Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability

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dc.contributor.authorAbdi, Sazdaen_US
dc.contributor.authorDwivedi, Anujen_US
dc.contributor.authorShashien_US
dc.contributor.authorKumar, Sureshen_US
dc.contributor.authorBhat, Vishnuen_US
dc.date.accessioned2020-11-18T10:20:46Z
dc.date.available2020-11-18T10:20:46Z
dc.date.issued2019-11
dc.description.abstractMost of the grasses of the genus Cenchrus (20–25 species) and Pennisetum (80–140 species) are distributed throughout the tropical and subtropical regions of the world and reproduce both by sexual and apomictic modes. However, the relationships among the Cenchrus–Pennisetum species are not very clear yet. Molecular markers like expressed sequence tag-simple sequence repeats (EST-SSRs) have been reported to be a better choice for resolving the phylogenetic relationships and to estimate the genetic diversity. The present study describes the identification of EST-SSR markers based on the transcriptome data of Cenchrus ciliaris inflorescence and illustrates the genetic diversity and phylogenetic relationships among these species. Of the 378 primer pairs used across 33 accessions of 21 Cenchrus, Pennisetum, and related grass (Bothriochloa, Dichanthium and Panicum) species, 116 EST-SSR markers were found to be polymorphic with an average polymorphism information content (PIC) of 0.49. Fifty-one EST-SSR loci and 520 alleles showed that where the PIC value is >0.5 there the GAG repeat motif was highly polymorphic. Two EST-SSR markers, CcSSR_80 and CcSSR_102, are polymorphic among the Cenchrus species, while they are absent in Pennisetum and the allied species. Five SSR markers (CcSSR_75, CcSSR_85, CcSSR_87, CcSSR_88 and CcSSR_114) showed 100% cross-transferability among the 21 Cenchrus–Pennisetum species. Species-specific alleles could also be detected for seven species of Cenchrus, Pennisetum and Panicum across 10 SSR markers. Assay of polymorphism across these agamic complexes showed that the three SSR markers (CcSSR_26, CcSSR_97 and CcSSR_109) were associated with Cenchrus–Pennisetum complex, and one (CcSSR_47) with Bothriochloa–Dichanthium complex. Markers with high discriminating power, namely CcSSR_4, CcSSR_38, CcSSR_48, CcSSR_66, CcSSR_67 and CcSSR_70, can be used to estimate the allelic sequence divergence across the sexual and apomictic lineages. Genetic diversity analysis using neighbour-joining (NJ) and principal co-ordinate analysis (PCoA) based approaches showed six and five clusters for the 33 accessions, respectively, having congruence in the pattern of clustering. These accessions were grouped according to their mode of reproduction. Cenchrus and Pennisetum species were grouped separately within the same clade, implying monophyletic group within a ‘bristle clade’. Thus, this study showed high discrimination power of microsatellite (EST-SSR) markers to resolve the phylogenetic relationships.en_US
dc.identifier.affiliationsDepartment of Botany, University of Delhi, Delhi 110 007, Indiaen_US
dc.identifier.affiliationsDivision of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, Indiaen_US
dc.identifier.citationAbdi Sazda, Dwivedi Anuj, Shashi, Kumar Suresh, Bhat Vishnu. Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability. Journal of Genetics. 2019 Nov; 98: 1-16en_US
dc.identifier.issn0022-1333
dc.identifier.issn0973-7731
dc.identifier.placeIndiaen_US
dc.identifier.urihttps://imsear.searo.who.int/handle/123456789/215390
dc.languageenen_US
dc.publisherIndian Academy of Sciencesen_US
dc.relation.volume98en_US
dc.source.urihttps://doi.org/10.1007/s12041-019-1142-xen_US
dc.subjectmicrosatellite markeren_US
dc.subjectCenchrusen_US
dc.subjectPennisetumen_US
dc.subjectapomixisen_US
dc.subjectagamic complexen_US
dc.subjectallelic sequence divergence.en_US
dc.titleDevelopment of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferabilityen_US
dc.typeJournal Articleen_US
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