Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize

dc.creatorJie Xu
dc.creatorLing Liu
dc.creatorYunbi Xu
dc.creatorChurun Chen
dc.creatorTingzhao Rong
dc.creatorFarhan Ali
dc.creatorShufeng Zhou
dc.creatorFengkai Wu
dc.creatorYaxi Liu
dc.creatorJing Wang
dc.creatorMoju Cao
dc.creatorYanli Lu
dc.date2014-03-05T17:51:01Z
dc.date2014-03-05T17:51:01Z
dc.date2013
dc.date.accessioned2023-07-17T19:57:31Z
dc.date.available2023-07-17T19:57:31Z
dc.identifier1340-2838
dc.identifierhttp://hdl.handle.net/10883/3409
dc.identifier10.1093/dnares/dst026
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7509181
dc.descriptionSimple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.
dc.description497-509
dc.formatPDF
dc.languageEnglish
dc.publisherOxford University Press
dc.publisherKazusa DNA Research Institute
dc.publisherhttp://dnaresearch.oxfordjournals.org/content/20/5/497.abstract
dc.rightsCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
dc.rightsOpen Access
dc.source20
dc.sourceDNA Research
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectSimple Sequence Repeat Markers
dc.subjectWhole-Genome Sequences
dc.subjectPolymorphic SSR Markers
dc.subjectMAIZE
dc.subjectGENETIC MARKERS
dc.subjectZEA MEXICANA
dc.titleDevelopment and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize
dc.typeArticle
dc.coverageOxford


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