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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #396543
Research Project: Genetic Improvement of Biotic and Abiotic Stress Tolerance and Nutritional Quality in Hard Winter Wheat

Location: Hard Winter Wheat Genetics Research

Title: Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat

Author
item LIU, ZHAO - Kansas State University
item LI, YAOGUANG - Kansas State University
item Bernardo, Amy
item St Amand, Paul
item ZHANG, PINGPING - Kansas State University
item SEHGAL, SUNISH - South Dakota State University
item Bai, Guihua

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2022
Publication Date: 11/2/2022
Citation: Liu, Z., Li, Y., Bernardo, A.E., St Amand, P.C., Zhang, P., Sehgal, S., Bai, G. 2022. Development of diagnostic SNP markers for identification of rye 1RS translocations in wheat. Crop Science. https://doi.org/10.1002/csc2.20841.
DOI: https://doi.org/10.1002/csc2.20841

Interpretive Summary: The short arm of rye chromosome1 (abbreviated 1RS) contains many genes for biotic and abiotic stress resistance. The 1RS chromosome arm has been transferred several times to bread wheat. One translocation to wheat chromosome 1A and another to 1B have been widely used in wheat breeding programs worldwide. To facilitate marker-assisted identification of the two translocations in wheat breeding, we developed a set of three breeder-friendly DNA-based KASP markers. 1RS translocations in wheat and validated in two additional U.S. hard winter wheat panels. The three markers together accurately identified the presence of 1RS translocations on either the 1A or 1B chromosome in the two hard winter wheat panels and can be used for routine screening in wheat.

Technical Abstract: Wheat (Triticum aestivum L.) wild relatives are rich genetic resources for genetic improvement of wheat. The short arm of rye (Secale cereale L.) chromosome 1 (1RS) contains many beneficial genes for resistance to drought, insects and diseases, therefore the 1RS wheat translocations have been widely used in wheat breeding programs worldwide. To facilitate marker-assisted identification of 1RS in wheat breeding, we designed a set of Kompetitive allele specific PCR (KASP) markers to detect the translocations of 1RS.1AL and 1RS.1BL based on the sequence flanking single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) between wheat and rye panels. We identified a set of three SNP markers for diagnosis and differentiation of the two 1RS translocations in wheat. Among the three KASP markers, 1AS-05056 is 1RS specific, and clearly separated the genotypes with 1RS (1RS.1AL and 1RS.1BL) from those without the two 1RS translocations; whereas 1AS-29875 clearly identified the 1RS.1AL translocation and 1BS-16654 separated 1RS.1BL from 1RS.1AL. The three new KASP markers together accurately identified the presence of 1RS translocation on either 1A or 1B chromosome in a panel of 95 representative U.S. winter wheat accessions, which were further validated in two additional U.S. hard winter wheat panels. Therefore, they can be used for routine screening of 1RS.1BL and 1RS.1AL translocation lines in wheat breeding programs.