Kumar Ajay, Seetan Raed, Mergoum Mohamed, Tiwari Vijay K, Iqbal Muhammad J, Wang Yi, Al-Azzam Omar, Šimková Hana, Luo Ming-Cheng, Dvorak Jan, Gu Yong Q, Denton Anne, Kilian Andrzej, Lazo Gerard R, Kianian Shahryar F
Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.
Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA.
BMC Genomics. 2015 Oct 16;16:800. doi: 10.1186/s12864-015-2030-2.
The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay.
In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii.
A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome.
This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
普通小麦（Triticum aestivum L.，约17 Gb）庞大而复杂的基因组需要高分辨率的基因组图谱以及饱和的标记支架，以便为全基因组组装锚定和定向BAC重叠群/序列支架。辐射杂种（RH）图谱已被证明是开发此类图谱的优秀工具，因为与遗传图谱相比，它在染色体全长上提供了更高且更均匀的标记分辨率，并且本身不需要标记多态性，因为它基于存在（保留）与缺失（缺失）标记分析。
在本研究中，对一个178个株系的RH群体进行了SSR和DArT标记基因分型，以构建节节麦（Aegilops tauschii）AL8/78整个D基因组的首张高分辨率RH图谱。为了确认图谱顺序的准确性，将AL8/78-RH图谱与以下图谱进行了比较：1）使用100多个双亲群体构建的DArT共识遗传图谱；2）参考六倍体小麦“中国春”的D基因组RH图谱；3）两个基于SNP的遗传图谱，一个带有锚定的D基因组BAC重叠群，另一个带有锚定的D基因组序列支架。利用标记序列，RH图谱还与基于BAC重叠群的物理图谱以及节节麦D基因组的草图序列进行了锚定。
总共609个标记被定位到7条D基因组染色体上的503个独特位置，总图长为14,706.7 cR。任意两个标记位点之间的平均距离为29.2 cR，相当于2.1 cM或9.8 Mb。整个D基因组的平均定位分辨率估计为0.34 Mb（Mb/cR）或0.07 cM（cM/cR）。RH图谱在标记的染色体分配方面与几份已发表的图谱几乎完全一致。AL8/78图谱上标记位置与四张已发表图谱之间的平均秩相关系数在0.75至0.92之间，表明标记顺序一致性良好。通过609个定位标记，共检测到整个D基因组的2481个缺失，平均缺失大小为42.0 Mb。总共52个标记被锚定到216个节节麦序列支架上，其中116个之前未锚定到D基因组上。
本研究报告了节节麦AL8/78 D基因组首张高分辨率RH图谱的构建，随后用于未分配序列支架的锚定。本研究证明了RH图谱如何在染色体全长上提供高且均匀的分辨率，从而有助于大型复杂植物基因组的完整序列组装。
