Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing. (December 2017)

• Record Type: Journal Article
• Authors: Wang, Haiyan; Dai, Keli; Xiao, Jin; Yuan, Chunxia; Zhao, Renhui; Doležel, Jaroslav; Wu, Yufeng; Cao, Aizhong; Chen, Peidu; Zhang, Shouzhong; Wang, Xiue
• Is Part Of: BMC genomics. Volume 18:Number 1(2017)
• Page Start: 1
• Page End: 9
• Publication Date: 2017-12
• Subjects: Triticum aestivum -- Haynaldia villosa -- Molecular marker -- Intron polymorphism; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-017-3567-z
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Haynaldia villosa (L.) Schur (syn.Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance geneWss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) ofH. villosa . We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as toH.villosa genome, as reflected by the lack of specific markers. Results This study aims to develop 4VS-specific markers by combination of chromosome sorting and next-generation sequencing. The short arm of chromosome 4VS ofH.villosa was flow-sorted using a FACSVantage SE flow cytometer and sorter, and then sequenced by Illumina sequencing. The sequence ofH. villosa 4VS was assembled by the software Hecate, and then was compared with the sequence assemblies of wheat chromosome arms 4AL, 4BS and 4DS andAe. tauschii 4DS, with the objectives of identifying exon-exon junctions and localizing introns on chromosome 4VS ofH. villosa . The intron length polymorphisms suitable for designingH. villosa primers were evaluated with criteria. Consequently, we designed a total of 359 intron targeting (IT) markers, among which 232 (64.62%) markers were specific for tracing the 4VS chromatin in the wheat background. Conclusion The combination of chromosome sorting and next-generation sequencing to develop specific IT markers for 4VS ofH. villosa has high success rate and specificity, thus being applicable for the development of chromosome-specific markers for alien chromatin in wheat breeding.