We performed homoeologous recombination-based partitioning and physical mapping of wheat chromosome 3B and Th. elongatum chromosome 3E, providing a unique physical framework of this homoeologous pair for genome studies. 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 in homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90-K 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 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.

中文翻译：

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小麦染色体3B及其同源物3E在长穗刺麦草中通过诱导同源重组进行分区和物理定位。

我们对小麦染色体 3B 和 Th 进行了基于同源重组的分区和物理作图。elongatum 3E 染色体，为基因组研究提供了这种同源对的独特物理框架。小麦 (Triticum aestivum, 2n = 6x = 42, AABBDD) 和 Thinopyrum elongatum (2n = 2x = 14, EE) 基因组可以通过荧光基因组原位杂交 (FGISH) 以及分子标记相互区分。这促进了基于同源重组的基因组分区和工程化，用于物理绘图和外星基因渗入。在这里，我们构建了一种特殊的小麦基因型，它是小麦染色体 3B 和 Th 的双单体。elongatum 3E染色体和纯合子为ph1b突变体，诱导3B-3E同源重组。完全，通过 FGISH 在一级、二级和三级同源重组循环中回收和检测了 81 个 3B-3E 重组体。与初级重组相比，由于配对伴侣之间同源性的增加，二级和三级重组向近端区域移动。通过高通量小麦 90-K 单核苷酸多态性 (SNP) 阵列对 3B-3E 重组体进行基因分型，并根据 FGISH 模式和 SNP 结果对它们的重组断点进行物理定位。3B-3E 重组将染色体 3B 物理划分为 38 个箱，并将 429 个 SNP 分配到不同的箱中。FGISH 和 SNP 结果的综合分析导致构建了 3B 染色体的复合 bin 图。此外，我们开发了 22 个 SNP 衍生的对 3E 染色体特异的半热不对称反向 PCR 标记，并构建了同源染色体 3E、3B、3A 和 3D 的比较图谱。总之，这项工作为进一步研究 3B-3E 同源对提供了独特的物理框架，并使小麦基因组多样化以促进小麦改良。