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Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis

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Title Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis
 
Creator Sethy, Niroj Kumar
Choudhary, Shalu
Shokeen, Bhumika
Bhatia, Sabhyata
 
Subject Cicer reticulatum
microsatellite markers
molecular variation
phylogenetic analysis
 
Description Microsatellite sequences were cloned and
sequenced from Cicer reticulatum, the wild annual progenitor of chickpea (C. arietinum L.). Based on the
flanking sequences of the microsatellite motifs, 11 sequence-tagged microsatellite site (STMS) markers were
developed. These markers were used for phylogenetic
analysis of 29 accessions representing all the nine annual
Cicer species. The 11 primer pairs amplified distinct
fragments in all the annual species demonstrating high
levels of sequence conservation at these loci. Efficient
marker transferability (97%) of the C. reticulatum STMS
markers across other species of the genus was observed as
compared to microsatellite markers from the cultivated
species. Variability in the size and number of alleles was
obtained with an average of 5.8 alleles per locus. Sequence analysis at three homologous microsatellite loci
revealed that the microsatellite allele variation was
mainly due to differences in the copy number of the
tandem repeats. However, other factors such as (1) point
mutations, (2) insertion/deletion events in the flanking
region, (3) expansion of closely spaced microsatellites and
(4) repeat conversion in the amplified microsatellite loci
were also responsible for allelic variation. An unweighted
pairgroup method with arithmetic averages (UPGMA)-
based dendrogram was obtained, which clearly distinguished all the accessions (except two C. judaicum accessions) from one another and revealed intra- as well
as inter-species variability in the genus. An annual Cicer
phylogeny was depicted which established the higher
similarity between C. arietinum and C. reticulatum. The
placement of C. pinnatifidum in the second crossability
group and its closeness to C. bijugum was supported. Two species, C. yamashitae and C. chorassanicum, were
grouped distinctly and seemed to be genetically diverse
from members of the first crossability group. Our data
support the distinct placement of C. cuneatum as well as a
revised classification regarding its placement.
The authors would like to thank NCPGR, an
autonomous institute of Department of Biotechnology, Government of India, for providing financial support to this work. NKS
and BS are recipients of fellowships from the Council for Scientific
and Industrial Research (CSIR), Government of India. SC is a
recipient of a fellowship from the University Grants Commission
(UGC), Government of India. We are grateful to ICRISAT, India,
and the Indian Agricultural Research Institute (IARI), India, for
providing seed material.
 
Date 2013-11-05T04:22:36Z
2013-11-05T04:22:36Z
2006
24 October 2005
 
Type Article
 
Identifier Theor. Appl. Genet., 112: 347-357
http://hdl.handle.net/123456789/59
 
Language en
 
Publisher Springer