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

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 BC 3 F 5 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. Electronic su...

Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

“…Li et al (2019) developed 76 molecular markers specific to the chromosome 1V to 7V of D . villosum #4 based on transcriptome data [31]. Furthermore, the transcription sequences were highly conserved and might be associated with the genes that related to a definite trait [57].…”

“…Furthermore, molecular markers of alien chromosome-specificity were limited for fine mapping of alien genes. Regardless, with the rapid development of high-throughput sequencing, sequencing-based technologies such as RNA-seq have been frequently used to develop molecular markers [1,30,31], detect expression pattern and level of genes responded to pathogens [32], exploit new genes and identify gene function without prior information of the particular reference genome sequences [33,34]. RNA-seq is very helpful to explore disease-resistant genes derived from wild relatives.…”

Discovery of powdery mildew resistance gene candidates fromAegilops biuncialischromosome 2Mbbased on transcriptome sequencing

“…longissima chromosome - specific markers by RNA-seq [30]. Li et al (2019) developed 76 molecular markers specific to the chromosome 1V to 7V of D. villosum #4 based on transcriptome data [31]. The transcription sequences were highly conserved and might be associated with the genes that related to a definite trait [57].…”

“…Furthermore, molecular markers of alien chromosome-specific were limited for fine mapping of alien genes. Regardless, with the rapid development of high-throughput sequencing, sequencing-based technologies such as RNA-seq have been frequently used to develop molecular markers [1,30,31], detect gene expression pattern and level responded to pathogens [32], exploit new genes and identify gene function without prior information of the particular reference genome [33,34]. RNA-seq is very helpful to explore disease-resistant genes (R) derived from wild relatives.…”

Molecular Characterization of the Dwarf53 Gene Homolog in Dasypyrum Villosum

“…Many researchers consider D. villosum as a valuable source of genes for improving wheat, primarily its resistance to abiotic stress and diseases. It is also known that D. villosum has a good tillering capacity and produces a large number of grains with a high protein content [10].…”