respectively. For marker Xgwm388, amplicons of 176 and 173 bp originate from Rusty and Joppa, respectively; and plants 1–5 have genotypes of RJ, RJ, RJ, RR, and RR, respectively. Therefore, plants 3 and 5 are recombinants (PDF 2413 KB)
122_2017_2875_MOESM2_ESM.docx (22 kb)
Supplemental Table S1. Complete listing of the markers investigated during this study, the reason for inclusion in the study, source of information, and PCR conditions for each primer pair (DOCX 22 KB)
122_2017_2875_MOESM3_ESM.pdf (149 kb)
Supplemental Table S2. Complete classification of all markers and plants in three backcross populations used for mapping. Data are ordered by bin (PDF 149 KB)


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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2017

Authors and Affiliations

  1. 1.USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research UnitRed River Valley Agricultural Research CenterFargoUSA
  2. 2.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  3. 3.USDA-ARS, Cereal Disease Laboratory, and Department of Plant PathologyUniversity of MinnesotaSt. PaulUSA

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