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Analysis of genetic diversity and structure in a genebank collection of red clover (Trifolium pratense L.) using SSR markers

Published online by Cambridge University Press:  04 March 2016

Mamta Gupta ,
Vikas Sharma ,
Sunil K. Singh ,
Rakesh K. Chahota  and
Tilak R. Sharma
Mamta Gupta
Affiliation:
Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University Palapmur-176 062, India National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi-110012, India
Vikas Sharma
Affiliation:
Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University Palapmur-176 062, India Department of Botany, Punjabi University Patiala, Punjab-147002, India
Sunil K. Singh
Affiliation:
Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University Palapmur-176 062, India National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi-110012, India
Rakesh K. Chahota
Affiliation:
Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University Palapmur-176 062, India
Tilak R. Sharma*
Affiliation:
Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University Palapmur-176 062, India
*
*Corresponding author. E-mail: sharmat88@yahoo.com
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Abstract

Genetic diversity of a red clover global collection was assessed using 36 simple sequence repeat (SSR) primers representing all seven linkage groups (LGs). The number of fragments amplified ranged from 1 to 6 for all the primers. Primer RCS0060 detected highest number of fragments, whereas four SSRs viz., RCS0899, RCS1594, TPSSR40 and RCS6927 amplified single fragment. Size range of amplicons generated by all the primers varied from 100 to 400 bp. Polymorphism information content values ranged from 0.301 to 0.719 with an average value of 0.605. LG wise diversity analysis showed that LG 3 was most diverse (I = 0.65, Ht = 0.44), whereas LG-1 showed minimum diversity (I = 0.48, Ht = 0.26) for the microsatellites used. Bayesian model-based clustering inferred three genetically distinct populations in the red clover germplasm holding and showed considerable admixture in individuals within clusters. Neighbour-joining analysis showed intermixing of accessions within groups. Principal component analysis plot complemented the clustering shown by Structure and distinguished three populations to greater extent. Analysis of molecular variance showed that 91% of the genetic variation was residing within populations, while 9% variation was among populations. Overall, the results showed that a high level of genetic diversity is prevailing in this worldwide collection of red clover, which can be exploited for its genetic improvement through breeding approaches.

Keywords

AMOVAgenetic diversitypolymorphismpopulation structurered cloverSSRTrifolium pratense
Type
Short Communication
Information
Plant Genetic Resources , Volume 15 , Issue 4 , August 2017 , pp. 376 - 379
Copyright
Copyright © NIAB 2016 

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