Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)

Publication Overview
TitleIdentification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)
AuthorsAgarwal G, Sabbavarapu MM, Singh VK, Thudi M, Sheelamary S, Guar PM, Varshney RK
TypeJournal Article
Journal NameEuphytica
Volume205
Year2015
Page(s)381-394
CitationAgarwal G, Sabbavarapu MM, Singh VK, Thudi M, Sheelamary S, Guar PM, Varshney RK. Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.). Euphytica. 2015; 205:381-394.

Abstract

The paucity of sequence information flanking the simple sequence repeat (SSR) motifs identified especially in the transcript sequences has been limiting factor in the development of SSR markers for plant genome analysis as well as breeding applications. To overcome this and enhance the genic SSR marker repertoire in chickpea, the draft genome sequence of kabuli chickpea (CDC Frontier) and publicly available transcript sequences consisting of in silico identified SSR motifs were deployed in the present study. In this direction, the 300 bp sequence flanking the SSR motifs were retrieved by aligning 566 SSR containing transcripts of ICCV 2 available in public domain on the reference chickpea genome. A set of 202 novel genic SSRs were developed from a set of 507 primer pairs designed, based on in silico amplification of single locus and having no similarity to the publicly available SSR markers. Further, 40 genic SSRs equally distributed on chickpea genome were validated on a select set of 44 chickpea genotypes (including 41 Cicer arietinum and 3 Cicer reticulatum), out of which 25 were reported to be polymorphic. The polymorphism information content (PIC) value of 25 polymorphic genic SSRs ranged from 0.11 to 0.77 and number of alleles varied from 2 to 9. Clear demarcation among founder lines of multi-parent advanced generation inter-cross (MAGIC) population developed at ICRISAT and near-isogenic nature of JG 11 and JG11+ demonstrates the usefulness of these markers in chickpea diversity analysis and breeding studies. Further, genic polymorphic SSRs reported between parental lines of 16 different mapping populations along with the novel SSRs can be deployed for trait mapping and breeding applications in chickpea.
Features
This publication contains information about 233 features:
Feature NameUniquenameType
CakTSSR00586CakTSSR00586genetic_marker
CakTSSR00612CakTSSR00612genetic_marker
CakTSSR00619CakTSSR00619genetic_marker
CakTSSR00621CakTSSR00621genetic_marker
CakTSSR00701CakTSSR00701genetic_marker
CakTSSR00729CakTSSR00729genetic_marker
CakTSSR00732CakTSSR00732genetic_marker
CakTSSR00739CakTSSR00739genetic_marker
CakTSSR00744CakTSSR00744genetic_marker
CakTSSR00748CakTSSR00748genetic_marker
CakTSSR01087CakTSSR01087genetic_marker
CakTSSR01097CakTSSR01097genetic_marker
CakTSSR01178CakTSSR01178genetic_marker
CakTSSR01213CakTSSR01213genetic_marker
CakTSSR01218CakTSSR01218genetic_marker
CakTSSR01279CakTSSR01279genetic_marker
CakTSSR01324CakTSSR01324genetic_marker
CakTSSR01380CakTSSR01380genetic_marker
CakTSSR01399CakTSSR01399genetic_marker
CakTSSR01464CakTSSR01464genetic_marker
CakTSSR01476CakTSSR01476genetic_marker
CakTSSR01484CakTSSR01484genetic_marker
CakTSSR01566CakTSSR01566genetic_marker
CakTSSR01621CakTSSR01621genetic_marker
CakTSSR01623CakTSSR01623genetic_marker

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URLhttps://link.springer.com/article/10.1007/s10681-015-1394-3