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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #315004
Title: Transposable element junctions in marker development and genomic characterization of barley

Author
item MAAZAHERI, MONA - North Dakota State University
item KIANIAN, PENNY - North Dakota State University
item MERGOUM, MOHAMMED - North Dakota State University
item VALENTINI, GIORGIO - University Of Luxembourg
item SEETAN, RAED - North Dakota State University
item PIRSEYEDI, SEYED - North Dakota State University
item KUMAR, AJAY - North Dakota State University
item Gu, Yong
item STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item KUBALAKOVA, MARIE - Institute Of Experimental Botany
item DOLEZEL, JAROSLAV - Institute Of Experimental Botany
item DENTON, ANNE - North Dakota State University
item Kianian, Shahryar

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2014
Publication Date: 3/28/2014
Citation: Maazaheri, M., Kianian, P., Mergoum, M., Valentini, G., Seetan, R., Pirseyedi, S., Kumar, A., Gu, Y.Q., Stein, N., Kubalakova, M., Dolezel, J., Denton, A., Kianian, S. 2014. Transposable element junctions in marker development and genomic characterization of barley. The Plant Genome. 7:1-8.

Interpretive Summary: Barley is a model plant for genomic studies of other species in the tribe Triticeae, which includes wheat and rye. The majority of the barley genome is composed of mobile transposable elements (TEs). In this study, the many junctions between TE and neighboring sequences was investigated with the aim of developing new molecular markers for linking together widespread regions of the genome and to determine whether the TE tended to insert into gene-rich or gene-poor regions of the barley genome. More than 10 gigabases of barley survey sequencing data were screened to detect TE repeat junctions (RJs). A total of 9,881,561 RJs were identified distributed evenly among the chromosomes and 400,538 of these were used to design RJ markers (RJMs), resulting in an average of 39 markers per million base pairs. The utility of a subset of the designed markers was tested in seven barley lines. Approximately 63% of the markers detected differences among the lines. The abundance of RJs makes them an ideal resource for high-density molecular marker design, which will aid breeders in fine mapping and genomic selection studies and will facilitate assembly of the sequence of the entire barley genome. In addition to marker design, identified RJs were also utilized to write a script for detecting TEs in short-read sequences. A total of 1,190,885 TEs were detected and their preferential insertion sites were identified in unassembled survey sequencing data. The script developed in this study allows for detecting TEs in species for which short-read sequence data, but not entire genome sequence assemblies, are available.

Technical Abstract: Barley is a model plant in genomic studies of Triticeae species. A complete barley genome sequence will facilitate not only barley breeding programs, but also those for related species. However, the large genome size and high repetitive sequence content complicate the barley genome assembly. The majority of the barley genome is composed of mobile transposable elements (TEs). In this study, the utility of abundant TE junctions was investigated to develop a large-scale molecular marker platform, as a prerequisite to genome assembly. Furthermore, TE junctions were utilized to characterize transposon insertion patterns in gene-rich and gene-poor regions of the barley genome. A total of 10.22 Gb of barley Roche 454 survey sequencing data were screened with RJPrimers pipeline to detect TE repeat junctions (RJs). In total, 9,881,561 RJs were identified distributed evenly among the chromosomes. From detected RJs, 400,538 RJ markers (RJMs) were designed as PCR-based markers across the genome, with an average of 39 markers per Mb. The utility of designed markers was tested using a subset of RJMs and examining their PCR amplification products in seven barley lines. Over 94% of the primer pairs amplified successfully, with ~63% producing polymorphic amplicons among the lines. In addition to marker design, identified RJs were utilized to write a script for detecting TEs in short-read sequences. In total 1,190,885 TEs were detected and their preferential insertion sites were identified in unassembled survey sequencing data. The majority of the genome was composed of Gypsy elements comprising ~65% of TEs, while in gene-rich regions Gypsy, Copia, and Mariner were the main transposons, each representing an average ~23% of total TEs. The abundance of RJs makes them an ideal resource for high-density molecular marker design. The numerous RJ markers developed in this study will have broad application in barley genomic studies including genomic selection, fine mapping, and genome assembly. In addition, the results of this study demonstrate that RJ identification is a powerful method for characterizing TEs, even when used with unassembled sequence reads. The script developed in this study allows for detecting TEs in species without a sequenced genome but for which short-read sequence data is available.