Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
College of Agronomy and Biotechnology/State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, 100193, China.
BMC Genomics. 2019 Apr 15;20(1):289. doi: 10.1186/s12864-019-5630-4.
Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D. villosum#4 still remains less studied. In particular, chromosomes of D. villosum#4 except 6V#4 have not been introduced into wheat by addition or substitution and translocation, which is an essential step to identify and apply the alien desired genes. RNA-seq technology can generate large amounts of transcriptome sequences and accelerate the development of chromosome-specific molecular markers and assisted selection of alien chromosome line.
We obtained the transcriptome of D. villosum#4 via a high-throughput sequencing technique, and then developed 76 markers specific to each chromosome arm of D. villosum#4 based on the bioinformatic analysis of the transcriptome data. The D. villosum#4 sequences containing the specific DNA markers were expected to be involved in different genes, among which most had functions in metabolic processes. Consequently, we mapped these newly developed molecular markers to the homologous chromosome of barley and obtained the chromosome localization of these markers on barley genome. Then we analyzed the collinearity of these markers among D. villosum, wheat, and barley. In succession, we identified six types of T. aestivum-D. villosum#4 alien chromosome lines which had one or more than one D. villosum#4 chromosome in the cross and backcross BCF populations between T. durum-D. villosum#4 amphidiploid TH3 and wheat cv. Wan7107 by employing the selected specific markers, some of which were further confirmed to be translocation or addition lines by genomic in situ hybridization (GISH).
Seventy-six PCR markers specific to chromosomes of D. villosum#4 based on transcriptome data were developed in the current study and their collinearity among D. villosum, wheat, and barley were carried out. Six types of Triticum aestivum-D. villosum#4 alien chromosome lines were identified by using 12 developed markers and some of which were further confirmed by GISH. These novel T. aestivum-D. villosum#4 chromosome lines have great potential to be used for the introduction of desirable genes from D. villosum#4 into wheat by chromosomal translocation to breed new wheat varieties.
长穗偃麦草是小麦（Triticum aestivum L.）的一个重要野生种，它蕴藏着许多可用于改良小麦各种性状的理想基因。与其他长穗偃麦草材料相比，长穗偃麦草#4 仍然研究较少。特别是，除 6V#4 以外的长穗偃麦草#4 染色体尚未通过附加或代换及易位导入小麦，这是鉴定和应用外源有利基因所必需的步骤。RNA-seq 技术可以产生大量转录组序列，并加速染色体特异性分子标记的开发和外源染色体系的辅助选择。
我们通过高通量测序技术获得了长穗偃麦草#4 的转录组，并基于转录组数据分析，开发了 76 个长穗偃麦草#4 每条染色体臂特异的标记。含有这些特异 DNA 标记的长穗偃麦草#4 序列预计涉及不同的基因，其中大多数基因具有代谢过程的功能。因此，我们将这些新开发的分子标记映射到大麦的同源染色体上，并获得了这些标记在大麦基因组上的染色体定位。然后，我们分析了这些标记在长穗偃麦草、小麦和大麦之间的共线性。随后，我们通过利用选择的特异标记，在 T. durum-D. villosum#4 双二倍体 TH3 与小麦品种 Wan7107 的杂交和回交 BCF 群体中鉴定出了 6 种含有一个或多个长穗偃麦草#4 染色体的 T. aestivum-D. villosum#4 外源染色体系，其中一些通过基因组原位杂交（GISH）进一步确认为易位或添加系。
本研究基于转录组数据开发了 76 个长穗偃麦草#4 染色体特异的 PCR 标记，并对其在长穗偃麦草、小麦和大麦中的共线性进行了分析。利用 12 个开发的标记鉴定出 6 种 T. aestivum-D. villosum#4 外源染色体系，其中一些通过 GISH 进一步证实。这些新的 T. aestivum-D. villosum#4 染色体系具有通过染色体易位将长穗偃麦草#4 中的有利基因导入小麦，从而培育新小麦品种的巨大潜力。
