Theoretical and Applied Genetics

, Volume 132, Issue 1, pp 195–204 | Cite as

Delimitation of wheat ph1b deletion and development of ph1b-specific DNA markers

  • Yadav Gyawali
  • Wei Zhang
  • Shiaoman Chao
  • Steven Xu
  • Xiwen CaiEmail author
Original Article


Key message

We detected the deletion breakpoints of wheat ph1b mutant and the actual size of the deletion. Also, we developed ph1b deletion-specific markers useful for ph1b-mediated gene introgression and genome studies.


The Ph1 (pairing homoeologous) locus has been considered a major genetic system for the diploidized meiotic behavior of the allopolyploid genome in wheat. It functions as a defense system against meiotic homoeologous pairing and recombination in polyploid wheat. A large deletion of the genomic region harboring Ph1 on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid wheat ‘Chinese Spring,’ which has been widely used to induce meiotic homoeologous recombination for gene introgression from wild grasses into wheat. However, the breakpoints and physical size of the deletion remain undetermined. In the present study, we first anchored the ph1b deletion on 5BL by the high-throughput wheat 90K SNP assay and then delimited the deletion to a genomic region of 60,014,523 bp by chromosome walking. DNA marker and sequence analyses detected the nucleotide positions of the distal and proximal breakpoints (DB and PB) of the ph1b deletion and the deletion junction as well. This will facilitate understanding of the genomic region harboring the Ph1 locus in wheat. In addition, we developed user-friendly DNA markers specific for the ph1b deletion. These new ph1b deletion-specific markers will dramatically improve the efficacy of the ph1b mutant in the meiotic homoeologous recombination-based gene introgression and genome studies in wheat and its relatives.



We thank members of the laboratories involved for their help to this research and Dr. Lili Qi for her critical review of the manuscript. This project is supported by Agriculture and Food Research Initiative Competitive Grant No. 2016-67014-24455 from the USDA National Institute of Food and Agriculture.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2018_3207_MOESM1_ESM.xlsx (30 kb)
Table S1 Genetic and physical analysis of the genomic region spanning the ph1b deletion on 5BL (XLSX 30 kb)
122_2018_3207_MOESM2_ESM.xlsx (35 kb)
Table S2 5BL-specific DNA markers used in chromosome walking toward the PB and DB (XLSX 34 kb)
122_2018_3207_MOESM3_ESM.xlsx (43 kb)
Table S3 Gene content within the Ph1 genomic region on 5BL (XLSX 42 kb)
122_2018_3207_MOESM4_ESM.pdf (98 kb)
File S1 The DNA sequences of the ph1b deletion region and the genomic regions flanking the deletion showing the nucleotide positions of the PB, DB, and their flanking markers. Dotted lines refer to the DNA sequences that are not written out, and dashed line to the deleted region in the ph1b mutant (PDF 98 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  2. 2.USDA-ARS, Red River Valley Agricultural Research CenterFargoUSA

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