Physical location of tandem repeats in the wheat genome and application for chromosome identification
Physical location of tandem repeats in the wheat genome and application for chromosome identification
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DOI：
10.1007/s00425-018-3033-4
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发表时间：
2019-03-01
期刊：
影响因子：
4.3
通讯作者：
Yang, Zujun
中科院分区：
文献类型：
--
作者：
Lang, Tao;Li, Guangrong;Yang, Zujun
主要结论预测了小麦基因组中串联重复序列（TR）的普遍分布，建立了一个新的网页，结合荧光原位杂交实验和新开发的Oligo探针，将提高小麦染色体鉴定的分辨率，对小麦参考基因组中的TR进行全面的序列分析，为发现和应用TR进行染色体鉴定奠定了基础。利用串联重复序列分析（TRF）技术，在中国春的参考序列中发现了TRs的全基因组定位。建立了小麦基因组中TRs重复单元大小、阵列数和物理覆盖长度的数据库。TRs的分布占小麦染色体的3-5%，在A、B和D基因组中呈非随机分布。比较了预测基因周围的三类TR。建立了一个优化的计算机辅助网页B2 DSC，以图形方式显示TR序列的一般分布和染色体富集区。B2 DSC预测的TRs在小麦基因组中的物理分布与荧光原位杂交（FISH）获得的相应杂交信号相匹配。我们开发了20个代表高拷贝数TR的20- 60 bp长度的寡核苷酸探针，并通过FISH验证。利用TR-Oligo探针构建了小麦染色体综合物理图谱。我们的研究结果表明，分子细胞遗传学和基因组研究的结合将显着有利于小麦育种通过染色体操作和工程。
Main conclusionA general distribution of tandem repeats (TRs) in the wheat genome was predicted and a new web page combined with fluorescence in situ hybridization experiments, and the newly developed Oligo probes will improve the resolution for wheat chromosome identification.Comprehensive sequence analysis of tandem repeats (TR) in the wheat reference genome permits discovery and application of TRs for chromosome identification. Genome-wide localization of TRs was identified in the reference sequences of Chinese Spring using Tandem Repeat Finder (TRF). A database of repeats unit size, array number, and physical coverage length of TRs in the wheat genome was built. The distribution of TRs occupied 3-5% of the wheat chromosomes, with non-random dispersal across the A, B, and D genomes. Three classes of TRs surrounding the predicted genes were compared. An optimized computer-assisted website page B2DSC was constructed for the general distribution and chromosomally enriched zones of TR sequences to be displayed graphically. The physical distribution of predicted TRs in the wheat genome by B2DSC matched well with the corresponding hybridization signals obtained with fluorescence in situ hybridization (FISH). We developed 20 oligonucleotide probes representing 20-60bp lengths of high copy number of TRs and verified by FISH. An integrated physical map of TR-Oligo probes for wheat chromosome identification was constructed. Our results suggest that the combination of both molecular cytogenetics and genomic research will significantly benefit wheat breeding through chromosome manipulation and engineering.