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      The application of GBS markers for extending the dense genetic map of rye ( Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm

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          Abstract

          Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye ( Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.

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          The online version of this article (doi:10.1007/s13353-016-0347-4) contains supplementary material, which is available to authorized users.

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          A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

          Huihui Li, Prashant Vikram, Ravi Singh … (2015)
          Background Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers. Results Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence. Conclusion The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1424-5) contains supplementary material, which is available to authorized users.
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            Chromosomal rearrangements in the rye genome relative to that of wheat.

            Jasmine Francis, D. Xie, K Devos … (1993)
            An RFLP-based genetic map of Secale Cereale has provided evidence for multiple evolutionary translocations in the rye genome relative to that of hexaploid wheat. DNA clones which have previously been mapped in wheat indicated that chromosome arms 2RS, 3RL, 4RL, 5RL, 6RS, 6RL, 7RS and 7RL have all been involved in at least one translocation. A possible evolutionary pathway, which accounts for the present day R genome relative to the A, B and D genomes of wheat, is presented. The relevance of these results for strategies designed to transfer useful genes from rye, and probably other related species, to wheat is discussed.
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              Unlocking the secondary gene-pool of barley with next-generation sequencing.

              Neele Wendler, Martin Mascher, Christiane Nöh … (2014)
              Crop wild relatives (CWR) provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. Hordeum bulbosum L. is representing the secondary gene pool of the genus Hordeum. It has been used as a source of genetic introgressions for improving elite barley germplasm (Hordeum vulgare L.). However, genetic introgressions from H. bulbosum have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker-assisted backcrossing the size of introgressed segments. We applied next-generation sequencing (NGS) based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative H. bulbosum. Firstly, exome capture-based (re)-sequencing revealed large numbers of single nucleotide polymorphisms (SNPs) enabling the precise allocation of H. bulbosum introgressions. This SNP resource was further exploited by designing a custom multiplex SNP genotyping assay. Secondly, two-enzyme-based genotyping-by-sequencing (GBS) was employed to allocate the introgressed H. bulbosum segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of H. bulbosum as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future.
              Article 0 comments Cited 42 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Stefan Stojałowski: sstojalowski@zut.edu.pl
                Journal
                Journal ID (nlm-ta): J Appl Genet
                Journal ID (iso-abbrev): J. Appl. Genet
                Title: Journal of Applied Genetics
                Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )
                ISSN (Print): 1234-1983
                ISSN (Electronic): 2190-3883
                Publication date (Electronic): 16 April 2016
                Publication date PMC-release: 16 April 2016
                Publication date (Print): 2016
                Volume: 57
                Issue: 4
                Pages: 439-451
                Affiliations
                [1 ]Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland
                [2 ]Department of Biochemistry and Biotechnology, Rzeszów University of Technology, Powstańców Warszawy 6, 35-959 Rzeszów, Poland
                Author notes

                Communicated by: Andrzej Górny

                Article
                Publisher ID: 347
                DOI: 10.1007/s13353-016-0347-4
                PMC ID: 5061839
                PubMed ID: 27085345
                SO-VID: b1a958b1-83c9-4d66-9cd4-3da8bf27fd36
                Copyright © © The Author(s) 2016
                License:

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                Date received : 2 February 2016
                Date revision received : 22 March 2016
                Date accepted : 27 March 2016
                Funding
                Funded by: National Science Center Poland
                Award ID: NN310 724540
                Categories
                Subject: Plant Genetics • Original Paper
                Custom metadata
                issue-copyright-statement © Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2016

                ScienceOpen disciplines: Genetics
                Keywords: cytoplasmic male sterility (cms),genetic map,genotyping by sequencing (gbs),rye
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: cytoplasmic male sterility (cms), genetic map, genotyping by sequencing (gbs), rye

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