Abstract
BackgroundShort read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps.ResultsUsing GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines.ConclusionWe envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species.
Highlights
Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies
Wheat can tolerate chromosomal deletions due to its buffered polyploid nature. This has enabled the development of complete sets of chromosome aneuploid stocks and many chromosome deletion stocks [5,6,7]. These genetic stocks are an important resource for wheat genetics, which have been used extensively in genetic mapping, the development of genomic resources, and genome mapping [6, 8,9,10,11]
Distribution of tag counts Genotyping-by-sequencing (GBS) resulted in a total of ~ 834 million 100 bp raw reads from 606 samples
Summary
Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. We present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromo‐ somal deletions These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps. The accurate characterization of the presence and dosage of chromosome deletions and aneuploidy in a high-throughput manner is an important objective for more efficient curation and utilization of these stocks. Subsets of these deletion and aneuploid stocks have been characterized before using C-banding, fluorescent- and genomic- in situ hybridization, and expressed sequenced tags (ESTs) [12,13,14]. We approached the question if genotyping-by-sequencing approaches could be utilized for characterizing
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