Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination

Authors: ZHANG, MINGYI - North Dakota State University; ZHANG, WEI - North Dakota State University; ZHU, XIANWEN - North Dakota State University; SUN, QING - North Dakota State University; Chao, Shiaoman; YAN, CHANGHUI - North Dakota State University; Xu, Steven; Fiedler, Jason; CAI, XIWEN - North Dakota State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/14/2020
Publication Date: 1/22/2020
Citation: Zhang, M., Zhang, W., Zhu, X., Sun, Q., Chao, S., Yan, C., Xu, S.S., Fiedler, J.D., Cai, X. 2020. Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination. Theoretical and Applied Genetics. 133:1277-1289. https://doi.org/10.1007/s00122-020-03547-7.
DOI: https://doi.org/10.1007/s00122-020-03547-7

Interpretive Summary: Wheat, one of the most important food crops worldwide, has narrow genetic diversity, which compromises the potential for improvement of the modern wheat crop. One strategy to broaden the genetic diversity of wheat is to induce genetic exchange or recombination between wheat chromosomes and their-related chromosomes from wild relative species. In this study, we developed many wheat lines carrying the genetic exchanges between a wheat chromosome and its-related chromosome from tall wheatgrass. By using these lines, we constructed a chromosome map with newly-developed DNA markers specific for the wheatgrass chromosome. This chromosome map is useful for genome studies of wheat and its relatives while the wheat lines carrying the chromosome segments from tall wheatgrass are a valuable genetic resource for wheat improvement.

Technical Abstract: The wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) and Thinopyrum elongatum (2n = 2x = 14, EE) genomes can be differentiated from each other by fluorescent genomic in situ hybridization (FGISH) as well as molecular markers. This has facilitated homoeologous recombination-based partitioning and engineering of their genomes for physical mapping and alien introgression. Here, we constructed a special wheat genotype, which was double monosomic for wheat chromosome 3B and Th. elongatum chromosome 3E and homozygous for the ph1b mutant, to induce 3B-3E homoeologous recombination. Totally, 81 3B-3E recombinants were recovered and detected in the primary, secondary, and tertiary homoeologous recombination cycles by FGISH. Comparing to the primary recombination, the secondary and tertiary recombination shifted toward the proximal regions due to the increase of homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90K single nucleotide polymorphism (SNP) arrays and their recombination breakpoints physically mapped based on the FGISH patterns and SNP results. The 3B-3E recombination physically partitioned chromosome 3B into 38 bins, and 429 SNPs were assigned to the distinct bins. Integrative analysis of FGISH and SNP results led to the construction of a composite bin map for chromosome 3B. Additionally, we developed 22 SNP-derived semi-thermal asymmetric reverse PCR (STARP) markers specific for chromosome 3E and constructed a comparative map of homoeologous chromosomes 3E, 3B, 3A, and 3D. In summary, this work provides a unique physical framework for further studies of the 3B-3E homoeologous pair and diversifies the wheat genome for wheat improvement.