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Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines.
BMC Genomics. 2019 Apr 15; 20(1):289.BG

Abstract

BACKGROUND

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.

RESULTS

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 BC3F5 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).

CONCLUSION

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.

Authors+Show Affiliations

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.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.School of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.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. nizf@cau.edu.cn.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. linzhishan@caas.cn. National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. linzhishan@caas.cn.Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. yexingguo@caas.cn. National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. yexingguo@caas.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30987602

Citation

Li, Shijin, et al. "Development of PCR Markers Specific to Dasypyrum Villosum Genome Based On Transcriptome Data and Their Application in Breeding Triticum aestivum-D. Villosum#4 Alien Chromosome Lines." BMC Genomics, vol. 20, no. 1, 2019, p. 289.
Li S, Wang J, Wang K, et al. Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines. BMC Genomics. 2019;20(1):289.
Li, S., Wang, J., Wang, K., Chen, J., Wang, K., Du, L., Ni, Z., Lin, Z., & Ye, X. (2019). Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines. BMC Genomics, 20(1), 289. https://doi.org/10.1186/s12864-019-5630-4
Li S, et al. Development of PCR Markers Specific to Dasypyrum Villosum Genome Based On Transcriptome Data and Their Application in Breeding Triticum aestivum-D. Villosum#4 Alien Chromosome Lines. BMC Genomics. 2019 Apr 15;20(1):289. PubMed PMID: 30987602.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines. AU - Li,Shijin, AU - Wang,Jing, AU - Wang,Kunyang, AU - Chen,Jingnan, AU - Wang,Ke, AU - Du,Lipu, AU - Ni,Zhongfu, AU - Lin,Zhishan, AU - Ye,Xingguo, Y1 - 2019/04/15/ PY - 2018/09/06/received PY - 2019/03/20/accepted PY - 2019/4/17/entrez PY - 2019/4/17/pubmed PY - 2019/8/3/medline KW - Alien chromosome lines KW - Dasypyrum villosum KW - Molecular markers KW - Transcriptome SP - 289 EP - 289 JF - BMC genomics JO - BMC Genomics VL - 20 IS - 1 N2 - BACKGROUND: 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. RESULTS: 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 BC3F5 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). CONCLUSION: 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/30987602/Development_of_PCR_markers_specific_to_Dasypyrum_villosum_genome_based_on_transcriptome_data_and_their_application_in_breeding_Triticum_aestivum_D__villosum L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5630-4 DB - PRIME DP - Unbound Medicine ER -