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      SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis

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          Abstract

          Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher ( P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub ( https://github.com/byemaxx/SSREnricher).

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          Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

          T Thiel, W Michalek, R. K. Varshney … (2003)
          A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.
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            Repeat instability: mechanisms of dynamic mutations.

            Christopher E Pearson, Kerrie Edamura, John Cleary (2005)
            Disease-causing repeat instability is an important and unique form of mutation that is linked to more than 40 neurological, neurodegenerative and neuromuscular disorders. DNA repeat expansion mutations are dynamic and ongoing within tissues and across generations. The patterns of inherited and tissue-specific instability are determined by both gene-specific cis-elements and trans-acting DNA metabolic proteins. Repeat instability probably involves the formation of unusual DNA structures during DNA replication, repair and recombination. Experimental advances towards explaining the mechanisms of repeat instability have broadened our understanding of this mutational process. They have revealed surprising ways in which metabolic pathways can drive or protect from repeat instability.
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              Microsatellite markers: an overview of the recent progress in plants

              Rajwant K Kalia, Manoj Rai, Sanjay Kalia … (2011)
              Article 0 comments Cited 184 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Zongjun Du
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (pmc): PeerJ
                Journal ID (publisher-id): PeerJ
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 2 July 2020
                Publication date Collection: 2020
                Volume: 8
                Electronic Location Identifier: e9372
                Affiliations
                College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan, China
                Author information
                http://orcid.org/0000-0002-0871-9840
                Article
                Publisher ID: 9372
                DOI: 10.7717/peerj.9372
                PMC ID: 7335497
                SO-VID: ce45a683-64f5-482e-95eb-09c3cacf72cc
                Copyright © © 2020 Luo et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 24 December 2019
                Date accepted : 27 May 2020
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 41706171
                Funded by: 13th Five-Year Aquaculture-Breeding Project
                Award ID: 2016NYZ0047
                This study was funded by the National Natural Science Foundation of China (No. 41706171) and the 13th five-year aquaculture-breeding project of Sichuan province (No. 2016NYZ0047), China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Bioinformatics
                Subject: Evolutionary Studies
                Subject: Genomics
                Subject: Data Mining and Machine Learning
                Subject: Data Science

                Keywords: microsatellites,simple sequence repeats,polymorphic,comparative transcriptome analysis,sequence alignment
                Data availability:
                Keywords: microsatellites, simple sequence repeats, polymorphic, comparative transcriptome analysis, sequence alignment

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