Identification of chromosome-specific SSR markers to characterize the Langdon durum D-genome disomic substitution lines

Authors: James, Heaven; Peters Haugrud, Amanda; Zhang, Zengcui; Faris, Justin

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2026
Publication Date: 3/10/2026
Citation: James, H.S., Peters Haugrud, A.R., Zhang, Z., Faris, J.D. 2026. Identification of chromosome-specific SSR markers to characterize the Langdon durum D-genome disomic substitution lines. Crop Science. 66(2). https://doi.org/10.1002/csc2.70251.
DOI: https://doi.org/10.1002/csc2.70251

Interpretive Summary: Durum wheat is used to make macaroni, pasta, and other semolina-based products, making it an economically important crop. Genetic studies of durum wheat provide valuable information for crop improvement. In the 1980s, specific durum lines developed to carry chromosomes from a common wheat line substituted for chromosomes in a durum variety called Langdon were developed. These durum wheat ‘chromosome substitution’ lines have been widely used for genetic analysis of various traits in durum wheat. However, the genetic integrity of the lines must be monitored and maintained. Until now, maintenance required the use of methods involving microscopic analysis of chromosome constitutions in dividing cells, which was not only extremely laborious but could also be somewhat inaccurate due to difficulties in obtaining adequate samples. Here, researchers developed methods using DNA markers to determine the chromosome constitution and genetic integrity of the Langdon substitution lines. The identified markers are highly effective, very user-friendly, and are inexpensive, thus making them suitable for use in most any laboratory equipped to do basic DNA analysis. The markers and associated protocols developed in this research will allow the use of the Langdon substitution lines to be used more broadly and accurately to address genetic questions in durum wheat, which will lead to improvement of durum wheat varieties.

Technical Abstract: Genetic studies of durum wheat provide valuable information for crop improvement. In the 1980s, D-genome disomic chromosome substitution (DS) lines were developed, which involved the substitution of a pair of D-genome chromosomes from hexaploid wheat for a pair of homoeologous A- or B-genome chromosomes in the tetraploid durum variety Langdon (LDN). DS lines were developed for each of the durum chromosomes, and they have been used extensively over the past 35 years for genetic studies. However, five of the LDN-DS lines are not true-breeding because the substituted chromosomes do not completely compensate for the homoeologous chromosomes they replace and are maintained with a monosome or telosome, which segregate in progeny and require cytogenetic analyses to determine the chromosome constitution of individual plants before evaluation. Here, our objective was to simplify the process by identifying chromosome-specific simple sequence repeat (SSR) markers that could be used to characterize the chromosome constitution of all 14 LDN-DS lines. Toward this goal, we identified two to five SSRs specific to each chromosome and showed they can be used to determine the chromosome constitution of each of the LDN-DS lines using a simple and cost-effective protocol involving basic PCR and agarose gel electrophoresis. In the process, we found that the LDN-4D(4A) substitution line has been lost and now exists only as a disomic chromosome 4D addition line. This work provides a simplified means for characterizing the LDN-DS lines suitable for most laboratories, which will allow more researchers to use the LDN-DS stocks for various genetic studies.