Transferability of gene based markers and population structure analyses of groundnut minicore
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Date
2008
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UAS, Dharwad
Abstract
Groundnut, Arachis hypogaea L., is an important oilseed crop grown all over the
world because of its economic importance and nutritional value. The yield of the groundnut
crop is low due to biotic and abiotic stresses and even breeding efforts are hindered due to the
limited knowledge of its genome. To improve the pace of breeding process, use of highly
efficient markers is imperative and a new set of markers called EST-SSRs have been found
advantageous in genetics and breeding as they are transferable. Through an analysis of Ah-
RGA database a set of 21 RGAs homologous to flax rust R gene was identified and clustered
into six classes. A set of 8 AhRGA-STS primers were designed and PCR screened for
polymorphisms in resistant and susceptible genotypes; primer pairs revealed seldom
polymorphism in chosen genotypes. In order to identify new gene based markers a set of 411
Sb-EST-SSRs were screened for their transferability to groundnut where a set of 161 primer
pairs amplified (39%) and a set of 24 (18%) were found polymorphic in groundnut.
Comparison of repeat motifs revealed predominance of di-(56.5%) and tri-(38%) nucleotide
repeats. Twelve of the transferred SbEST-SSRs markers were used to understand the
population genetic structure of 184 ground minicore accessions. Total of 51 alleles from 12
markers were available for analyses. Primer iabtgs384 was found to be the most informative
markers and AMOVA among population was 2.2% and 97.8% respectively between and
within population pairs. Dissimilarity dendrogram depicted five clusters. Population structure
analysis using STRUCTURE software resulted 7 sub populations and with ancestry sharing
of >70 per cent. Genetic distances between sub-populations ranged from 0.0844 to 0.3637
which is low compared to observed phenotypic difference among groundnut minicore
accessions.
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Plant Biotechnology